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Can not get the results #16

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liaochenlanruo opened this issue Oct 8, 2021 · 2 comments
Closed

Can not get the results #16

liaochenlanruo opened this issue Oct 8, 2021 · 2 comments

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@liaochenlanruo
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When I running the following command, the errors happened, and I can not gain the results.

islandpath LHL010.gbk LHL010.island

Smartmatch is experimental at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 674.
Smartmatch is experimental at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 677.
Smartmatch is experimental at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 852.
/home/liu/miniconda3/envs/component/opt/islandpath/logger.conf2021/10/08 20:06:51 [main] Logging initialized
2021/10/08 20:06:51 [main] Creating temp directory with needed files
2021/10/08 20:06:51 [main] This is the /mnt/c/Users/ADMIN/Downloads/islandpath-1.0.6-conda/islandpath-1.0.6-conda/dimob_tmpKunmimIPyx/LHL010
2021/10/08 20:06:51 [GenomeUtils] From filename /mnt/c/Users/ADMIN/Downloads/islandpath-1.0.6-conda/islandpath-1.0.6-conda/dimob_tmpKunmimIPyx/LHL010.gbk got /mnt/c/Users/ADMIN/Downloads/islandpath-1.0.6-conda/islandpath-1.0.6-conda/dimob_tmpKunmimIPyx/LHL010, gbk
2021/10/08 20:06:51 [GenomeUtils] Reading genbank format file
2021/10/08 20:06:51 [GenomeUtils] The genome sequence in /mnt/c/Users/ADMIN/Downloads/islandpath-1.0.6-conda/islandpath-1.0.6-conda/dimob_tmpKunmimIPyx/LHL010.gbk has been read.
2021/10/08 20:06:52 [GenomeUtils] Checking contig unknown
2021/10/08 20:06:52 [GenomeUtils] Found sequence in the genbank/embl file
2021/10/08 20:06:52 [GenomeUtils] Checking contig unknown
2021/10/08 20:06:52 [GenomeUtils] Found sequence in the genbank/embl file
2021/10/08 20:06:52 [GenomeUtils] Checking contig unknown
2021/10/08 20:06:52 [GenomeUtils] Found sequence in the genbank/embl file
2021/10/08 20:06:52 [GenomeUtils] Checking contig unknown
2021/10/08 20:06:52 [GenomeUtils] Found sequence in the genbank/embl file
2021/10/08 20:06:52 [GenomeUtils] Checking contig unknown
2021/10/08 20:06:52 [GenomeUtils] Found sequence in the genbank/embl file
2021/10/08 20:06:52 [GenomeUtils] Checking contig unknown
2021/10/08 20:06:52 [GenomeUtils] Found sequence in the genbank/embl file
2021/10/08 20:06:52 [GenomeUtils] Checking contig unknown
2021/10/08 20:06:52 [GenomeUtils] Found sequence in the genbank/embl file
2021/10/08 20:06:52 [GenomeUtils] Checking contig unknown
2021/10/08 20:06:52 [GenomeUtils] Found sequence in the genbank/embl file
2021/10/08 20:06:52 [GenomeUtils] Checking contig unknown
2021/10/08 20:06:52 [GenomeUtils] Found sequence in the genbank/embl file
2021/10/08 20:06:52 [GenomeUtils] Checking contig unknown
2021/10/08 20:06:52 [GenomeUtils] Found sequence in the genbank/embl file
2021/10/08 20:06:52 [GenomeUtils] Checking contig unknown
2021/10/08 20:06:52 [GenomeUtils] Found sequence in the genbank/embl file
2021/10/08 20:06:52 [GenomeUtils] Checking contig unknown
2021/10/08 20:06:52 [GenomeUtils] Found sequence in the genbank/embl file
2021/10/08 20:06:52 [GenomeUtils] Checking contig unknown
2021/10/08 20:06:52 [GenomeUtils] Found sequence in the genbank/embl file
2021/10/08 20:06:52 [GenomeUtils] Checking contig unknown
2021/10/08 20:06:52 [GenomeUtils] Found sequence in the genbank/embl file
2021/10/08 20:06:52 [GenomeUtils] Checking contig unknown
2021/10/08 20:06:52 [GenomeUtils] Found sequence in the genbank/embl file
2021/10/08 20:06:52 [GenomeUtils] We have 15 contigs
2021/10/08 20:06:52 [GenomeUtils] From filename /mnt/c/Users/ADMIN/Downloads/islandpath-1.0.6-conda/islandpath-1.0.6-conda/dimob_tmpKunmimIPyx/LHL010.gbk got /mnt/c/Users/ADMIN/Downloads/islandpath-1.0.6-conda/islandpath-1.0.6-conda/dimob_tmpKunmimIPyx/LHL010, gbk
2021/10/08 20:06:52 [GenomeUtils] No base filename given in args, trying to use object default: /mnt/c/Users/ADMIN/Downloads/islandpath-1.0.6-conda/islandpath-1.0.6-conda/dimob_tmpKunmimIPyx/LHL010
2021/10/08 20:06:52 [GenomeUtils] Found formats:
2021/10/08 20:06:52 [GenomeUtils] The genome sequence in /mnt/c/Users/ADMIN/Downloads/islandpath-1.0.6-conda/islandpath-1.0.6-conda/dimob_tmpKunmimIPyx/LHL010.gbk has been read.
2021/10/08 20:06:52 [GenomeUtils] Now generating required file formats (faa, ffn and ptt)
2021/10/08 20:06:53 [GenomeUtils] No base filename given in args, trying to use object default: /mnt/c/Users/ADMIN/Downloads/islandpath-1.0.6-conda/islandpath-1.0.6-conda/dimob_tmpKunmimIPyx/LHL010
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 372, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 373, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 374, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
print() on closed filehandle $PTT_OUT at /home/liu/miniconda3/envs/component/opt/islandpath/lib/GenomeUtils.pm line 471, line 67589.
.
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2021/10/08 20:10:24 [GenomeUtils] No base filename given in args, trying to use object default: /mnt/c/Users/ADMIN/Downloads/islandpath-1.0.6-conda/islandpath-1.0.6-conda/dimob_tmpc0DVqO72Hn/LHL010
2021/10/08 20:10:24 [main] Running IslandPath-DIMOB
2021/10/08 20:10:24 [Dimob] Genome /mnt/c/Users/ADMIN/Downloads/islandpath-1.0.6-conda/islandpath-1.0.6-conda/dimob_tmpc0DVqO72Hn/LHL010, found formats: .faa .ffn .ptt
2021/10/08 20:10:24 [Dimob] Looking for mobility genes using hmmer
2021/10/08 20:10:24 [Dimob] Running hmmer command hmmscan /home/liu/miniconda3/envs/component/opt/islandpath/hmmpfam/Pfam-A_mobgenes_201512_prok /mnt/c/Users/ADMIN/Downloads/islandpath-1.0.6-conda/islandpath-1.0.6-conda/dimob_tmpc0DVqO72Hn/LHL010.faa >/mnt/c/Users/ADMIN/Downloads/islandpath-1.0.6-conda/islandpath-1.0.6-conda/dimob_tmpc0DVqO72Hn/blasttmpLevQ2Wqw_j
2021/10/08 20:10:41 [Dimob] Parsing hmmer results with Mobgene
2021/10/08 20:10:41 [Dimob::Mobgene] Using extended ids
2021/10/08 20:10:42 [Dimob] Retrieving mobility genes from ptt file
Use of uninitialized value in numeric eq (==) at /home/liu/miniconda3/envs/component/opt/islandpath/lib/Dimob/tabdelimitedfiles.pm line 67.
2021/10/08 20:10:42 [Dimob] Calculating dinucleotide bias
Use of uninitialized value in concatenation (.) or string at /home/liu/miniconda3/envs/component/opt/islandpath/lib/Dimob/genomicislands.pm line 372, line 4077.
Use of uninitialized value in numeric eq (==) at /home/liu/miniconda3/envs/component/opt/islandpath/lib/Dimob/tabdelimitedfiles.pm line 67.
2021/10/08 20:10:52 [Dimob] Looking for regions with dinuc bias and mobility genes
2021/10/08 20:10:52 [Dimob] Cleaning temporary files
2021/10/08 20:10:52 [Dimob] Cleaning up temp files for Dimob
2021/10/08 20:10:52 [main] Printing results
2021/10/08 20:10:52 [main] Removing tmp files
@innovate-invent
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Hi @liaochenlanruo, and thanks for your interest in islandpath. This appears to be the same issue as #14 . Please make sure you are running islandpath on a genbank file with only one contig.

@liaochenlanruo
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@innovate-invent Thanks a lot! It works!

@gavinmdouglas gavinmdouglas mentioned this issue Jul 22, 2022
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@innovate-invent @liaochenlanruo