[Iplant-api-dev] LMOD errors
Barthelson, Roger A - (rogerab)
rogerab at email.arizona.edu
Fri May 22 11:07:25 MST 2015
I am still seeing job failures that start out with LMOD warning…
Here are 2, one for Interproscan and one for Bayesembler again:
Interproscan
{
"status" : "success",
"message" : null,
"version" : "2.1.0-r6d11c",
"result" : { }
}Lmod Warning: /opt/modulefiles/TACC-paths: (TACC-paths): couldn't read file
"/opt/modulefiles/TACC-paths": no such file or directory
While processing the following module(s):
Module fullname Module Filename
--------------- ---------------
TACC-paths /opt/modulefiles/TACC-paths
TACC /opt/modulefiles/TACC
Lmod Warning: /opt/modulefiles/cluster-paths: (cluster-paths): couldn't read
file "/opt/modulefiles/cluster-paths": no such file or directory
While processing the following module(s):
Module fullname Module Filename
--------------- ---------------
cluster-paths /opt/modulefiles/cluster-paths
splitfasta.pl -f blattrinity_pep.fa -o split_fasta -n 1000
splitfasta DONE
/opt/apps/launcher/launcher-2.0/paramrun: line 136: [: -ne: unary operator expected
/opt/apps/launcher/launcher-2.0/paramrun: line 136: [: -ne: unary operator expected
/opt/apps/launcher/launcher-2.0/paramrun: line 136: [: -ne: unary operator expected
/opt/apps/launcher/launcher-2.0/paramrun: line 136: [: -ne: unary operator expected
/opt/apps/launcher/launcher-2.0/paramrun: line 136: [: -ne: unary operator expected
/opt/apps/launcher/launcher-2.0/paramrun: line 136: [: -ne: unary operator expected
/opt/apps/launcher/launcher-2.0/paramrun: line 136: [: -ne: unary operator expected
/opt/apps/launcher/launcher-2.0/paramrun: line 136: [: -ne: unary operator expected
Warning: Permanently added 'c460-201,129.114.75.83' (RSA) to the list of known hosts.
Warning: Permanently added 'c460-203,129.114.75.85' (RSA) to the list of known hosts.
Warning: Permanently added 'c453-203,129.114.74.59' (RSA) to the list of known hosts.
Warning: Permanently added 'c460-104,129.114.75.82' (RSA) to the list of known hosts.
/opt/apps/launcher/launcher-2.0/init_launcher: line 23: [: : integer expression expected
/opt/apps/launcher/launcher-2.0/init_launcher: line 23: [: : integer expression expected
/opt/apps/launcher/launcher-2.0/init_launcher: line 23: [: : integer expression expected
/opt/apps/launcher/launcher-2.0/init_launcher: line 23: [: : integer expression expected
/opt/apps/launcher/launcher-2.0/init_launcher: line 23: [: : integer expression expected
/opt/apps/launcher/launcher-2.0/init_launcher: line 23: [: : integer expression expected
/opt/apps/launcher/launcher-2.0/init_launcher: line 23: [: : integer expression expected
/opt/apps/launcher/launcher-2.0/init_launcher: line 23: [: : integer expression expected
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details
real 0m27.539s
user 0m44.979s
sys 0m1.143s
real 0m27.563s
user 0m44.943s
sys 0m1.161s
real 0m27.455s
user 0m45.138s
sys 0m1.072s
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details
real 0m27.486s
user 0m44.947s
sys 0m1.131s
real 0m27.401s
user 0m45.386s
sys 0m1.068s
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details
real 0m27.467s
user 0m45.323s
sys 0m1.108s
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details
real 0m27.702s
user 0m45.321s
sys 0m1.141s
real 0m27.738s
user 0m45.166s
sys 0m1.202s
real 0m27.668s
user 0m45.292s
sys 0m1.060s
real 0m27.693s
user 0m45.382s
sys 0m1.077s
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details
real 0m27.810s
user 0m45.217s
sys 0m1.110s
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details
real 0m28.771s
user 0m46.059s
sys 0m1.088s
real 0m28.005s
user 0m45.967s
sys 0m1.108s
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details
real 0m29.073s
user 0m46.786s
sys 0m1.132s
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details
real 0m28.879s
user 0m48.734s
sys 0m1.107s
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details
real 0m28.985s
user 0m48.929s
sys 0m1.097s
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details
real 0m20.393s
user 0m47.167s
sys 0m1.112s
real 0m52.706s
user 0m0.437s
sys 0m0.154s
egrep: output/seqfile.8.xml: No such file or directory
cat: output/seqfile.8.tsv: No such file or directory
cat: output/seqfile.8.gff3: No such file or directory
egrep: output/seqfile.6.xml: No such file or directory
cat: output/seqfile.6.tsv: No such file or directory
cat: output/seqfile.6.gff3: No such file or directory
egrep: output/seqfile.7.xml: No such file or directory
cat: output/seqfile.7.tsv: No such file or directory
cat: output/seqfile.7.gff3: No such file or directory
egrep: output/seqfile.10.xml: No such file or directory
cat: output/seqfile.10.tsv: No such file or directory
cat: output/seqfile.10.gff3: No such file or directory
egrep: output/seqfile.4.xml: No such file or directory
cat: output/seqfile.4.tsv: No such file or directory
cat: output/seqfile.4.gff3: No such file or directory
egrep: output/seqfile.11.xml: No such file or directory
cat: output/seqfile.11.tsv: No such file or directory
cat: output/seqfile.11.gff3: No such file or directory
egrep: output/seqfile.13.xml: No such file or directory
cat: output/seqfile.13.tsv: No such file or directory
cat: output/seqfile.13.gff3: No such file or directory
egrep: output/seqfile.15.xml: No such file or directory
cat: output/seqfile.15.tsv: No such file or directory
cat: output/seqfile.15.gff3: No such file or directory
egrep: output/seqfile.14.xml: No such file or directory
cat: output/seqfile.14.tsv: No such file or directory
cat: output/seqfile.14.gff3: No such file or directory
egrep: output/seqfile.16.xml: No such file or directory
cat: output/seqfile.16.tsv: No such file or directory
cat: output/seqfile.16.gff3: No such file or directory
egrep: output/seqfile.2.xml: No such file or directory
cat: output/seqfile.2.tsv: No such file or directory
cat: output/seqfile.2.gff3: No such file or directory
egrep: output/seqfile.9.xml: No such file or directory
cat: output/seqfile.9.tsv: No such file or directory
cat: output/seqfile.9.gff3: No such file or directory
egrep: output/seqfile.1.xml: No such file or directory
cat: output/seqfile.1.tsv: No such file or directory
cat: output/seqfile.1.gff3: No such file or directory
egrep: output/seqfile.5.xml: No such file or directory
cat: output/seqfile.5.tsv: No such file or directory
cat: output/seqfile.5.gff3: No such file or directory
egrep: output/seqfile.3.xml: No such file or directory
cat: output/seqfile.3.tsv: No such file or directory
cat: output/seqfile.3.gff3: No such file or directory
egrep: output/seqfile.12.xml: No such file or directory
cat: output/seqfile.12.tsv: No such file or directory
cat: output/seqfile.12.gff3: No such file or directory
egrep: output/seqfile.0.xml: No such file or directory
cat: output/seqfile.0.tsv: No such file or directory
cat: output/seqfile.0.gff3: No such file or directory
{
"status" : "success",
"message" : null,
"version" : "2.1.0-r6d11c",
"result" : { }
}
BAYESEMBLER
{
"status" : "success",
"message" : null,
"version" : "2.1.0-r6d11c",
"result" : { }
}Lmod Warning: /opt/modulefiles/TACC-paths: (TACC-paths): couldn't read file
"/opt/modulefiles/TACC-paths": no such file or directory
While processing the following module(s):
Module fullname Module Filename
--------------- ---------------
TACC-paths /opt/modulefiles/TACC-paths
TACC /opt/modulefiles/TACC
Lmod Warning: /opt/modulefiles/cluster-paths: (cluster-paths): couldn't read
file "/opt/modulefiles/cluster-paths": no such file or directory
While processing the following module(s):
Module fullname Module Filename
--------------- ---------------
cluster-paths /opt/modulefiles/cluster-paths
[bam_cat] ERROR: fail to open file 'TrmPr1_SRR567164.sra_1.fastq.bam' 'TrmPr1_SRR567166.sra_1.fastq.bam' 'TrmPr1_SRR567167.sra_1.fastq.bam'.
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated.
[bam_sort_core] truncated file. Continue anyway.
[bam_cat] ERROR: fail to open file 'TrmPr1_SRR567164.sra_1.fastq.bam' 'TrmPr1_SRR567166.sra_1.fastq.bam' 'TrmPr1_SRR567167.sra_1.fastq.bam'.
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated.
[bam_sort_core] truncated file. Continue anyway.
bayesembler: /seqdata/krogh/jola/projects/transcriptome_assembly/code/release/bayesembler_1_1_1_pub_release/src/assembler.cpp:382: std::vector<std::pair<std::list<GraphInfo>, std::basic_string<char> > > Assembler::generateSpliceGraphs(double*): Assertion `unique_reads.empty()' failed.
/tmp/slurmd/job5300501/slurm_script: line 92: 31244 Aborted ./bayesembler -p 14 $runthis --output-mode full -b baybams2.bam
real 0m36.094s
user 0m33.433s
sys 0m0.293s
{
"status" : "success",
"message" : null,
"version" : "2.1.0-r6d11c",
"result" : { }
}bayesembler: /seqdata/krogh/jola/projects/transcriptome_assembly/code/release/bayesembler_1_1_1_pub_release/src/assembler.cpp:382: std::vector<std::pair<std::list<GraphInfo>, std::basic_string<char> > > Assembler::generateSpliceGraphs(double*): Assertion `unique_reads.empty()' failed.
/tmp/slurmd/job5300502/slurm_script: line 92: 30457 Aborted ./bayesembler -p 14 $runthis --output-mode full -b baybams2.bam
real 0m35.520s
user 0m33.392s
sys 0m0.306s
{
"status" : "success",
"message" : null,
"version" : "2.1.0-r6d11c",
"result" : { }
}
Roger
--
Roger Barthelson Ph.D.
Scientific Analyst
iPlant Collaborative
BIO5 Institute, University of Arizona
Phone: 520-977-5249
Email: rogerab at email.arizona.edu<mailto:rogerab at email.arizona.edu>
Web: www.iplantcollaborative.org/<http://www.iplantcollaborative.org/>
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