glennhickey
commented
1 year ago Please try the latest release. It should be fixed there
On Thu, May 18, 2023 at 7:10 AM xuxingyubio @.***> wrote:
My code is as follows： cactus-pangenome ./js grch38_pan.seqfile --reference GRCh38 --outDir ./grch38_pan --outName grch38_pan --gbz --giraffe --vcf --chrom-vg --refContigs $(for i in seq 22; do printf "chr$i "; done ; echo "chrX chrY chrM") --otherContig chrOther --maxCores 40 --indexCores 20 --mapCores 6 --permissiveContigFilter 0.05 --workDir work_final --logFile grch38_pan.log error is as follows: join_wrapper' kind-export_join_wrapper/instance-t9ez1nr2 v4 Traceback (most recent call last): File "/home/users/xyxu/pangenome/demo/cactus-bin-v2.5.1/cactus_env/lib/python3.9/site-packages/toil/worker.py", line 403, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/home/users/xyxu/pangenome/demo/cactus-bin-v2.5.1/cactus_env/lib/python3.9/site-packages/toil/job.py", line 2743, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/home/users/xyxu/pangenome/demo/cactus-bin-v2.5.1/cactus_env/lib/python3.9/site-packages/toil/job.py", line 2660, in _run return self.run(fileStore) File "/home/users/xyxu/pangenome/demo/cactus-bin-v2.5.1/cactus_env/lib/python3.9/site-packages/toil/job.py", line 2888, in run rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) File "/home/users/xyxu/pangenome/demo/cactus-bin-v2.5.1/cactus_env/lib/python3.9/site-packages/cactus/refmap/cactus_pangenome.py", line 288, in export_join_wrapper export_join_data(job.fileStore, options, wf_output[0], wf_output[1], wf_output[2], wf_output[3], wf_output[4]) File "/home/users/xyxu/pangenome/demo/cactus-bin-v2.5.1/cactus_env/lib/python3.9/site-packages/cactus/refmap/cactus_graphmap_join.py", line 753, in export_join_data name = os.path.splitext(vg_path)[0] + '.vg' File "/home/users/xyxu/miniconda3/lib/python3.9/posixpath.py", line 118, in splitext p = os.fspath(p) TypeError: expected str, bytes or os.PathLike object, not NoneType [2023-05-17T22:34:42+0800] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host node13 If I don't use " --chrom-vg", it can run successfully.
— Reply to this email directly, view it on GitHub https://github.com/ComparativeGenomicsToolkit/cactus/issues/1018, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAG373X43Y4BEJJZEQC656LXGX7UDANCNFSM6AAAAAAYGKFXBM . You are receiving this because you are subscribed to this thread.Message ID: @.***>
xuxingyubio
My code is as follows： cactus-pangenome ./js grch38_pan.seqfile --reference GRCh38 --outDir ./grch38_pan --outName grch38_pan --gbz --giraffe --vcf --chrom-vg --refContigs $(for i in
seq 22; do printf "chr$i "; done ; echo "chrX chrY chrM") --otherContig chrOther --maxCores 40 --indexCores 20 --mapCores 6 --permissiveContigFilter 0.05 --workDir work_final --logFile grch38_pan.log error is as follows: join_wrapper' kind-export_join_wrapper/instance-t9ez1nr2 v4 Traceback (most recent call last): File "/home/users/xyxu/pangenome/demo/cactus-bin-v2.5.1/cactus_env/lib/python3.9/site-packages/toil/worker.py", line 403, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/home/users/xyxu/pangenome/demo/cactus-bin-v2.5.1/cactus_env/lib/python3.9/site-packages/toil/job.py", line 2743, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/home/users/xyxu/pangenome/demo/cactus-bin-v2.5.1/cactus_env/lib/python3.9/site-packages/toil/job.py", line 2660, in _run return self.run(fileStore) File "/home/users/xyxu/pangenome/demo/cactus-bin-v2.5.1/cactus_env/lib/python3.9/site-packages/toil/job.py", line 2888, in run rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) File "/home/users/xyxu/pangenome/demo/cactus-bin-v2.5.1/cactus_env/lib/python3.9/site-packages/cactus/refmap/cactus_pangenome.py", line 288, in export_join_wrapper export_join_data(job.fileStore, options, wf_output[0], wf_output[1], wf_output[2], wf_output[3], wf_output[4]) File "/home/users/xyxu/pangenome/demo/cactus-bin-v2.5.1/cactus_env/lib/python3.9/site-packages/cactus/refmap/cactus_graphmap_join.py", line 753, in export_join_data name = os.path.splitext(vg_path)[0] + '.vg' File "/home/users/xyxu/miniconda3/lib/python3.9/posixpath.py", line 118, in splitext p = os.fspath(p) TypeError: expected str, bytes or os.PathLike object, not NoneType [2023-05-17T22:34:42+0800] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host node13 If I don't use " --chrom-vg", it can run successfully.