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xiaoli-dong
panic: runtime error: slice bounds out of range
I've been able to run metaerg successfully with and without providing a depth file on some of my datasets using:
metaerg.pl --dbdir /projects/p30777/db --depth /projects/p30777/metagenome_data/bams/[sample_ID]/depth.txt /projects/p30777/metagenome_data/contigs/[sample_ID]_contigs.fa --sp --tm --outdir /projects/p30777/Omics_methods_pub/metaerg/[sample_ID]_depth --force
However, on a few of my datasets (which are formatted the same way as the others) I get the error 'panic: runtime error: slice bounds out of range" (output pasted below). Does anybody know what causes this error? Thanks!
OUTPUT: [Wed Dec 4 06:00:08 2019] Running: signalp -verbose=false -org gram- -format short -gff3 -tmp /projects/p30777/Omics_methods_pub/metaerg/DeMMO6_depth/tmp -prefix /projects/p30777/Omics_methods_pub/metaerg/DeMMO6_depth/tmp/cds.faa.signalp.gramn -fasta /projects/p30777/Omics_methods_pub/metaerg/DeMMO6_depth/tmp/cds.faa [Wed Dec 4 06:00:14 2019] Running: signalp -verbose=false -org gram+ -format short -gff3 -tmp /projects/p30777/Omics_methods_pub/metaerg/DeMMO6_depth/tmp -prefix /projects/p30777/Omics_methods_pub/metaerg/DeMMO6_depth/tmp/cds.faa.signalp.gramp -fasta /projects/p30777/Omics_methods_pub/metaerg/DeMMO6_depth/tmp/cds.faa [Wed Dec 4 06:00:20 2019] Running: signalp -verbose=false -org euk -format short -gff3 -tmp /projects/p30777/Omics_methods_pub/metaerg/DeMMO6_depth/tmp -prefix /projects/p30777/Omics_methods_pub/metaerg/DeMMO6_depth/tmp/cds.faa.signalp.euk -fasta /projects/p30777/Omics_methods_pub/metaerg/DeMMO6_depth/tmp/cds.faa [Wed Dec 4 06:00:27 2019] Running: signalp -verbose=false -org arch -format short -gff3 -tmp /projects/p30777/Omics_methods_pub/metaerg/DeMMO6_depth/tmp -prefix /projects/p30777/Omics_methods_pub/metaerg/DeMMO6_depth/tmp/cds.faa.signalp.arch -fasta /projects/p30777/Omics_methods_pub/metaerg/DeMMO6_depth/tmp/cds.faa panic: runtime error: slice bounds out of range
goroutine 1 [running]: github.com/tensorflow/tensorflow/tensorflow/go.tensorData(0x2b05c4001890, 0xc5ee7610c0, 0x678880, 0x6e6688) /home/people/jjalma/go/src/github.com/tensorflow/tensorflow/tensorflow/go/tensor.go:210 +0xa1 github.com/tensorflow/tensorflow/tensorflow/go.NewTensor(0x674000, 0xc5ee7610a0, 0x674000, 0xc5ee7610a0, 0x0) /home/people/jjalma/go/src/github.com/tensorflow/tensorflow/tensorflow/go/tensor.go:94 +0x221 main.main() /home/people/jjalma/SignalP-5.0b/signalp.go:607 +0x5870 [Wed Dec 4 12:17:24 2019] Could not run command:signalp -verbose=false -org gram- -format short -gff3 -tmp /projects/p30777/Omics_methods_pub/metaerg/DeMMO6_depth/tmp -prefix /projects/p30777/Omics_methods_pub/metaerg/DeMMO6_depth/tmp/cds.faa.signalp.gramn -fasta /projects/p30777/Omics_methods_pub/metaerg/DeMMO6_depth/tmp/cds.faa,
Perl exited with active threads: 3 running and unjoined 0 finished and unjoined 0 running and detached [Wed Dec 4 12:17:25 2019] Could not run command:/home/cpc7770/metaerginstall/bin/perl /home/cpc7770/metaerginstall/metaerg/bin/predictFeatures.pl --dbdir /projects/p30777/db --evalue 1e-05 --gtype meta --gc 11 --minorflen 180 --prefix metaerg.pl_12042019 --cpus 8 --outdir /projects/p30777/Omics_methods_pub/metaerg/DeMMO6_depth/tmp --sp --tm --force /projects/p30777/Omics_methods_pub/metaerg/DeMMO6_depth/metaerg.pl_12042019.fna,
Hi again, I was/am having the same problem with one of my samples. This seems to be a problem in the current SignalP version. Because the deadline for my bachelor thesis approaches I just disabled SignalP. It is weird, that the error happens in the TensorFlow library. The web service for SignalP 5 is limited to 5.000 sequences and 10.000aa long CDS. SignalP 4 had this integrated into its script.
According to this blogpost the input layer is 70*20. The length shouldn't a problem.
I will prepare a R script to check the length of the sequences and amino acid characters. Gram - also fails for me, but it is the first to be called, this may be just the reason for that.
Ah thank you I will try running without SignalP. Good luck with your thesis!