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Command line failed with exit code: 1 #389

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yinziiiiii opened this issue Nov 29, 2024 · 8 comments
Open

Command line failed with exit code: 1 #389

yinziiiiii opened this issue Nov 29, 2024 · 8 comments

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@yinziiiiii
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Something goes wrong when I use interproscan Help me plz.
There is no problem running the instance file.But with any other protein file, this is the problem
f4079cadc3d37640f2bfd44ade96387

the sequence is

A147-Vu04G1087-RA
MKAANGTPKGVALIIGDNNVRGSLQFLQHPNGTTHVTGRITGLSPGFHGFHIHAFGDTTN
GCNSTGPHFNPLKKDHGAPSDDERHAGDLGNIVAGPDGVAEISIRDTQIPLTGVHSIIGR
AVVVHADPDDLGKGGHELSKSTGNAGARIACGIIGLQSSV

./interproscan.sh -i test.fasta -appl Pfam,Gene3D,SUPERFAMILY,PRINTS,SMART,CDD,ProSiteProfiles -f gff3
@matthiasblum
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matthiasblum commented Dec 3, 2024 •
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Hello, @yinziiiiii,

I had no problem annotating your sequence. Here is the GFF3 output:

##gff-version 3
##feature-ontology http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269
##interproscan-version 5.72-103.0
##sequence-region A147-Vu04G1087-RA 1 160
A147-Vu04G1087-RA	.	polypeptide	1	160	.	+	.	ID=A147-Vu04G1087-RA;md5=82ecd1a20690abf6b7c9c96e42b178f7
A147-Vu04G1087-RA	Gene3D	protein_match	8	157	2.4E-65	+	.	date=03-12-2024;Target=A147-Vu04G1087-RA 8 157;ID=match$1_8_157;Name=G3DSA:2.60.40.200;status=T;Dbxref="InterPro:IPR036423"
A147-Vu04G1087-RA	PRINTS	protein_match	85	94	4.1E-45	+	.	date=03-12-2024;Target=A147-Vu04G1087-RA 85 94;ID=match$2_85_94;signature_desc=Cu-Zn-superoxide dismutase family signature;Name=PR00068;status=T;Dbxref="InterPro:IPR001424"
A147-Vu04G1087-RA	PRINTS	protein_match	49	71	4.1E-45	+	.	date=03-12-2024;Target=A147-Vu04G1087-RA 49 71;ID=match$2_49_71;signature_desc=Cu-Zn-superoxide dismutase family signature;Name=PR00068;status=T;Dbxref="InterPro:IPR001424"
A147-Vu04G1087-RA	PRINTS	protein_match	104	126	4.1E-45	+	.	date=03-12-2024;Target=A147-Vu04G1087-RA 104 126;ID=match$2_104_126;signature_desc=Cu-Zn-superoxide dismutase family signature;Name=PR00068;status=T;Dbxref="InterPro:IPR001424"
A147-Vu04G1087-RA	PRINTS	protein_match	129	155	4.1E-45	+	.	date=03-12-2024;Target=A147-Vu04G1087-RA 129 155;ID=match$2_129_155;signature_desc=Cu-Zn-superoxide dismutase family signature;Name=PR00068;status=T;Dbxref="InterPro:IPR001424"
A147-Vu04G1087-RA	Pfam	protein_match	20	154	5.1E-47	+	.	date=03-12-2024;Target=A147-Vu04G1087-RA 20 154;ID=match$3_20_154;signature_desc=Copper/zinc superoxide dismutase (SODC);Name=PF00080;status=T;Dbxref="InterPro:IPR001424"
A147-Vu04G1087-RA	CDD	protein_match	16	151	6.91753E-58	+	.	date=03-12-2024;Target=A147-Vu04G1087-RA 16 151;ID=match$4_16_151;signature_desc=Cu-Zn_Superoxide_Dismutase;Name=cd00305;status=T;Dbxref="InterPro:IPR001424"
A147-Vu04G1087-RA	SUPERFAMILY	protein_match	11	156	4.71E-58	+	.	date=03-12-2024;Target=A147-Vu04G1087-RA 11 156;ID=match$5_11_156;Name=SSF49329;status=T;Dbxref="InterPro:IPR036423"
##FASTA
>A147-Vu04G1087-RA
MKAANGTPKGVALIIGDNNVRGSLQFLQHPNGTTHVTGRITGLSPGFHGFHIHAFGDTTN
GCNSTGPHFNPLKKDHGAPSDDERHAGDLGNIVAGPDGVAEISIRDTQIPLTGVHSIIGR
AVVVHADPDDLGKGGHELSKSTGNAGARIACGIIGLQSSV
>match$1_8_157
PKGVALIIGDNNVRGSLQFLQHPNGTTHVTGRITGLSPGFHGFHIHAFGDTTNGCNSTGP
HFNPLKKDHGAPSDDERHAGDLGNIVAGPDGVAEISIRDTQIPLTGVHSIIGRAVVVHAD
PDDLGKGGHELSKSTGNAGARIACGIIGLQ
>match$2_49_71
GFHIHAFGDTTNGCNSTGPHFNP
>match$2_85_94
HAGDLGNIVA
>match$2_104_126
IRDTQIPLTGVHSIIGRAVVVHA
>match$2_129_155
DDLGKGGHELSKSTGNAGARIACGIIG
>match$3_20_154
VRGSLQFLQHPNGTTHVTGRITGLSPGFHGFHIHAFGDTTNGCNSTGPHFNPLKKDHGAP
SDDERHAGDLGNIVAGPDGVAEISIRDTQIPLTGVHSIIGRAVVVHADPDDLGKGGHELS
KSTGNAGARIACGII
>match$4_16_151
GDNNVRGSLQFLQHPNGTTHVTGRITGLSPGFHGFHIHAFGDTTNGCNSTGPHFNPLKKD
HGAPSDDERHAGDLGNIVAGPDGVAEISIRDTQIPLTGVHSIIGRAVVVHADPDDLGKGG
HELSKSTGNAGARIAC
>match$5_11_156
VALIIGDNNVRGSLQFLQHPNGTTHVTGRITGLSPGFHGFHIHAFGDTTNGCNSTGPHFN
PLKKDHGAPSDDERHAGDLGNIVAGPDGVAEISIRDTQIPLTGVHSIIGRAVVVHADPDD
LGKGGHELSKSTGNAGARIACGIIGL

Would you mind sharing the full error log?

@yinziiiiii
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yinziiiiii commented Dec 4, 2024 via email

@yinziiiiii
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yinziiiiii commented Dec 4, 2024 via email

@matthiasblum
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/public/home/wangyinzi/software/bio-software/interproscan-5.71-102.0/interproscan.sh: line 61: 52156 Killed

This line seems to indicate that the InterProScan process was killed by the operating system. This can happen when running computationally intensive programs on shared environments, like compute farms. If you're trying the run InterProScan on your institution's cluster, you most likely need to submit a job through a job scheduler (such as LSF, SLURM, etc.) to allocate resources.

$ ./interproscan.sh -i t.fa -appl Pfam,Gene3D,SUPERFAMILY,PRINTS,SMART,CDD,ProSiteProfiles -o output.tsv -f gff3
04/12/2024 17:12:13:043 Welcome to InterProScan-5.71-102.0
04/12/2024 17:12:13:045 Running InterProScan v5 in STANDALONE mode... on Linux
04/12/2024 17:12:33:455 RunID: login2_20241204_171232493_elit
04/12/2024 17:12:46:785 Loading file /public/home/sunshichao02/software/interproscan-5.71-102.0/t.fa
04/12/2024 17:12:46:787 Running the following analyses:
[CDD-3.20,Gene3D-4.3.0,Pfam-37.0,PRINTS-42.0,ProSiteProfiles-2023_05,SMART-9.0,SUPERFAMILY-1.75]
Available matches will be retrieved from the pre-calculated match lookup service.


Matches for any sequences that are not represented in the lookup service will be calculated locally.
2024-12-04 17:12:51,985 [Thread-6] [uk.ac.ebi.interpro.scan.business.sequence.BerkeleyPrecalculatedProteinLookup:748] WARN - 


The version of InterProScan you are using is 5.71-102.0
The version of the lookup service you are using is 5.72-103.0
As the data in these versions is not the same, you cannot use this match lookup service.
InterProScan will now run locally
If you would like to use the match lookup service, you have the following options:
i) Download the newest version of InterProScan5 from our FTP site by following the instructions on:
   https://www.ebi.ac.uk/interpro/interproscan.html
ii) Download the match lookup service for your version of InterProScan from our FTP site and install it locally.
    You will then need to edit the following property in your configuration file to point to your local installation:
    precalculated.match.lookup.service.url=


In the meantime, the analysis will continue to run locally.




2024-12-04 17:12:57,740 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 1
Command: bin/hmmer/hmmer3/3.3/hmmsearch -Z 61295632 --cut_ga 10 -o /public/home/sunshichao02/software/interproscan-5.71-102.0/temp/login2_20241204_1

I don't think that is the full log.

But if you only have one sequence, or a limited number of sequences to analyze, it might be easier for you to use the InterPro website: https://www.ebi.ac.uk/interpro/search/sequence/
You can submit 100 sequences at a time, and download the results when they become available.

@yinziiiiii
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yinziiiiii commented Dec 4, 2024 via email

@matthiasblum
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You may have forgotten to attach the file, or the file didn't reach GitHub. You may have to post directory on GitHub to attach files.

@yinziiiiii
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interproscan.zip
Can you see it now？

@matthiasblum
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Yes. Sorry for the late reply. I'll give it a go in the next few days.

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@matthiasblum @yinziiiiii