search

Dill-PICL / GOMAP-singularity

GOMAP-Singularity is the containerized version of GOMAP
http://gomap.blunderingbioinformatics.org/
MIT License
11 stars 5 forks source link

GOMAP-singularity: IndexError (Aggregate step) #31

Open mmtohm opened 1 year ago

mmtohm commented 1 year ago

Hi, I ran this command "./run-GOMAP-SINGLE.sh --step=aggregate --config=min-config.yml" and text error show this:

Running Aggregate Step Traceback (most recent call last): File "./gomap.py", line 105, in aggregate(config) File "/opt/GOMAP/code/gomap_aggregate.py", line 24, in aggregate download_argot2(config) File "/opt/GOMAP/code/pipeline/run_argot2.py", line 201, in download_argot2 csv_href = argot_config["baseurl"]+"/"+[ link.attrib["href"] for link in all_links if "getTSVFile.php" in link.attrib["href"] ][0] IndexError: list index out of range

Someone help me please

wkpalan commented 1 year ago

@mmtohm,

The GOMAP pipeline cannot run without the output files from Argot2.5 step that are created in the mixmeth step. Have you been able to run mixmeth step without any errors?