(velocyto) feike@feike-desktop:~/users/HJJ/ASNEO/test$ bash run_ASNEO.sh /media/feike/HJJ/index/hg19.fa
/home/feike/miniconda3/envs/velocyto/lib/python3.7/site-packages/Bio/SubsMat/init.py:131: BiopythonDeprecationWarning: Bio.SubsMat has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.substitution_matrices as a replacement, and contact the Biopython developers if you still need the Bio.SubsMat module.
BiopythonDeprecationWarning,
################################################################################
2021-09-28 15:17:40,166 [INFO]: Start the program with Namespace(allele='HLA-C05:01,HLA-B18:01,HLA-C07:02,HLA-A03:01,HLA-A30:02,HLA-B07:02', bam=None, bind=2, columns=False, genome='/media/feike/HJJ/index/hg19.fa', junc='SRR2660032.SJ.out.tab', length='9', outdir='result', process=10, psi=0.1, reads=10, rpkm=1)
2021-09-28 15:17:40,187 [INFO]: Begin Junction to Isoform Process ...
2021-09-28 15:17:52,463 [INFO]: Origin junctions number is: 293941
2021-09-28 15:17:55,640 [INFO]: After filter, Remain junctions number is: 1026
2021-09-28 15:17:55,640 [INFO]: Generate novel isoforms
2021-09-28 15:19:06,949 [INFO]: Novel isoforms number is 256
2021-09-28 15:19:06,959 [INFO]: Begin Isoform to Epitope Process ...
2021-09-28 15:19:06,959 [INFO]: Translate isoforms to protein
index file /media/feike/HJJ/index/hg19.fa.fai not found, generating...
2021-09-28 15:19:34,501 [INFO]: Cut protein to short peptide
2021-09-28 15:19:51,005 [INFO]: All short pep number is: 871
2021-09-28 15:19:51,006 [INFO]: Call netMHCpan
/bin/sh: 1: /home/feike/users/HJJ/ASNEO/src/netMHCpan-4.0/netMHCpan: not found
Traceback (most recent call last):
File "../ASNEO.py", line 491, in
main()
File "../ASNEO.py", line 483, in main
ProcessIsoform(args.genome, args.length, args.allele, args.bind)
File "../ASNEO.py", line 256, in ProcessIsoform
RunMHCpan(allele=allele, peptxt=path['pep_txt'], affit=path['affit'])
File "../ASNEO.py", line 221, in RunMHCpan
line = f.readlines()[-1].strip()
IndexError: list index out of range
(velocyto) feike@feike-desktop:~/users/HJJ/ASNEO/test$ bash run_ASNEO.sh /media/feike/HJJ/index/hg19.fa /home/feike/miniconda3/envs/velocyto/lib/python3.7/site-packages/Bio/SubsMat/init.py:131: BiopythonDeprecationWarning: Bio.SubsMat has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.substitution_matrices as a replacement, and contact the Biopython developers if you still need the Bio.SubsMat module. BiopythonDeprecationWarning,
################################################################################ 2021-09-28 15:17:40,166 [INFO]: Start the program with Namespace(allele='HLA-C05:01,HLA-B18:01,HLA-C07:02,HLA-A03:01,HLA-A30:02,HLA-B07:02', bam=None, bind=2, columns=False, genome='/media/feike/HJJ/index/hg19.fa', junc='SRR2660032.SJ.out.tab', length='9', outdir='result', process=10, psi=0.1, reads=10, rpkm=1)
2021-09-28 15:17:40,187 [INFO]: Begin Junction to Isoform Process ... 2021-09-28 15:17:52,463 [INFO]: Origin junctions number is: 293941 2021-09-28 15:17:55,640 [INFO]: After filter, Remain junctions number is: 1026 2021-09-28 15:17:55,640 [INFO]: Generate novel isoforms 2021-09-28 15:19:06,949 [INFO]: Novel isoforms number is 256 2021-09-28 15:19:06,959 [INFO]: Begin Isoform to Epitope Process ... 2021-09-28 15:19:06,959 [INFO]: Translate isoforms to protein index file /media/feike/HJJ/index/hg19.fa.fai not found, generating... 2021-09-28 15:19:34,501 [INFO]: Cut protein to short peptide 2021-09-28 15:19:51,005 [INFO]: All short pep number is: 871 2021-09-28 15:19:51,006 [INFO]: Call netMHCpan /bin/sh: 1: /home/feike/users/HJJ/ASNEO/src/netMHCpan-4.0/netMHCpan: not found Traceback (most recent call last): File "../ASNEO.py", line 491, in
main()
File "../ASNEO.py", line 483, in main
ProcessIsoform(args.genome, args.length, args.allele, args.bind)
File "../ASNEO.py", line 256, in ProcessIsoform
RunMHCpan(allele=allele, peptxt=path['pep_txt'], affit=path['affit'])
File "../ASNEO.py", line 221, in RunMHCpan
line = f.readlines()[-1].strip()
IndexError: list index out of range