Problem with falco tool

usegalaxy.eu support
,
1

Hi! I’m working on a university assignment and I’m first practicing in Galaxy using an NCBI dataset (SRR17898727). I downloaded it using the tool “faster download and extract reads in FASTQ”.

Now I want to apply Falco to analyze the data quality (my data is in FASTQ format, single-end data, RNA). However, I get an error when running Falco. This is what appears in the error details:

Execution resulted in the following messages:

Fatal error: Exit code 139 ()

Tool generated the following standard error:

/data/jwd08/main/000/100/133/100133565/tool_script.sh: line 23: 17 Segmentation fault (core dumped) falco --threads ${GALAXY_SLOTS:-2} --quiet -f ‘fastq’ ‘SRR17898727’ -skip-summary

I’m not sure how to fix it. Thank you!

2

@Teresa I’m confused because the bug report you submitted in parallel is not at all about that NCBI dataset, but for data you seem to have uploaded. Very most likely that input data is either mal-formatted or got corrupted durin upload.

You can try to run fastqc on just that problematic file - it’s usually a little better with error messages.

3

Thank you very much! The problem was that the file was apparently too heavy. I tried with one that was smaller and it worked.