Dear all,
thank your for reviewing this post. I am invoking qiime cutadapt trim-paired
on a cluster as follows:
for ((i=1;i<=2;i++)); do
qiime cutadapt trim-paired \
--i-demultiplexed-sequences "$trpth"/"${inpth[$i]}" \
--p-cores "$cores" \
--p-front-f "${fwdcut[$i]}" \
--p-front-r "${revcut[$i]}" \
--p-error-rate 0.1 \
--o-trimmed-sequences "$trpth"/"${otpth[$i]}" \
--verbose | tee "$trpth"/"${log[$i]}"
done
I am looping over a imported .qza
file containing 18S data, and receive a trimmed .qza
file as expected. However this is not the case for a 16S data set, where only the log file gets written --verbose | tee "$trpth"/"${log[$i]}"
. So trimming is taking place for both files, but for the 16S data no files are written. Is this a possibly known bug? Perhaps I should just skip this step, as not read are filtered out anyways? Can't update Qiime in the target environment easily, it's a big remote machine. Looking forward to hearing from you in due course.
Thank you.
Paul
Dear all,
thank you very much, I resolved this. The error message was in the log file but quite far up. Looks like the data has some errors that didn't get caught during importing. I will be excluding the offending data and retry. Error message was:
This is cutadapt 1.16 with Python 3.5.5
Command line parameters: --cores 40 --error-rate 0.1 --times 1 --overlap 3 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-bpmdr3da/585A_150_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-bpmdr3da/585A_151_L001_R2_001.fastq.gz --front AGAGTTTGATCMTGGCTCAG -G GWATTACCGCGGCKGCTG /tmp/qiime2-archive-e7k4n5h7/49b8914c-474b-4d85-acc2-5978cc10d5ef/data/585A_150_L001_R1_001.fastq.gz /tmp/qiime2-archive-e7k4n5h7/49b8914c-474b-4d85-acc2-5978cc10d5ef/data/585A_151_L001_R2_001.fastq.gz
Running on 40 cores
Trimming 2 adapters with at most 10.0% errors in paired-end mode ...
ERROR: Traceback (most recent call last):
File "/programs/Anaconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/cutadapt/pipeline.py", line 456, in run
(n, bp1, bp2) = self._pipeline.process_reads()
File "/programs/Anaconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/cutadapt/pipeline.py", line 284, in process_reads
for read1, read2 in self._reader:
File "/programs/Anaconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/cutadapt/seqio.py", line 414, in __iter__
r2 = next(it2)
File "src/cutadapt/_seqio.pyx", line 214, in __iter__ (src/cutadapt/_seqio.c:5619)
cutadapt.seqio.FormatError: Line 3 in FASTQ file is expected to start with '+', but found '@M01153:41'
Kind regards,
Paul
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