Comments (8)
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may be based on outdated information for both of these datasets.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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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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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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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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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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@nbokulich, can this issue be closed now?
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@gregcaporaso I am waiting for PR #58 to merge, which includes related edits to READMEs. Thanks!
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The README files have been updated with #58. Thanks @fwhelan for catching this!
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Related Issues (20)
- Permanent "issues" or notes pages for each mock community dataset HOT 4
- Automatic taxonomy string extraction
- Update required metadata
- Unable to replicate community composition of Mock-3 HOT 3
- Shotgun Mock HOT 2
- new data integrity checks HOT 5
- Potential issue demultiplexing mock-8 HOT 2
- Failing to demultiplex mock-3 HOT 3
- Error preprocessing mock 7 and 8 : Failed qual conversion HOT 1
- Question about barcode length in mock2 and mock6 HOT 1
- Demultiplexing Reverse Reads HOT 5
- CONTRIBUTING.md not found HOT 1
- Trouble generating a pull request HOT 3
- add accuracy data and recommendations for mock communities on README
- Mock2 expected abundance replication issue HOT 4
- replace QIIME 1 commands with QIIME 2 commands
- Mock 11 primers HOT 1
- Is Mock-1 HiSeq or MiSeq? HOT 2
- How can I distinguish those three mock communities from Mock-10 data? HOT 2
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