fastq-dl: ModuleNotFoundError: No module named 'executor'

Hello and thank you for this useful tool! I have made a docker with the installation of fastq-dl and I tried to run one example but it seems is not working. the dockerfile can be found here: https://github.com/ConYel/docker_sncRNA_workflow/blob/master/Dockerfile

Do you believe there are some issues with the installation or the way the container is created?

fastq-dl SRX477044 ENA
2020-12-16 14:46:36:root:INFO - Aspera Connect not available, using FTP for ENA downloads
2020-12-16 14:46:37:root:INFO - Query: SRX477044
2020-12-16 14:46:37:root:INFO - Archive: ENA
2020-12-16 14:46:37:root:INFO - Total Runs To Download: 1
2020-12-16 14:46:37:root:INFO - 	Working on run SRR1178104...
Traceback (most recent call last):
  File "/root/miniconda/bin/fastq-dl", line 462, in <module>
    fastqs = ena_download(run, outdir, aspera=aspera,
  File "/root/miniconda/bin/fastq-dl", line 216, in ena_download
    fastq = download_ena_fastq(
  File "/root/miniconda/bin/fastq-dl", line 250, in download_ena_fastq
    execute(f'mkdir -p {outdir}')
  File "/root/miniconda/bin/fastq-dl", line 94, in execute
    from executor import ExternalCommand, ExternalCommandFailed
ModuleNotFoundError: No module named 'executor'

About this issue

Original URL
State: closed
Created 4 years ago
Comments: 15 (9 by maintainers)

Most upvoted comments

Glad you were able to get it working!

I’ll look into adding progress for downloads, and I agree I think and option to overwrite should be added. Looking at the pigz error, it wasn’t very helpful. I’ll add a “I found this, please use --force to overwrite” type of message before any downloads start.

rpetit3 on Dec 17, 2020

Well, thank you very much! I will check tomorrow with a new build of the docker plus the ENV to see if it could help.

ConYel on Dec 16, 2020

I submitted a new release (v1.0.6) with a fix for ENA downloads. It will be available from conda today or tomorrow.

I also created a work flow (https://github.com/rpetit3/fastq-dl/runs/1565163292) to make sure downloads are working.

Thank you very much for your help!

rpetit3 on Dec 16, 2020

Ok looks like somethign has changed on ENA side.

In the past, this worked:

wget -O ./SRR1178104_1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR117/004/SRR1178104/SRR1178104_1.fastq.gz

Now, ftp:// is needed for it to work:

wget -O ./SRR1178104_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR117/004/SRR1178104/SRR1178104_1.fastq.gz

As a temporary solution you could try downloading from SRA

/root/miniconda/bin/python3 /root/miniconda/bin/fastq-dl  SRX477044 SRA

rpetit3 on Dec 16, 2020

That’s a different error though, so progress!

Looks like the service is unavailable at the moment:

http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR117/004/SRR1178104/SRR1178104_1.fastq.gz

rpetit3 on Dec 16, 2020