AndreaGuarracino
commented
5 months ago Can you share the 'Rice.fa.gz.bf3285f.mappings.wfmash.paf' file?
Andrea
From: Shuo Cao @.> Sent: Friday, April 26, 2024 04:59 To: pangenome/pggb @.> Cc: Subscribed @.***> Subject: [pangenome/pggb] erro about paf2net.py (Issue #393)
Hi ~ I ran into a problem when using partition-before-pggb.
here is my command line "partition-before-pggb -i Rice.fa.gz -o output -n 6 -t 30 -p 90 -s 5000 -D ./"
I've standardized the names of the chromosomes to the format "rice#1#1".
The error encountered was reported as follows
''' python3 /public/tools/miniconda3/envs/pggb/bin/scripts/paf2net.py -p .//Rice.fa.gz.bf3285f.mappings.wfmash.paf 0.02s user 0.01s system 58% cpu 0.06s total 9320Kb max memory Traceback (most recent call last): File "/public/tools/miniconda3/envs/pggb/bin/scripts/net2communities.py", line 24, in weight_list = [float(x) for x in open(args.edge_weights).read().strip().split('\n')] File "/public/tools/miniconda3/envs/pggb/bin/scripts/net2communities.py", line 24, in weight_list = [float(x) for x in open(args.edge_weights).read().strip().split('\n')] ValueError: could not convert string to float: '' Command exited with non-zero status 1 python3 /public/tools/miniconda3/envs/pggb/bin/scripts/net2communities.py -e .//Rice.fa.gz.bf3285f.mappings.wfmash.paf.edges.list.txt -w .//Rice.fa.gz.bf3285f.mappings.wfmash.paf.edges.weights.txt -n .//Rice.fa.gz.bf3285f.mappings.wfmash.paf.vertices.id2name.txt --accurate-detection --output-prefix output/Rice.fa.g 4.22s user 0.13s system 579% cpu 0.75s total 57724Kb max memory '''
— Reply to this email directly, view it on GitHubhttps://github.com/pangenome/pggb/issues/393, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AO26XHVJ3AW7AJO63TAEWQLY7IQPNAVCNFSM6AAAAABG2PLD26VHI2DSMVQWIX3LMV43ASLTON2WKOZSGI3DKNBSHE3DGMI. You are receiving this because you are subscribed to this thread.Message ID: @.***>
unavailable-2374
Hi ~ I ran into a problem when using partition-before-pggb.
here is my command line "partition-before-pggb -i Rice.fa.gz -o output -n 6 -t 30 -p 90 -s 5000 -D ./"
I've standardized the names of the chromosomes to the format "rice#1#1".
The error encountered was reported as follows
''' python3 /public/tools/miniconda3/envs/pggb/bin/scripts/paf2net.py -p .//Rice.fa.gz.bf3285f.mappings.wfmash.paf 0.02s user 0.01s system 58% cpu 0.06s total 9320Kb max memory Traceback (most recent call last): File "/public/tools/miniconda3/envs/pggb/bin/scripts/net2communities.py", line 24, in
weight_list = [float(x) for x in open(args.edge_weights).read().strip().split('\n')]
File "/public/tools/miniconda3/envs/pggb/bin/scripts/net2communities.py", line 24, in
weight_list = [float(x) for x in open(args.edge_weights).read().strip().split('\n')]
ValueError: could not convert string to float: ''
Command exited with non-zero status 1
python3 /public/tools/miniconda3/envs/pggb/bin/scripts/net2communities.py -e .//Rice.fa.gz.bf3285f.mappings.wfmash.paf.edges.list.txt -w .//Rice.fa.gz.bf3285f.mappings.wfmash.paf.edges.weights.txt -n .//Rice.fa.gz.bf3285f.mappings.wfmash.paf.vertices.id2name.txt --accurate-detection --output-prefix output/Rice.fa.g
4.22s user 0.13s system 579% cpu 0.75s total 57724Kb max memory
'''