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huangs001 / AlignGraph2

Similar genome assisted reassembly pipeline for PacBio long reads
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"Align and split" error #2

Closed elcortegano closed 1 year ago

elcortegano commented 1 year ago

I recently installed this tool, and run it as:

python3 AlignGraph2.py -t 60 -r reads.fq -c assembly.fa -g similar_genome.fa -o /scratch/elopez/poolfounders

But I get the following error:

Total read=4149430 Read iterator Done Filter Done All Done /scratch/elopez/AlignGraph2/thirdparty/mecat/Linux-amd64/bin/mecat2ref: error while loading shared libraries: libgomp.so.1: cannot open shared object file: No such file or directory K-Mer counting... Done Read to Contig... Done Read to Ref... Done Contig to Ref... Done Pre process... Done PAGraph... Done Extract and split... Done Align and split... Traceback (most recent call last): File "/scratch/elopez/AlignGraph2/./AlignGraph2.py", line 486, in cns_helper.split_ref(os.path.join(cns_wrk_mecat_dir, 'merge.ref'), cns_wrk_ref_dir, mapping) File "/scratch/elopez/AlignGraph2/script/cns_helper.py", line 43, in split_ref with open(ref_path) as f: ^^^^^^^^^^^^^^ FileNotFoundError: [Errno 2] No such file or directory: '/scratch/elopez/AlignGraph2/poolfounders/working_dir/cns/wrk/mecat/merge.ref'

What could be causing the problem? In relation with the error message, libgomp.so.1 is in my PATH variable.

In case it helps, these are the versions of the dependencies in my system:

elcortegano commented 1 year ago

Solved. I run the exact same script on a different node and for some reason there it worked. Looks like a subtle problem, but definitely one on my side.

Have a different issue now, which is that the program seems to be stuck at one step without progress (I also see it using only one thread, even when -t 60 was used). But that's a different issue.