# Error occured while running for MAFFT in qiime2
**URL:** https://forum.qiime2.org/t/error-occured-while-running-for-mafft-in-qiime2/29269
**Category:** Technical Support
**Tags:** phylogeny, tree
**Created:** [February 15, 2024, 5:08pm UTC](https://forum.qiime2.org/t/error-occured-while-running-for-mafft-in-qiime2/29269 "2024-02-15T17:08:31Z")
**Posts on this page:** 13
**Page:** 1
### Author:  [@pulak](https://forum.qiime2.org/u/pulak)
#### Post date: [February 15, 2024, 5:08pm UTC](https://forum.qiime2.org/t/error-occured-while-running-for-mafft-in-qiime2/29269/1 "2024-02-15T17:08:31Z")
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/commands.py", line 520, in **call**
results = self.\_execute\_action(
File "/home/pulakesw/anaconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/q2cli/commands.py", 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/action.py", 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/action.py", 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/\_visualizer.py", 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/\_demux.py", 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/gzip.py", line 305, in read1
return self.\_buffer.read1(size)
File "/home/pulakesw/anaconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/\_compression.py", line 68, in readinto
data = self.read(len(byte\_view))
File "/home/pulakesw/anaconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/gzip.py", line 470, in read
self.\_read\_eof()
File "/home/pulakesw/anaconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/gzip.py", line 516, in \_read\_eof
raise BadGzipFile("CRC check failed %s != %s" % (hex(crc32),
gzip.BadGzipFile: CRC check failed 0x11b726dd != 0x1399e02d
"
---
### Author:  [@colinvwood](https://forum.qiime2.org/u/colinvwood)
#### Post date: [February 15, 2024, 8:44pm UTC](https://forum.qiime2.org/t/error-occured-while-running-for-mafft-in-qiime2/29269/2 "2024-02-15T20:44:40Z")
Hello @pulak,
What command did you run? It looks like one of the fastq.gz files may be corrupt.
---
### Author:  [@pulak](https://forum.qiime2.org/u/pulak)
#### Post date: [February 16, 2024, 11:17am UTC](https://forum.qiime2.org/t/error-occured-while-running-for-mafft-in-qiime2/29269/3 "2024-02-16T11:17:07Z")
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
---
### Author:  [@colinvwood](https://forum.qiime2.org/u/colinvwood)
#### Post date: [February 16, 2024, 4:45pm UTC](https://forum.qiime2.org/t/error-occured-while-running-for-mafft-in-qiime2/29269/4 "2024-02-16T16:45:39Z")
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.
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### Author:  [@pulak](https://forum.qiime2.org/u/pulak)
#### Post date: [February 17, 2024, 7:15pm UTC](https://forum.qiime2.org/t/error-occured-while-running-for-mafft-in-qiime2/29269/5 "2024-02-17T19:15:55Z")
My rep-seqs.qza file is 44mb, its a large collection of samples over 4500.
And sequences.fasta file size is 76mb.
---
### Author:  [@cherman2](https://forum.qiime2.org/u/cherman2)
#### Post date: [February 19, 2024, 3:16pm UTC](https://forum.qiime2.org/t/error-occured-while-running-for-mafft-in-qiime2/29269/6 "2024-02-19T15:16:55Z")
---
### Author:  [@colinvwood](https://forum.qiime2.org/u/colinvwood)
#### Post date: [February 19, 2024, 4:45pm UTC](https://forum.qiime2.org/t/error-occured-while-running-for-mafft-in-qiime2/29269/7 "2024-02-19T16:45:11Z")
Hello @pulak,
Can you run `qiime tools validate rep-seqs.qza` and post the output?
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### Author:  [@colinvwood](https://forum.qiime2.org/u/colinvwood)
#### Post date: [February 19, 2024, 4:45pm UTC](https://forum.qiime2.org/t/error-occured-while-running-for-mafft-in-qiime2/29269/8 "2024-02-19T16:45:14Z")
---
### Author:  [@pulak](https://forum.qiime2.org/u/pulak)
#### Post date: [February 22, 2024, 8:05am UTC](https://forum.qiime2.org/t/error-occured-while-running-for-mafft-in-qiime2/29269/9 "2024-02-22T08:05:25Z")
It shows
"Result rep-seqs.qza appears to be valid at level=max".
---
### Author:  [@cherman2](https://forum.qiime2.org/u/cherman2)
#### Post date: [February 22, 2024, 3:30pm UTC](https://forum.qiime2.org/t/error-occured-while-running-for-mafft-in-qiime2/29269/10 "2024-02-22T15:30:39Z")
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### Author:  [@colinvwood](https://forum.qiime2.org/u/colinvwood)
#### Post date: [February 22, 2024, 4:35pm UTC](https://forum.qiime2.org/t/error-occured-while-running-for-mafft-in-qiime2/29269/11 "2024-02-22T16:35:31Z")
Hello @pulak,
Can you run the same command with the `--verbose` flag?
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### Author:  [@colinvwood](https://forum.qiime2.org/u/colinvwood)
#### Post date: [February 22, 2024, 4:35pm UTC](https://forum.qiime2.org/t/error-occured-while-running-for-mafft-in-qiime2/29269/12 "2024-02-22T16:35:34Z")
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### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [March 24, 2024, 10:35pm UTC](https://forum.qiime2.org/t/error-occured-while-running-for-mafft-in-qiime2/29269/13 "2024-03-24T22:35:57Z")
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