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test cutadapt 4.0+galaxy1 #68

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jennaj opened this issue Nov 10, 2022 · 4 comments
Closed

test cutadapt 4.0+galaxy1 #68

jennaj opened this issue Nov 10, 2022 · 4 comments

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@jennaj
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jennaj commented Nov 10, 2022

toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1
@jennaj
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jennaj commented Nov 10, 2022

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1

@mvdbeek
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mvdbeek commented Nov 10, 2022

Results (powered by Planemo)

Summary

State Count
Total 33
Passed 24
Error 0
Failure 9
Skipped 0
Failed s
Passed s
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test tool test #1)

    Command Line:

    • 

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Output:
    

      

    • 

      This is cutadapt 4.0 with Python 3.9.12
Command line parameters: -j=8 -a AGATCGGAAGAGC --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim cutadapt_small_fastq.fq
Processing single-end reads on 8 cores ...
Finished in 0.02 s (7086 µs/read; 0.01 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         0 (0.0%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):            102 bp (100.0%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 0 times

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
library
{"__current_case__": 0, "input_1": {"values": [{"id": 104837505, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}

      

      
adapter_options
{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}

      

      
filter_options
{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}

      

      
read_mod_options
{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"}

      

      
output_selector
None

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test test against test.galaxyproject.org #2)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Output:
    

      

    • 

      This is cutadapt 4.0 with Python 3.9.12
Command line parameters: -j=8 -a AGATCGGAAGAGC --output=out1.fq.gz --error-rate=0.1 --times=1 --overlap=3 --action=trim bwa-mem-fastq1_fq_gz.fq.gz
Processing single-end reads on 8 cores ...
Finished in 0.03 s (276 µs/read; 0.22 M reads/minute).

=== Summary ===

Total reads processed:                      99
Reads with adapters:                         2 (2.0%)
Reads written (passing filters):            99 (100.0%)

Total basepairs processed:        24,849 bp
Total written (filtered):         24,843 bp (100.0%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 50.0%
  G: 50.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	2	1.5	0	2

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
library
{"__current_case__": 0, "input_1": {"values": [{"id": 104837506, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}

      

      
adapter_options
{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}

      

      
filter_options
{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}

      

      
read_mod_options
{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"}

      

      
output_selector
None

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test racon 1.3.1.1 #11)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Output:
    

      

    • 

      This is cutadapt 4.0 with Python 3.9.12
Command line parameters: -j=8 -g file:/jetstream2/scratch/main/jobs/46781853/inputs/dataset_99a97fdd-580d-4a7d-ad65-397689d70b61.dat --output=split/{name}.fastq.gz --error-rate=0.1 --times=1 --overlap=3 --action=trim cutadapt_in_split_fastq_gz.fq.gz
Processing single-end reads on 8 cores ...
Finished in 0.05 s (4681 µs/read; 0.01 M reads/minute).

=== Summary ===

Total reads processed:                      11
Reads with adapters:                        10 (90.9%)
Reads written (passing filters):            11 (100.0%)

Total basepairs processed:         1,210 bp
Total written (filtered):          1,130 bp (93.4%)

=== Adapter A2 ===

Sequence: AGGTCACT; Type: anchored 5'; Length: 8; Trimmed: 5 times

No. of allowed errors: 0

Overview of removed sequences
length	count	expect	max.err	error counts
8	5	0.0	0	5


=== Adapter A1 ===

Sequence: GTCGGTAA; Type: anchored 5'; Length: 8; Trimmed: 5 times

No. of allowed errors: 0

Overview of removed sequences
length	count	expect	max.err	error counts
8	5	0.0	0	5

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
library
{"__current_case__": 0, "input_1": {"values": [{"id": 104837426, "src": "hda"}]}, "r1": {"adapters": [], "anywhere_adapters": [], "cut": "0", "front_adapters": [{"__index__": 0, "front_adapter_source": {"__current_case__": 2, "front_adapter_file": {"values": [{"id": 104837431, "src": "hda"}]}, "front_adapter_source_list": "file"}, "single_noindels": "false"}]}, "type": "single"}

      

      
adapter_options
{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}

      

      
filter_options
{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}

      

      
read_mod_options
{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"}

      

      
output_selector
"multiple_output"

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test mafft 7.221.3 #12)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Output:
    

      

    • 

      This is cutadapt 4.0 with Python 3.9.12
Command line parameters: -j=8 -a AAAT --untrimmed-output=untrimmed_output.fq --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim cutadapt_small_fastq.fq
Processing single-end reads on 8 cores ...
Finished in 0.04 s (14568 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         1 (33.3%)

== Read fate breakdown ==
Reads discarded as untrimmed:                2 (66.7%)
Reads written (passing filters):             1 (33.3%)

Total basepairs processed:           102 bp
Total written (filtered):             30 bp (29.4%)

=== Adapter 1 ===

Sequence: AAAT; Type: regular 3'; Length: 4; Trimmed: 1 times

Minimum overlap: 3
No. of allowed errors:
1-4 bp: 0

Bases preceding removed adapters:
  A: 0.0%
  C: 100.0%
  G: 0.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
4	1	0.0	0	1

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
library
{"__current_case__": 0, "input_1": {"values": [{"id": 104837505, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AAAT", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}

      

      
adapter_options
{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}

      

      
filter_options
{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}

      

      
read_mod_options
{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"}

      

      
output_selector
"untrimmed_file"

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test ebi_metagenomics_run_downloader 0.1.0 #13)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Output:
    

      

    • 

      This is cutadapt 4.0 with Python 3.9.12
Command line parameters: -j=8 -a AGATCGGAAGAGC --untrimmed-output=untrimmed_output.fq.gz --output=out1.fq.gz --error-rate=0.1 --times=1 --overlap=3 --action=trim bwa-mem-fastq1_fq_gz.fq.gz
Processing single-end reads on 8 cores ...
Finished in 0.04 s (427 µs/read; 0.14 M reads/minute).

=== Summary ===

Total reads processed:                      99
Reads with adapters:                         2 (2.0%)

== Read fate breakdown ==
Reads discarded as untrimmed:               97 (98.0%)
Reads written (passing filters):             2 (2.0%)

Total basepairs processed:        24,849 bp
Total written (filtered):            496 bp (2.0%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 50.0%
  G: 50.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	2	1.5	0	2

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
library
{"__current_case__": 0, "input_1": {"values": [{"id": 104837573, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}

      

      
adapter_options
{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}

      

      
filter_options
{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}

      

      
read_mod_options
{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"}

      

      
output_selector
"untrimmed_file"

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test tp_sort_rows 1.0.0 #15)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Output:
    

      

    • 

      This is cutadapt 4.0 with Python 3.9.12
Command line parameters: -j=8 -a AGATCGGAAGAGC -u 5 --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim cutadapt_small_fastq.fq
Processing single-end reads on 8 cores ...
Finished in 0.03 s (8485 µs/read; 0.01 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         0 (0.0%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):             87 bp (85.3%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 0 times

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
library
{"__current_case__": 0, "input_1": {"values": [{"id": 104837595, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "5", "front_adapters": []}, "type": "single"}

      

      
adapter_options
{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}

      

      
filter_options
{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}

      

      
read_mod_options
{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"}

      

      
output_selector
None

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test tp_sorted_uniq 1.0.0 #16)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Output:
    

      

    • 

      This is cutadapt 4.0 with Python 3.9.12
Command line parameters: -j=8 -a AGATCGGAAGAGC -u 5 --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim --rename={id} barcode={cut_prefix} cutadapt_small_fastq.fq
Processing single-end reads on 8 cores ...
Finished in 0.03 s (10545 µs/read; 0.01 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         0 (0.0%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):             87 bp (85.3%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 0 times

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
library
{"__current_case__": 0, "input_1": {"values": [{"id": 104837611, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "5", "front_adapters": []}, "type": "single"}

      

      
adapter_options
{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}

      

      
filter_options
{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}

      

      
read_mod_options
{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": "{id} barcode={cut_prefix}", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"}

      

      
output_selector
None

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test hyphy_gard 2.5.31+galaxy1 #17)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Output:
    

      

    • 

      This is cutadapt 4.0 with Python 3.9.12
Command line parameters: -j=8 -a CGTCCGAANTAG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=retain cutadapt_small_fastq.fq
Processing single-end reads on 8 cores ...
Finished in 0.03 s (8723 µs/read; 0.01 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         1 (33.3%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):             80 bp (78.4%)

=== Adapter 1 ===

Sequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-11 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 0.0%
  T: 0.0%
  none/other: 100.0%

Overview of removed sequences
length	count	expect	max.err	error counts
34	1	0.0	1	1

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
library
{"__current_case__": 0, "input_1": {"values": [{"id": 104837631, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "CGTCCGAANTAG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}

      

      
adapter_options
{"action": "retain", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}

      

      
filter_options
{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}

      

      
read_mod_options
{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"}

      

      
output_selector
None

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test prokka 1.14.6+galaxy1 #18)
    

    Command Line:
    

      

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      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Output:
    

      

    • 

      This is cutadapt 4.0 with Python 3.9.12
Command line parameters: -j=8 -a CGTCCGAANTAG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=mask cutadapt_small_fastq.fq
Processing single-end reads on 8 cores ...
Finished in 0.03 s (8708 µs/read; 0.01 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         1 (33.3%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):            102 bp (100.0%)

=== Adapter 1 ===

Sequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-11 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 0.0%
  T: 0.0%
  none/other: 100.0%

Overview of removed sequences
length	count	expect	max.err	error counts
34	1	0.0	1	1

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
library
{"__current_case__": 0, "input_1": {"values": [{"id": 104837638, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "CGTCCGAANTAG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}

      

      
adapter_options
{"action": "mask", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}

      

      
filter_options
{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}

      

      
read_mod_options
{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"}

      

      
output_selector
None

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test build_ucsc_custom_track_1 1.0.0 (+ 1.0.1 once updated on org) #19)
    

    Command Line:
    

      

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      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Output:
    

      

    • 

      This is cutadapt 4.0 with Python 3.9.12
Command line parameters: -j=8 -a CGTCCGAANTAG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=lowercase cutadapt_small_fastq.fq
Processing single-end reads on 8 cores ...
Finished in 0.03 s (10107 µs/read; 0.01 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         1 (33.3%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):            102 bp (100.0%)

=== Adapter 1 ===

Sequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-11 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 0.0%
  T: 0.0%
  none/other: 100.0%

Overview of removed sequences
length	count	expect	max.err	error counts
34	1	0.0	1	1

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
library
{"__current_case__": 0, "input_1": {"values": [{"id": 104837638, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "CGTCCGAANTAG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}

      

      
adapter_options
{"action": "lowercase", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}

      

      
filter_options
{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}

      

      
read_mod_options
{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"}

      

      
output_selector
None

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test roary 3.13.0+galaxy2 #20)
    

    Command Line:
    

      

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    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Output:
    

      

    • 

      This is cutadapt 4.0 with Python 3.9.12
Command line parameters: -j=8 -a CGTCCGAANTAG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=none cutadapt_small_fastq.fq
Processing single-end reads on 8 cores ...
Finished in 0.04 s (13007 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         1 (33.3%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):            102 bp (100.0%)

=== Adapter 1 ===

Sequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-11 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 0.0%
  T: 0.0%
  none/other: 100.0%

Overview of removed sequences
length	count	expect	max.err	error counts
34	1	0.0	1	1

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
library
{"__current_case__": 0, "input_1": {"values": [{"id": 104837653, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "CGTCCGAANTAG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}

      

      
adapter_options
{"action": "none", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}

      

      
filter_options
{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}

      

      
read_mod_options
{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"}

      

      
output_selector
None

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test mothur_align_seqs 1.39.5.0 #21)
    

    Command Line:
    

      

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    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Output:
    

      

    • 

      This is cutadapt 4.0 with Python 3.9.12
Command line parameters: -j=8 -a TAAACAGATTAGT --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim --revcomp cutadapt_small_fastq.fq
Processing single-end reads on 8 cores ...
Finished in 0.03 s (8749 µs/read; 0.01 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         1 (33.3%)
Reverse-complemented:                        0 (0.0%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):             97 bp (95.1%)

=== Adapter 1 ===

Sequence: TAAACAGATTAGT; Type: regular 3'; Length: 13; Trimmed: 1 times; Reverse-complemented: 0 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 0.0%
  T: 100.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
5	1	0.0	0	1

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
library
{"__current_case__": 0, "input_1": {"values": [{"id": 104837661, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "TAAACAGATTAGT", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}

      

      
adapter_options
{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "true", "times": "1"}

      

      
filter_options
{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}

      

      
read_mod_options
{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"}

      

      
output_selector
None

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test circos 0.69.8+galaxy7 #26)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Output:
    

      

    • 

      This is cutadapt 4.0 with Python 3.9.12
Command line parameters: -j=8 -a AGCCGCTANGACG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim --length=10 cutadapt_small_fastq.fq
Processing single-end reads on 8 cores ...
Finished in 0.02 s (8298 µs/read; 0.01 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         1 (33.3%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):             20 bp (19.6%)

=== Adapter 1 ===

Sequence: AGCCGCTANGACG; Type: regular 3'; Length: 13; Trimmed: 1 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 0.0%
  T: 0.0%
  none/other: 100.0%

Overview of removed sequences
length	count	expect	max.err	error counts
34	1	0.0	1	1

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
dbkey
"?"

      

      
__input_ext
"input"

      

      
library
{"__current_case__": 0, "input_1": {"values": [{"id": 104837686, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGCCGCTANGACG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}

      

      
adapter_options
{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}

      

      
filter_options
{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}

      

      
read_mod_options
{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 0, "length": "10", "shorten_end": "3prime", "shorten_values": "True"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"}

      

      
output_selector
None

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test macs2_callpeak 2.1.1.20160309.6 #27)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Output:
    

      

    • 

      This is cutadapt 4.0 with Python 3.9.12
Command line parameters: -j=8 -a AGCCGCTANGACG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim --length=-10 cutadapt_small_fastq.fq
Processing single-end reads on 8 cores ...
Finished in 0.03 s (10478 µs/read; 0.01 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         1 (33.3%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):             20 bp (19.6%)

=== Adapter 1 ===

Sequence: AGCCGCTANGACG; Type: regular 3'; Length: 13; Trimmed: 1 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 0.0%
  T: 0.0%
  none/other: 100.0%

Overview of removed sequences
length	count	expect	max.err	error counts
34	1	0.0	1	1

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
library
{"__current_case__": 0, "input_1": {"values": [{"id": 104837695, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGCCGCTANGACG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}

      

      
adapter_options
{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}

      

      
filter_options
{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}

      

      
read_mod_options
{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 0, "length": "10", "shorten_end": "5prime", "shorten_values": "True"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"}

      

      
output_selector
None

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test table_annovar 0.2 #28)
    

    Command Line:
    

      

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    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Output:
    

      

    • 

      This is cutadapt 4.0 with Python 3.9.12
Command line parameters: -j=8 -a AGCGGCTTAGACG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim --max-expected-errors=10 cutadapt_small_fastq.fq
Processing single-end reads on 8 cores ...
Finished in 0.02 s (8307 µs/read; 0.01 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         0 (0.0%)

== Read fate breakdown ==
Reads with too many exp. errors:             0 (0.0%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):            102 bp (100.0%)

=== Adapter 1 ===

Sequence: AGCGGCTTAGACG; Type: regular 3'; Length: 13; Trimmed: 0 times

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
library
{"__current_case__": 0, "input_1": {"values": [{"id": 104837716, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGCGGCTTAGACG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}

      

      
adapter_options
{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}

      

      
filter_options
{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "10", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}

      

      
read_mod_options
{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"}

      

      
output_selector
None

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test roary 3.13.0+galaxy2 #4)
    

    Command Line:
    

      

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    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Output:
    

      

    • 

      This is cutadapt 4.0 with Python 3.9.12
Command line parameters: -j=8 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --output=out1.fq.gz --paired-output=out2.fq.gz --error-rate=0.1 --times=1 --overlap=3 --action=trim --pair-filter=any Unnamed Collection_1.fq.gz Unnamed Collection_2.fq.gz
Processing paired-end reads on 8 cores ...
Finished in 0.03 s (340 µs/read; 0.18 M reads/minute).

=== Summary ===

Total read pairs processed:                 99
  Read 1 with adapter:                       2 (2.0%)
  Read 2 with adapter:                       4 (4.0%)
Pairs written (passing filters):            99 (100.0%)

Total basepairs processed:        49,698 bp
  Read 1:        24,849 bp
  Read 2:        24,849 bp
Total written (filtered):         49,677 bp (100.0%)
  Read 1:        24,843 bp
  Read 2:        24,834 bp

=== First read: Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 50.0%
  G: 50.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	2	1.5	0	2


=== Second read: Adapter 2 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 50.0%
  T: 50.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	2	1.5	0	2
4	1	0.4	0	1
5	1	0.1	0	1

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
library
{"__current_case__": 2, "input_1": {"values": [{"id": 1779373, "src": "hdca"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "r2": {"adapters2": [{"__index__": 0, "adapter_source2": {"__current_case__": 0, "adapter2": "AGATCGGAAGAGC", "adapter_name2": "", "adapter_source_list2": "user"}, "single_noindels": "false"}], "anywhere_adapters2": [], "cut2": "0", "front_adapters2": [], "quality_cutoff2": null}, "type": "paired_collection"}

      

      
adapter_options
{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}

      

      
filter_options
{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}

      

      
read_mod_options
{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"}

      

      
output_selector
None

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test circos 0.69.8+galaxy10 #32)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Output:
    

      

    • 

      This is cutadapt 4.0 with Python 3.9.12
Command line parameters: -j=8 -a AGATCGGAAGAGC;noindels -A AGATCGGAAGAGC;noindels --output=out1.fq.gz --paired-output=out2.fq.gz --error-rate=0.1 --times=1 --overlap=3 --action=trim --pair-filter=any Unnamed Collection_1.fq.gz Unnamed Collection_2.fq.gz
Processing paired-end reads on 8 cores ...
Finished in 0.04 s (450 µs/read; 0.13 M reads/minute).

=== Summary ===

Total read pairs processed:                 99
  Read 1 with adapter:                       2 (2.0%)
  Read 2 with adapter:                       4 (4.0%)
Pairs written (passing filters):            99 (100.0%)

Total basepairs processed:        49,698 bp
  Read 1:        24,849 bp
  Read 2:        24,849 bp
Total written (filtered):         49,677 bp (100.0%)
  Read 1:        24,843 bp
  Read 2:        24,834 bp

=== First read: Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 50.0%
  G: 50.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	2	1.5	0	2


=== Second read: Adapter 2 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 50.0%
  T: 50.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	2	1.5	0	2
4	1	0.4	0	1
5	1	0.1	0	1

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
library
{"__current_case__": 2, "input_1": {"values": [{"id": 1779420, "src": "hdca"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "true"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "r2": {"adapters2": [{"__index__": 0, "adapter_source2": {"__current_case__": 0, "adapter2": "AGATCGGAAGAGC", "adapter_name2": "", "adapter_source_list2": "user"}, "single_noindels": "true"}], "anywhere_adapters2": [], "cut2": "0", "front_adapters2": [], "quality_cutoff2": null}, "type": "paired_collection"}

      

      
adapter_options
{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}

      

      
filter_options
{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}

      

      
read_mod_options
{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"}

      

      
output_selector
None

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test strelka #33)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Output:
    

      

    • 

      This is cutadapt 4.0 with Python 3.9.12
Command line parameters: -j=8 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --output=out1.fq.gz --paired-output=out2.fq.gz --error-rate=0.1 --times=1 --overlap=3 --action=trim --pair-filter=any --quality-cutoff=5 Unnamed Collection_1.fq.gz Unnamed Collection_2.fq.gz -Q=15,20
Processing paired-end reads on 8 cores ...
Finished in 0.29 s (2928 µs/read; 0.02 M reads/minute).

=== Summary ===

Total read pairs processed:                 99
  Read 1 with adapter:                       2 (2.0%)
  Read 2 with adapter:                       2 (2.0%)
Pairs written (passing filters):            99 (100.0%)

Total basepairs processed:        49,698 bp
  Read 1:        24,849 bp
  Read 2:        24,849 bp
Quality-trimmed:                     747 bp (1.5%)
  Read 1:             0 bp
  Read 2:           747 bp
Total written (filtered):         48,938 bp (98.5%)
  Read 1:        24,843 bp
  Read 2:        24,095 bp

=== First read: Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 50.0%
  G: 50.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	2	1.5	0	2


=== Second read: Adapter 2 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 100.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	1	1.5	0	1
4	1	0.4	0	1

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
library
{"__current_case__": 2, "input_1": {"values": [{"id": 1779422, "src": "hdca"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "r2": {"adapters2": [{"__index__": 0, "adapter_source2": {"__current_case__": 0, "adapter2": "AGATCGGAAGAGC", "adapter_name2": "", "adapter_source_list2": "user"}, "single_noindels": "false"}], "anywhere_adapters2": [], "cut2": "0", "front_adapters2": [], "quality_cutoff2": "15,20"}, "type": "paired_collection"}

      

      
adapter_options
{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}

      

      
filter_options
{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}

      

      
read_mod_options
{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "5", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"}

      

      
output_selector
None

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test pangolin 3.1.17+galaxy1 #7)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Output:
    

      

    • 

      This is cutadapt 4.0 with Python 3.9.12
Command line parameters: -j=8 --json stats.json -a AAAGATG --rest-file=rest_output.fa --output=out1.fa --error-rate=0.1 --times=1 --overlap=3 --action=trim cutadapt_rest_fa.fa
Processing single-end reads on 8 cores ...
Finished in 0.03 s (5916 µs/read; 0.01 M reads/minute).

=== Summary ===

Total reads processed:                       5
Reads with adapters:                         5 (100.0%)
Reads written (passing filters):             5 (100.0%)

Total basepairs processed:            97 bp
Total written (filtered):             35 bp (36.1%)

=== Adapter 1 ===

Sequence: AAAGATG; Type: regular 3'; Length: 7; Trimmed: 5 times

Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 100.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
7	1	0.0	0	1
12	1	0.0	0	1
14	2	0.0	0	2
15	1	0.0	0	1

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
library
{"__current_case__": 0, "input_1": {"values": [{"id": 104837423, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AAAGATG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}

      

      
adapter_options
{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}

      

      
filter_options
{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}

      

      
read_mod_options
{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"}

      

      
output_selector
["rest_file", "json_stats"]

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test SEACR 1.3+galaxy1 on usegalaxy.org #8)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Output:
    

      

    • 

      This is cutadapt 4.0 with Python 3.9.12
Command line parameters: -j=8 -a AGATCGGAAGAGC --output=out1.fq.gz --error-rate=0.1 --times=1 --overlap=3 --action=trim --nextseq-trim=20 bwa-mem-fastq1_fq_gz.fq.gz
Processing single-end reads on 8 cores ...
Finished in 0.03 s (296 µs/read; 0.20 M reads/minute).

=== Summary ===

Total reads processed:                      99
Reads with adapters:                         4 (4.0%)
Reads written (passing filters):            99 (100.0%)

Total basepairs processed:        24,849 bp
Quality-trimmed:                     286 bp (1.2%)
Total written (filtered):         24,550 bp (98.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 75.0%
  G: 25.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	3	1.5	0	3
4	1	0.4	0	1

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
library
{"__current_case__": 0, "input_1": {"values": [{"id": 104837506, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}

      

      
adapter_options
{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}

      

      
filter_options
{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}

      

      
read_mod_options
{"length_tag": null, "nextseq_trim": "20", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"}

      

      
output_selector
None

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test gffread 2.2.1.3+galaxy0 #9)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
library
{"__current_case__": 0, "input_1": {"values": [{"id": 104837420, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}

      

      
adapter_options
{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}

      

      
filter_options
{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}

      

      
read_mod_options
{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"}

      

      
output_selector
["report", "info_file"]

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test trim_galore 0.6.7+galaxy0 #10)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Output:
    

      

    • 

      This is cutadapt 4.0 with Python 3.9.12
Command line parameters: -j=8 -g A1=^GTCGGTAA -g A2=^AGGTCACT --output=split/{name}.fastq --error-rate=0.1 --times=1 --overlap=3 --action=trim cutadapt_in_split_fastq.fq
Processing single-end reads on 8 cores ...
Finished in 0.03 s (2471 µs/read; 0.02 M reads/minute).

=== Summary ===

Total reads processed:                      11
Reads with adapters:                        10 (90.9%)
Reads written (passing filters):            11 (100.0%)

Total basepairs processed:         1,210 bp
Total written (filtered):          1,130 bp (93.4%)

=== Adapter A1 ===

Sequence: GTCGGTAA; Type: anchored 5'; Length: 8; Trimmed: 5 times

No. of allowed errors: 0

Overview of removed sequences
length	count	expect	max.err	error counts
8	5	0.0	0	5


=== Adapter A2 ===

Sequence: AGGTCACT; Type: anchored 5'; Length: 8; Trimmed: 5 times

No. of allowed errors: 0

Overview of removed sequences
length	count	expect	max.err	error counts
8	5	0.0	0	5

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
library
{"__current_case__": 0, "input_1": {"values": [{"id": 104837419, "src": "hda"}]}, "r1": {"adapters": [], "anywhere_adapters": [], "cut": "0", "front_adapters": [{"__index__": 0, "front_adapter_source": {"__current_case__": 0, "front_adapter": "^GTCGGTAA", "front_adapter_name": "A1", "front_adapter_source_list": "user"}, "single_noindels": "false"}, {"__index__": 1, "front_adapter_source": {"__current_case__": 0, "front_adapter": "^AGGTCACT", "front_adapter_name": "A2", "front_adapter_source_list": "user"}, "single_noindels": "false"}]}, "type": "single"}

      

      
adapter_options
{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}

      

      
filter_options
{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}

      

      
read_mod_options
{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"}

      

      
output_selector
"multiple_output"

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 




      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
      



  

  @jennaj





  


    

      

  

    

        
    
    

  


      
          
  
      
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            jennaj
  

      

      

      commented


        Nov 11, 2022


      
    


  





      


        


  
    

      
          
old version failed (expected) + new version successful (good!)

      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
            

    

      
    

    


      

          @jennaj
jennaj




            closed this as completed


      Nov 11, 2022

    

  


    







      

  
      



  

  @jennaj





  


    

      

  

    

        
    
    

  


      
          
  
      
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            jennaj
  

      

      

      commented


        Nov 12, 2022


      
    


  





      


        


  
    

      
          
Passed here as well https://usegalaxy.org/u/jen/h/test-cutadapt

      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
            

    

      
    

    


      

          @jennaj
jennaj




            closed this as completed


      Nov 12, 2022

    

  


    











  
  

    

      

  





  




  
  

              

  
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          @mvdbeek 
        
          @jennaj