Importing files in Casava format - md5sum not found

[Ashoi_Dantra]

Hi, student here.
I have used CASAVA format before and have never faced this issue. I just used the code
qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path /export/home/a-e/adantra/iydata
--input-format CasavaOneEightSingleLanePerSampleDirFmt
--output-path /export/home/a-e/adantra/outputiy/demux-paired-end.qza

and i get an error:
Traceback (most recent call last):
File "/cm/shared/apps/conda/anaconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/builtin/tools.py", line 852, in _import
artifact = qiime2.sdk.Artifact.import_data(
File "/cm/shared/apps/conda/anaconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/result.py", line 325, in import_data
md5sums = util.md5sum_directory(path)
File "/cm/shared/apps/conda/anaconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/core/util.py", line 174, in md5sum_directory
sums[os.path.relpath(path, start=directory)] = md5sum(path)
File "/cm/shared/apps/conda/anaconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/core/util.py", line 141, in md5sum_native
result = subprocess.run(['md5sum', str(filepath)],
File "/cm/shared/apps/conda/anaconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['md5sum', '/export/home/a-e/adantra/iydata/138821_01_L001_R1_001.fastq.gz']' returned non-zero exit status 1.

An unexpected error has occurred:

Command '['md5sum', '/export/home/a-e/adantra/iydata/138821_01_L001_R1_001.fastq.gz']' returned non-zero exit status 1.

I am not sure what this means. I have validated that my files are all correct and have the necessary data. I also checked the permissions I have for this file which is all good. I do not know what md5sum is and when i used the code: which md5sum, it printed usr/bin/md5sum. I have also moved this file into the current folder i am working in (outputiy).

Anyone have any reasoning as to why this is happening and what I can do? I have spent two week on renaming, merging data and am very frustrated.

[Mike_Stevenson]

Hi Ashoi.

I think the Md5 command didn’t work correctly. I’ve had similar issues before and the problem for me was simply a corrupted download. I would try downloading again as one option. You could also try running the export command again but put ‘sudo’ before it if it’s perhaps related to permissions. Other than that, I’m not sure.

[Ashoi_Dantra]

Hi Mike, Yes you are right! It was a few files that had not downloaded in the correct format. Thankyou!!