R scripting front-end version 3.6.1 (2019-07-05)
Write arguments to /ibex/scratch/projects/c2042/analysis/sqanti3/all_samples.chained.params.txt...
**** Running SQANTI3...
launching worker on on splits/0/all_samples.chained.gff.split0....
launching worker on on splits/1/all_samples.chained.gff.split1....
**** Parsing provided files....
Reading genome fasta /home/albadenm/c2042/analysis/IsoSeq_Ocoarcata/maker/OcoaRS1.PZYT01.fa.maker.output/round4/OcoaRS1.PZYT01.fa.masked....
launching worker on on splits/2/all_samples.chained.gff.split2....
**** Parsing provided files....
Reading genome fasta /home/albadenm/c2042/analysis/IsoSeq_Ocoarcata/maker/OcoaRS1.PZYT01.fa.maker.output/round4/OcoaRS1.PZYT01.fa.masked....
launching worker on on splits/3/all_samples.chained.gff.split3....
**** Parsing provided files....
Reading genome fasta /home/albadenm/c2042/analysis/IsoSeq_Ocoarcata/maker/OcoaRS1.PZYT01.fa.maker.output/round4/OcoaRS1.PZYT01.fa.masked....
launching worker on on splits/4/all_samples.chained.gff.split4....
**** Parsing provided files....
Reading genome fasta /home/albadenm/c2042/analysis/IsoSeq_Ocoarcata/maker/OcoaRS1.PZYT01.fa.maker.output/round4/OcoaRS1.PZYT01.fa.masked....
launching worker on on splits/5/all_samples.chained.gff.split5....
**** Parsing provided files....
Reading genome fasta /home/albadenm/c2042/analysis/IsoSeq_Ocoarcata/maker/OcoaRS1.PZYT01.fa.maker.output/round4/OcoaRS1.PZYT01.fa.masked....
launching worker on on splits/6/all_samples.chained.gff.split6....
**** Parsing provided files....
Reading genome fasta /home/albadenm/c2042/analysis/IsoSeq_Ocoarcata/maker/OcoaRS1.PZYT01.fa.maker.output/round4/OcoaRS1.PZYT01.fa.masked....
launching worker on on splits/7/all_samples.chained.gff.split7....
**** Parsing provided files....
Reading genome fasta /home/albadenm/c2042/analysis/IsoSeq_Ocoarcata/maker/OcoaRS1.PZYT01.fa.maker.output/round4/OcoaRS1.PZYT01.fa.masked....
**** Parsing provided files....
Reading genome fasta /home/albadenm/c2042/analysis/IsoSeq_Ocoarcata/maker/OcoaRS1.PZYT01.fa.maker.output/round4/OcoaRS1.PZYT01.fa.masked....
Skipping aligning of sequences because GTF file was provided.
Skipping aligning of sequences because GTF file was provided.
Skipping aligning of sequences because GTF file was provided.
Skipping aligning of sequences because GTF file was provided.
Skipping aligning of sequences because GTF file was provided.
Skipping aligning of sequences because GTF file was provided.
Skipping aligning of sequences because GTF file was provided.
Skipping aligning of sequences because GTF file was provided.
Indels will be not calculated since you ran SQANTI3 without alignment step (SQANTI3 with gtf format as transcriptome input).
Indels will be not calculated since you ran SQANTI3 without alignment step (SQANTI3 with gtf format as transcriptome input).
Indels will be not calculated since you ran SQANTI3 without alignment step (SQANTI3 with gtf format as transcriptome input).
Indels will be not calculated since you ran SQANTI3 without alignment step (SQANTI3 with gtf format as transcriptome input).
**** Predicting ORF sequences...
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to a fallback locale ("en_US.UTF-8").
Indels will be not calculated since you ran SQANTI3 without alignment step (SQANTI3 with gtf format as transcriptome input).
**** Predicting ORF sequences...
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to a fallback locale ("en_US.UTF-8").
**** Predicting ORF sequences...
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to a fallback locale ("en_US.UTF-8").
**** Predicting ORF sequences...
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to a fallback locale ("en_US.UTF-8").
Indels will be not calculated since you ran SQANTI3 without alignment step (SQANTI3 with gtf format as transcriptome input).
**** Predicting ORF sequences...
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to a fallback locale ("en_US.UTF-8").
Indels will be not calculated since you ran SQANTI3 without alignment step (SQANTI3 with gtf format as transcriptome input).
**** Predicting ORF sequences...
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to a fallback locale ("en_US.UTF-8").
Indels will be not calculated since you ran SQANTI3 without alignment step (SQANTI3 with gtf format as transcriptome input).
**** Predicting ORF sequences...
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to a fallback locale ("en_US.UTF-8").
**** Predicting ORF sequences...
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to a fallback locale ("en_US.UTF-8").
error: data input empty
GeneMarkS: error on last system call, error code 256
Abort program!!!
Process Process-1:
Traceback (most recent call last):
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 1748, in run
orfDict = correctionPlusORFpred(args, genome_dict)
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 583, in correctionPlusORFpred
if subprocess.check_call(cmd, shell=True, cwd=gmst_dir)!=0:
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/subprocess.py", line 363, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'perl /ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/utilities/gmst/gmst.pl -faa --strand direct --fnn --output /ibex/scratch/projects/c2042/analysis/sqanti3/splits/0/GMST/GMST_tmp /ibex/scratch/projects/c2042/analysis/sqanti3/splits/0/all_samples.chained_corrected.fasta' returned non-zero exit status 1.
**** Parsing Reference Transcriptome....
/home/albadenm/c2042/analysis/IsoSeq_Ocoarcata/maker/OcoaRS1.PZYT01.fa.maker.output/round4/OcoaRS1.PZYT01.fa.all.maker.functional_ipr.gff doesn't appear to be a GTF file (GFF not supported by this program)
Process Process-8:
Traceback (most recent call last):
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 1751, in run
refs_1exon_by_chr, refs_exons_by_chr, junctions_by_chr, junctions_by_gene, start_ends_by_gene = reference_parser(args, list(genome_dict.keys()))
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 653, in reference_parser
for r in genePredReader(referenceFiles):
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 134, in __init__
self.f = open(filename)
FileNotFoundError: [Errno 2] No such file or directory: '/ibex/scratch/projects/c2042/analysis/sqanti3/splits/7/refAnnotation_all_samples.chained.genePred'
**** Parsing Reference Transcriptome....
/home/albadenm/c2042/analysis/IsoSeq_Ocoarcata/maker/OcoaRS1.PZYT01.fa.maker.output/round4/OcoaRS1.PZYT01.fa.all.maker.functional_ipr.gff doesn't appear to be a GTF file (GFF not supported by this program)
Process Process-3:
Traceback (most recent call last):
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 1751, in run
refs_1exon_by_chr, refs_exons_by_chr, junctions_by_chr, junctions_by_gene, start_ends_by_gene = reference_parser(args, list(genome_dict.keys()))
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 653, in reference_parser
for r in genePredReader(referenceFiles):
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 134, in __init__
self.f = open(filename)
FileNotFoundError: [Errno 2] No such file or directory: '/ibex/scratch/projects/c2042/analysis/sqanti3/splits/2/refAnnotation_all_samples.chained.genePred'
**** Parsing Reference Transcriptome....
/home/albadenm/c2042/analysis/IsoSeq_Ocoarcata/maker/OcoaRS1.PZYT01.fa.maker.output/round4/OcoaRS1.PZYT01.fa.all.maker.functional_ipr.gff doesn't appear to be a GTF file (GFF not supported by this program)
Process Process-3:
Traceback (most recent call last):
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 1751, in run
refs_1exon_by_chr, refs_exons_by_chr, junctions_by_chr, junctions_by_gene, start_ends_by_gene = reference_parser(args, list(genome_dict.keys()))
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 653, in reference_parser
for r in genePredReader(referenceFiles):
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 134, in __init__
self.f = open(filename)
FileNotFoundError: [Errno 2] No such file or directory: '/ibex/scratch/projects/c2042/analysis/sqanti3/splits/2/refAnnotation_all_samples.chained.genePred'
^[[B**** Parsing Reference Transcriptome....
/home/albadenm/c2042/analysis/IsoSeq_Ocoarcata/maker/OcoaRS1.PZYT01.fa.maker.output/round4/OcoaRS1.PZYT01.fa.all.maker.functional_ipr.gff doesn't appear to be a GTF file (GFF not supported by this program)
Process Process-4:
Traceback (most recent call last):
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 1751, in run
refs_1exon_by_chr, refs_exons_by_chr, junctions_by_chr, junctions_by_gene, start_ends_by_gene = reference_parser(args, list(genome_dict.keys()))
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 653, in reference_parser
for r in genePredReader(referenceFiles):
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 134, in __init__
self.f = open(filename)
FileNotFoundError: [Errno 2] No such file or directory: '/ibex/scratch/projects/c2042/analysis/sqanti3/splits/3/refAnnotation_all_samples.chained.genePred'
error: data input empty
GeneMarkS: error on last system call, error code 256
Abort program!!!
Process Process-7:
Traceback (most recent call last):
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 1748, in run
orfDict = correctionPlusORFpred(args, genome_dict)
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 583, in correctionPlusORFpred
if subprocess.check_call(cmd, shell=True, cwd=gmst_dir)!=0:
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/subprocess.py", line 363, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'perl /ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/utilities/gmst/gmst.pl -faa --strand direct --fnn --output /ibex/scratch/projects/c2042/analysis/sqanti3/splits/6/GMST/GMST_tmp /ibex/scratch/projects/c2042/analysis/sqanti3/splits/6/all_samples.chained_corrected.fasta' returned non-zero exit status 1.
error: data input empty
GeneMarkS: error on last system call, error code 256
Abort program!!!
Process Process-5:
Traceback (most recent call last):
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 1748, in run
orfDict = correctionPlusORFpred(args, genome_dict)
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 583, in correctionPlusORFpred
if subprocess.check_call(cmd, shell=True, cwd=gmst_dir)!=0:
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/subprocess.py", line 363, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'perl /ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/utilities/gmst/gmst.pl -faa --strand direct --fnn --output /ibex/scratch/projects/c2042/analysis/sqanti3/splits/4/GMST/GMST_tmp /ibex/scratch/projects/c2042/analysis/sqanti3/splits/4/all_samples.chained_corrected.fasta' returned non-zero exit status 1.
error: data input empty
GeneMarkS: error on last system call, error code 256
Abort program!!!
Process Process-6:
Traceback (most recent call last):
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 1748, in run
orfDict = correctionPlusORFpred(args, genome_dict)
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 583, in correctionPlusORFpred
if subprocess.check_call(cmd, shell=True, cwd=gmst_dir)!=0:
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/subprocess.py", line 363, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'perl /ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/utilities/gmst/gmst.pl -faa --strand direct --fnn --output /ibex/scratch/projects/c2042/analysis/sqanti3/splits/5/GMST/GMST_tmp /ibex/scratch/projects/c2042/analysis/sqanti3/splits/5/all_samples.chained_corrected.fasta' returned non-zero exit status 1.
error: data input empty
GeneMarkS: error on last system call, error code 256
Abort program!!!
Process Process-2:
Traceback (most recent call last):
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 1748, in run
orfDict = correctionPlusORFpred(args, genome_dict)
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 583, in correctionPlusORFpred
if subprocess.check_call(cmd, shell=True, cwd=gmst_dir)!=0:
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/subprocess.py", line 363, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'perl /ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/utilities/gmst/gmst.pl -faa --strand direct --fnn --output /ibex/scratch/projects/c2042/analysis/sqanti3/splits/1/GMST/GMST_tmp /ibex/scratch/projects/c2042/analysis/sqanti3/splits/1/all_samples.chained_corrected.fasta' returned non-zero exit status 1.
Traceback (most recent call last):
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 2337, in <module>
main()
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 2328, in main
combine_split_runs(args, split_dirs)
File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 2151, in combine_split_runs
with open(_orf) as h: f_faa.write(h.read())
FileNotFoundError: [Errno 2] No such file or directory: '/ibex/scratch/projects/c2042/analysis/sqanti3/splits/0/all_samples.chained_corrected.faa'