join reads demux error

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1

Hi everyone.
I denoise my data using deblur. If I understand well i must join my reads with vsearch but
I'm having problems with

qiime vsearch join-pairs --i-demultiplexed-seqs demux-filtered.qza --o-joined-sequences demux-joined.qza --verbose

the error is a little bit big because of the numer of samples. let me share you the last one:

"vsearch v2.7.0_linux_x86_64, 15.9GB RAM, 8 cores

Merging reads 69%

Fatal error: More forward reads than reverse reads
Traceback (most recent call last):
File "/home/cruiz/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2cli/commands.py", line 329, in call
results = action(**arguments)
File "", line 2, in join_pairs
File "/home/cruiz/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/sdk/action.py", line 244, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/home/cruiz/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/sdk/action.py", line 390, in callable_executor
output_views = self._callable(**view_args)
File "/home/cruiz/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2_vsearch/_join_pairs.py", line 56, in join_pairs
_, result = _join_pairs_w_command_output(
File "/home/cruiz/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2_vsearch/_join_pairs.py", line 147, in _join_pairs_w_command_output
run_command(cmd)
File "/home/cruiz/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2_vsearch/_cluster_features.py", line 33, in run_command
subprocess.run(cmd, check=True)
File "/home/cruiz/miniconda3/envs/qiime2-2021.4/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['vsearch', '--fastq_mergepairs', '/tmp/qiime2-archive-mlp00o_1/986bf56f-249b-4252-b9a9-fe2c68bc5671/data/150516.MT4.CR13_102_L001_R1_001.fastq.gz', '--reverse', '/tmp/qiime2-archive-mlp00o_1/986bf56f-249b-4252-b9a9-fe2c68bc5671/data/150516.MT4.CR13_103_L001_R2_001.fastq.gz', '--fastqout', '/tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-_pfe1pbk/150516.MT4.CR13_50_L001_R1_001.fastq', '--fastq_ascii', '33', '--fastq_minlen', '1', '--fastq_minovlen', '10', '--fastq_maxdiffs', '10', '--fastq_qmin', '0', '--fastq_qminout', '0', '--fastq_qmax', '41', '--fastq_qmaxout', '41', '--minseqlength', '1', '--fasta_width', '0', '--threads', '1']' returned non-zero exit status 1.

Plugin error from vsearch:

Command '['vsearch', '--fastq_mergepairs', '/tmp/qiime2-archive-mlp00o_1/986bf56f-249b-4252-b9a9-fe2c68bc5671/data/150516.MT4.CR13_102_L001_R1_001.fastq.gz', '--reverse', '/tmp/qiime2-archive-mlp00o_1/986bf56f-249b-4252-b9a9-fe2c68bc5671/data/150516.MT4.CR13_103_L001_R2_001.fastq.gz', '--fastqout', '/tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-_pfe1pbk/150516.MT4.CR13_50_L001_R1_001.fastq', '--fastq_ascii', '33', '--fastq_minlen', '1', '--fastq_minovlen', '10', '--fastq_maxdiffs', '10', '--fastq_qmin', '0', '--fastq_qminout', '0', '--fastq_qmax', '41', '--fastq_qmaxout', '41', '--minseqlength', '1', '--fasta_width', '0', '--threads', '1']' returned non-zero exit status 1.

about the Fatal error: More forward reads than reverse reads Why could this happen?

vsearch version 2.7
qiime2-2021.4

Thanks in advance,
César

2

Hello @Cesar_Ruiz
I am not sure if I understood you correctly, but I have an impression that you processed your forward and reverse reads by Deblur and now trying to merge them by vsearch.
If it is a case, then I will suggest you to merge reads first (after primers removal by cutadapt plugin) and then process them by Deblur.

If I am incorrect, then there is another possibility.
The error you are facing occurs because number of your forward and reverse reads do not match (some of reads are unpaired). You can use bbtools (not in Qiime2) to filter your reads so only paired reads will remain.

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