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Error in Build RPGG for my own datasets #29
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Hi Lee, Could you trying using the latest commit? The Cheers, |
Hi Tony, /rd1/laixh/soft/danbing-tk-1.3.2//bin/vntr2kmers_thread -g -m <(cut -f if [ 0 == "1" ]; then /bin/bash: line 3: module: command not found set -eu /rd1/laixh/soft/danbing-tk-1.3.2//bin/vntr2kmers_thread -g -m <(cut -f if [ 0 == "1" ]; then
/bin/bash: line 3: module: command not found set -eu /rd1/laixh/soft/danbing-tk-1.3.2//bin/vntr2kmers_thread -g -m <(cut -f if [ 0 == "1" ]; then
Shutting down, this might take some time. It's seems that lack of module make the command failed. Because our platform do not support this software, so I delete all the module load command in file GoodPanGenomeGraph.snakefile. The pan.tr.kmers, pan.ntr.kmers and pan.graph.kmers successfully generated but error message occur when run rule GenSerializedGraphAndIndex, error message below: Error in rule GenSerializedGraphAndIndex: cd /rd1/laixh/soft/danbing-tk-1.3.2/test/output/ /rd1/laixh/soft/danbing-tk-1.3.2//bin/ktools serialize /rd1/laixh/soft/danbing-tk-1.3.2/test/output//pan
**I tried command line "/rd1/laixh/soft/danbing-tk-1.3.2//bin/ktools serialize /rd1/laixh/soft/danbing-tk-1.3.2/test/output//pan", this command returns Segmentation fault (core dumped). best wishes, |
Hi Lee, Thanks for reporting this error. I just removed the strict dependency for Thanks! |
Hi, set -eu /rd1/laixh/soft/danbing-tk-1.3.2//bin/vntr2kmers_thread -g -m <(cut -f if [ 0 == "1" ]; then
Best wishes, |
Fixed again! Forgot to make sure return code is zero. Hope it works now. |
Hi,
I use 35 hyplotypes to build RPGG for my VNTR sets, I find that the program always reports the following error when I run /soft/danbing-tk-1.1//script/preMBE.py /35Hyplto/genome.bam.tsv pan.tr.mbe.v0.bed:
beds[hi,m] = np.loadtxt(f"{g}/tmp1.{h}.bed", dtype=object, usecols=[0,1,2,6], ndmin=2)
ValueError: shape mismatch: value array of shape (101497,4) could not be broadcast to indexing result of shape (37920,4)
I checked f"{g}/tmp1.{h}.bed" file, it's seems that every hyplotype file have different number of mapping locations, what should I do to solve this problem, any suggestion will be appreciated.
Best wishes
Lee
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