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Comments (8)

nbokulich avatar nbokulich commented on August 10, 2024

I apologize for this issue — I think the recommendations in README.md may be based on outdated information for both of these datasets. Could you try:

split_libraries_fastq.py -i mock-forward-read.fastq.gz -o split_libraries -m sample-metadata.tsv -b mock-index-read.fastq.gz --rev_comp_mapping_barcodes

and see if that does the trick?

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fwhelan avatar fwhelan commented on August 10, 2024

Thanks for your quick response! For mock-5, I get the following:

mock-5$ split_libraries_fastq.py -i mock-forward-read.fastq.gz -o split_libraries -m sample-metadata.tsv -b mock-index-read.corrected.fastq.gz --rev_comp_mapping_barcodes
Traceback (most recent call last):
  File "/usr/local/bin/split_libraries_fastq.py", line 365, in <module>
    main()
  File "/usr/local/bin/split_libraries_fastq.py", line 344, in main
    for fasta_header, sequence, quality, seq_id in seq_generator:
  File "/usr/local/lib/python2.7/dist-packages/qiime/split_libraries_fastq.py", line 322, in process_fastq_single_end_read_file
    raise FastqParseError("Headers of barcode and read do not match. Can't continue. "
qiime.split_libraries_fastq.FastqParseError: Headers of barcode and read do not match. Can't continue. Confirm that the barcode fastq and read fastq that you are passing match one another.

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nbokulich avatar nbokulich commented on August 10, 2024

This issue is my fault — I recently uploaded the fixed files per the recommendation in README.md and forgot to remove this note. The unmodified files (mock-index-read.fastq.gz) should work without error.

I have been making a number of fixes to data files recently and am currently working on a few updates, including to README.md files, so I apologize if you run into any more issues — just let me know and I will fix asap. Thanks!

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fwhelan avatar fwhelan commented on August 10, 2024

That worked! ..for mock-5. To be honest, I'm looking for a working set, so I can stick with mock-3-5. But for the purposes of furthering your project:

mock-7$ split_libraries_fastq.py -i mock-forward-read.fastq -o split_libraries -m sample-metadata.edit.tsv -b mock-index-read.fastq --rev_comp_mapping_barcodes
Traceback (most recent call last):
  File "/usr/local/bin/split_libraries_fastq.py", line 365, in <module>
    main()
  File "/usr/local/bin/split_libraries_fastq.py", line 344, in main
    for fasta_header, sequence, quality, seq_id in seq_generator:
  File "/usr/local/lib/python2.7/dist-packages/qiime/split_libraries_fastq.py", line 317, in process_fastq_single_end_read_file
    parse_fastq(fastq_read_f, strict=False, phred_offset=phred_offset)):
  File "/usr/local/lib/python2.7/dist-packages/skbio/parse/sequences/fastq.py", line 174, in parse_fastq
    seqid)
skbio.parse.sequences._exception.FastqParseError: Failed qual conversion for seq id: ILLUMINA_0275:2:1101:1357:1952#ATAGGCGATCNN. This may be because you passed an incorrect value for phred_offset.

Thanks so much for your help!

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nbokulich avatar nbokulich commented on August 10, 2024

Thanks for confirming! And thanks for the error report on mock-7.

Please let me know if you run into any additional issues.

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gregcaporaso avatar gregcaporaso commented on August 10, 2024

@nbokulich, can this issue be closed now?

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nbokulich avatar nbokulich commented on August 10, 2024

@gregcaporaso I am waiting for PR #58 to merge, which includes related edits to READMEs. Thanks!

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nbokulich avatar nbokulich commented on August 10, 2024

The README files have been updated with #58. Thanks @fwhelan for catching this!

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