Error occured while running for MAFFT in qiime2

The following problem occured while running for MAFFT sequence alignment for rep-seqs.qza file in HPC.

"Plugin error from phylogeny:
Command '['mafft', '--preservecase', '--inputorder', '--thread', '1', '/tmp/qiime2/pulakesw/data/68b72d9c-419e-46a2-98aa-4420b3480a5 2/data/dna-sequences.fasta']' returned non-zero exit status 1.
Debug info has been saved to /tmp/qiime2-q2cli-err-ozsjsu38.log"

Could anyone help me understand the main reason.

Following is the /tmp/qiime2-q2cli-err-ozsjsu38.log texts.

"Traceback (most recent call last):
File "/home/pulakesw/anaconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/q2cli/", line 520, in call
results = self._execute_action(
File "/home/pulakesw/anaconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/q2cli/", line 581, in _execute_action
results = action(**arguments)
File "", line 2, in summarize
File "/home/pulakesw/anaconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/qiime2/sdk/", line 342, in bound_callable
outputs = self.callable_executor(
File "/home/pulakesw/anaconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/qiime2/sdk/", line 615, in callable_executor
ret_val = self._callable(output_dir=temp_dir, **view_args)
File "/home/pulakesw/anaconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/q2_demux/_summarize/", line 140, in summarize
for seq in _read_fastq_seqs(filename):
File "/home/pulakesw/anaconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/q2_demux/", line 68, in _read_fastq_seqs
for seq_header, seq, qual_header, qual in itertools.zip_longest(*[fh] * 4):
File "/home/pulakesw/anaconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/", line 305, in read1
return self._buffer.read1(size)
File "/home/pulakesw/anaconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/", line 68, in readinto
data =
File "/home/pulakesw/anaconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/", line 470, in read
File "/home/pulakesw/anaconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/", line 516, in _read_eof
raise BadGzipFile("CRC check failed %s != %s" % (hex(crc32),
gzip.BadGzipFile: CRC check failed 0x11b726dd != 0x1399e02d

Hello @pulak,

What command did you run? It looks like one of the fastq.gz files may be corrupt.

I run for the following command.

qiime phylogeny align-to-tree-mafft-fasttree
--i-sequences rep-seqs.qza
--o-alignment aligned-rep-seqs.qza
--o-masked-alignment masked-aligned-rep-seqs.qza
--o-tree unrooted-tree.qza
--o-rooted-tree rooted-tree.qza

Hello @pulak,

If you're comfortable sharing your rep-seqs.qza file I can try to reproduce the error and see what's going on.

My rep-seqs.qza file is 44mb, its a large collection of samples over 4500.

And sequences.fasta file size is 76mb.

Hello @pulak,

Can you run qiime tools validate rep-seqs.qza and post the output?

1 Like

It shows

"Result rep-seqs.qza appears to be valid at level=max".

Hello @pulak,

Can you run the same command with the --verbose flag?

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