bounlu
commented
4 years ago If you are having problems, alternatively, you can use RNA-Editing pipeline on CSI NGS Portal:
https://github.com/a2iEditing/RNAEditingIndexer/issues/13#issuecomment-561713668
Open jalalsiddiqui opened 4 years ago
bounlu
commented
4 years ago If you are having problems, alternatively, you can use RNA-Editing pipeline on CSI NGS Portal:
https://github.com/a2iEditing/RNAEditingIndexer/issues/13#issuecomment-561713668
shalomhillelroth
commented
4 years ago Hi,
Sorry for the very belayed answer, with the whole COVID-19 happening I have very limited access to my computer.
Can you kindly attach the log and the stdout?
Best,
Shalom Hillel Roth
jalalsiddiqui
commented
4 years ago @bounlu I can look up the alternate pipeline as well.
@shalomhillelroth The log and stdout are as below.
-bash-4.2$ cat test_rei_10cores.sh.e10032064 [bam_sort_core] merging from 0 files and 10 in-memory blocks... [bam_sort_core] merging from 0 files and 10 in-memory blocks... [bam_sort_core] merging from 0 files and 10 in-memory blocks... [bam_sort_core] merging from 0 files and 10 in-memory blocks... Arguments in effect: Input file : /fs/project/PAS1348/RNAEditingIndex_test/output_directory/BAMs/SRR5962217/SRR5962217_sampled/SRR5962217_sampled_region_ucscHg38RefSeqCurated.OnlyChr1.bed.gz_alignments_strand_1.bam Output file : /fs/project/PAS1348/RNAEditingIndex_test/output_directory/BAMs/SRR5962217/SRR5962217_sampled/SRR5962217_sampled_region_ucscHg38RefSeqCurated.OnlyChr1.bed.gz_alignments_strand_1.bam.trimmed_5.bam
Number of records read = 76230 Number of records written = 76230 Arguments in effect: Input file : /fs/project/PAS1348/RNAEditingIndex_test/output_directory/BAMs/SRR5962217/SRR5962217_sampled/SRR5962217_sampled_region_ucscHg38RefSeqCurated.OnlyChr1.bed.gz_alignments_strand_2.bam Output file : /fs/project/PAS1348/RNAEditingIndex_test/output_directory/BAMs/SRR5962217/SRR5962217_sampled/SRR5962217_sampled_region_ucscHg38RefSeqCurated.OnlyChr1.bed.gz_alignments_strand_2.bam.trimmed_5.bam
Number of records read = 76338 Number of records written = 76338 Arguments in effect: Input file : /fs/project/PAS1348/RNAEditingIndex_test/output_directory/BAMs/SRR5962209/SRR5962209_sampled/SRR5962209_sampled_region_ucscHg38RefSeqCurated.OnlyChr1.bed.gz_alignments_strand_1.bam Output file : /fs/project/PAS1348/RNAEditingIndex_test/output_directory/BAMs/SRR5962209/SRR5962209_sampled/SRR5962209_sampled_region_ucscHg38RefSeqCurated.OnlyChr1.bed.gz_alignments_strand_1.bam.trimmed_5.bam
[mpileup] 1 samples in 1 input files Arguments in effect: Input file : /fs/project/PAS1348/RNAEditingIndex_test/output_directory/BAMs/SRR5962219/SRR5962219_sampled/SRR5962219_sampled_region_ucscHg38RefSeqCurated.OnlyChr1.bed.gz_alignments_strand_1.bam Output file : /fs/project/PAS1348/RNAEditingIndex_test/output_directory/BAMs/SRR5962219/SRR5962219_sampled/SRR5962219_sampled_region_ucscHg38RefSeqCurated.OnlyChr1.bed.gz_alignments_strand_1.bam.trimmed_5.bam
Number of records read = 62293 Number of records written = 62293 Arguments in effect: Input file : /fs/project/PAS1348/RNAEditingIndex_test/output_directory/BAMs/SRR5962209/SRR5962209_sampled/SRR5962209_sampled_region_ucscHg38RefSeqCurated.OnlyChr1.bed.gz_alignments_strand_2.bam Output file : /fs/project/PAS1348/RNAEditingIndex_test/output_directory/BAMs/SRR5962209/SRR5962209_sampled/SRR5962209_sampled_region_ucscHg38RefSeqCurated.OnlyChr1.bed.gz_alignments_strand_2.bam.trimmed_5.bam
Arguments in effect: Input file : /fs/project/PAS1348/RNAEditingIndex_test/output_directory/BAMs/SRR5962201/SRR5962201_sampled/SRR5962201_sampled_region_ucscHg38RefSeqCurated.OnlyChr1.bed.gz_alignments_strand_1.bam Output file : /fs/project/PAS1348/RNAEditingIndex_test/output_directory/BAMs/SRR5962201/SRR5962201_sampled/SRR5962201_sampled_region_ucscHg38RefSeqCurated.OnlyChr1.bed.gz_alignments_strand_1.bam.trimmed_5.bam
Number of records read = 63750 Number of records written = 63750
Number of records read = 106797 Number of records written = 106797 Arguments in effect: Input file : /fs/project/PAS1348/RNAEditingIndex_test/output_directory/BAMs/SRR5962219/SRR5962219_sampled/SRR5962219_sampled_region_ucscHg38RefSeqCurated.OnlyChr1.bed.gz_alignments_strand_2.bam Output file : /fs/project/PAS1348/RNAEditingIndex_test/output_directory/BAMs/SRR5962219/SRR5962219_sampled/SRR5962219_sampled_region_ucscHg38RefSeqCurated.OnlyChr1.bed.gz_alignments_strand_2.bam.trimmed_5.bam
[mpileup] 1 samples in 1 input files
Number of records read = 123921 Number of records written = 123921 Arguments in effect: Input file : /fs/project/PAS1348/RNAEditingIndex_test/output_directory/BAMs/SRR5962201/SRR5962201_sampled/SRR5962201_sampled_region_ucscHg38RefSeqCurated.OnlyChr1.bed.gz_alignments_strand_2.bam Output file : /fs/project/PAS1348/RNAEditingIndex_test/output_directory/BAMs/SRR5962201/SRR5962201_sampled/SRR5962201_sampled_region_ucscHg38RefSeqCurated.OnlyChr1.bed.gz_alignments_strand_2.bam.trimmed_5.bam
Number of records read = 103573 Number of records written = 103573 [mpileup] 1 samples in 1 input files
Number of records read = 130933
Number of records written = 130933
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[2020-04-21 13:34:34,322] general_functions WARNING GGPSResources.general_functions.remove_files Failed To Remove 21-04-2020-17.cnf
[2020-04-21 13:34:34,323] general_functions WARNING GGPSResources.general_functions.remove_files Failed To Remove 21-04-2020-17.cnf
Traceback (most recent call last):
File "Tools/EditingIndex/A2IEditingIndex.py", line 1341, in
For the stdout, I have
-bash-4.2$ cat test_rei_10cores.sh.o10032064 | head GenerateIndex - Starting! Running: bedtools getfasta -name -bedOut -fi '/fs/project/PAS1348/Software/RNAEditingIndexer/Resources/Genomes/HomoSapiens/ucscHg38Genome.fa' -bed '/fs/project/PAS1348/Software/RNAEditingIndexer/TestResources/AnnotationAndRegions/ucscHg38RefSeqCurated.OnlyChr1.bed.gz' GenerateIndex - Indexing FASTA Records! GenerateIndex - Done Converting, Outputted to /fs/project/PAS1348/RNAEditingIndex_test/output_directory/ucscHg38Genome.fa.GenomeIndex.jsd PileupToCount - Warning: Found Coverage Out Of index! (Ignoring) PileupToCount - Warning: Found Coverage Out Of index! (Ignoring) PileupToCount - Warning: Found Coverage Out Of index! (Ignoring) PileupToCount - Warning: Found Coverage Out Of index! (Ignoring) PileupToCount - Warning: Found Coverage Out Of index! (Ignoring) PileupToCount - Warning: Found Coverage Out Of index! (Ignoring)
It keeps going down with PileupToCount.
No worries about the belated response. Take your time. I appreciate all your help.
jalalsiddiqui
commented
4 years ago One question. Do you think this could be on my end (the cluster I am running)? If so I can work with our supercomputing group at my university.
I tried increasing the memory but to no avail. What is causing this ValueError for the test data set?
Any help will be appreciated. BTW has anyone gotten this to work?
[bam_sort_core] merging from 0 files and 10 in-memory blocks... [bam_sort_core] merging from 0 files and 10 in-memory blocks... [bam_sort_core] merging from 0 files and 10 in-memory blocks... [bam_sort_core] merging from 0 files and 10 in-memory blocks... Arguments in effect: Input file : /fs/project/PAS1348/RNAEditingIndex_test/output_directory/BAMs/SRR5962217/SRR5962217_sampled/SRR5962217_sampled_region_ucscHg38RefSeqCurated.OnlyChr1.bed.gz_alignments_strand_1.bam Output file : /fs/project/PAS1348/RNAEditingIndex_test/output_directory/BAMs/SRR5962217/SRR5962217_sampled/SRR5962217_sampled_region_ucscHg38RefSeqCurated.OnlyChr1.bed.gz_alignments_strand_1.bam.trimmed_5.bam
Bases to trim from each side : 5
Number of records read = 76230 Number of records written = 76230 Arguments in effect: Input file : /fs/project/PAS1348/RNAEditingIndex_test/output_directory/BAMs/SRR5962217/SRR5962217_sampled/SRR5962217_sampled_region_ucscHg38RefSeqCurated.OnlyChr1.bed.gz_alignments_strand_2.bam Output file : /fs/project/PAS1348/RNAEditingIndex_test/output_directory/BAMs/SRR5962217/SRR5962217_sampled/SRR5962217_sampled_region_ucscHg38RefSeqCurated.OnlyChr1.bed.gz_alignments_strand_2.bam.trimmed_5.bam
Bases to trim from each side : 5
Number of records read = 76338 Number of records written = 76338 Arguments in effect: Input file : /fs/project/PAS1348/RNAEditingIndex_test/output_directory/BAMs/SRR5962209/SRR5962209_sampled/SRR5962209_sampled_region_ucscHg38RefSeqCurated.OnlyChr1.bed.gz_alignments_strand_1.bam Output file : /fs/project/PAS1348/RNAEditingIndex_test/output_directory/BAMs/SRR5962209/SRR5962209_sampled/SRR5962209_sampled_region_ucscHg38RefSeqCurated.OnlyChr1.bed.gz_alignments_strand_1.bam.trimmed_5.bam
Bases to trim from each side : 5
[mpileup] 1 samples in 1 input files Arguments in effect: Input file : /fs/project/PAS1348/RNAEditingIndex_test/output_directory/BAMs/SRR5962219/SRR5962219_sampled/SRR5962219_sampled_region_ucscHg38RefSeqCurated.OnlyChr1.bed.gz_alignments_strand_1.bam Output file : /fs/project/PAS1348/RNAEditingIndex_test/output_directory/BAMs/SRR5962219/SRR5962219_sampled/SRR5962219_sampled_region_ucscHg38RefSeqCurated.OnlyChr1.bed.gz_alignments_strand_1.bam.trimmed_5.bam
Bases to trim from each side : 5
Number of records read = 62293 Number of records written = 62293 Arguments in effect: Input file : /fs/project/PAS1348/RNAEditingIndex_test/output_directory/BAMs/SRR5962209/SRR5962209_sampled/SRR5962209_sampled_region_ucscHg38RefSeqCurated.OnlyChr1.bed.gz_alignments_strand_2.bam Output file : /fs/project/PAS1348/RNAEditingIndex_test/output_directory/BAMs/SRR5962209/SRR5962209_sampled/SRR5962209_sampled_region_ucscHg38RefSeqCurated.OnlyChr1.bed.gz_alignments_strand_2.bam.trimmed_5.bam
Bases to trim from each side : 5
Arguments in effect: Input file : /fs/project/PAS1348/RNAEditingIndex_test/output_directory/BAMs/SRR5962201/SRR5962201_sampled/SRR5962201_sampled_region_ucscHg38RefSeqCurated.OnlyChr1.bed.gz_alignments_strand_1.bam Output file : /fs/project/PAS1348/RNAEditingIndex_test/output_directory/BAMs/SRR5962201/SRR5962201_sampled/SRR5962201_sampled_region_ucscHg38RefSeqCurated.OnlyChr1.bed.gz_alignments_strand_1.bam.trimmed_5.bam
Bases to trim from each side : 5
Number of records read = 63750 Number of records written = 63750
Number of records read = 106797 Number of records written = 106797 Arguments in effect: Input file : /fs/project/PAS1348/RNAEditingIndex_test/output_directory/BAMs/SRR5962219/SRR5962219_sampled/SRR5962219_sampled_region_ucscHg38RefSeqCurated.OnlyChr1.bed.gz_alignments_strand_2.bam Output file : /fs/project/PAS1348/RNAEditingIndex_test/output_directory/BAMs/SRR5962219/SRR5962219_sampled/SRR5962219_sampled_region_ucscHg38RefSeqCurated.OnlyChr1.bed.gz_alignments_strand_2.bam.trimmed_5.bam
Bases to trim from each side : 5
[mpileup] 1 samples in 1 input files
Number of records read = 123921 Number of records written = 123921 Arguments in effect: Input file : /fs/project/PAS1348/RNAEditingIndex_test/output_directory/BAMs/SRR5962201/SRR5962201_sampled/SRR5962201_sampled_region_ucscHg38RefSeqCurated.OnlyChr1.bed.gz_alignments_strand_2.bam Output file : /fs/project/PAS1348/RNAEditingIndex_test/output_directory/BAMs/SRR5962201/SRR5962201_sampled/SRR5962201_sampled_region_ucscHg38RefSeqCurated.OnlyChr1.bed.gz_alignments_strand_2.bam.trimmed_5.bam
Bases to trim from each side : 5
Number of records read = 103573 Number of records written = 103573 [mpileup] 1 samples in 1 input files
Number of records read = 130933 Number of records written = 130933 [mpileup] 1 samples in 1 input files [mpileup] 1 samples in 1 input files [mpileup] 1 samples in 1 input files [mpileup] 1 samples in 1 input files [mpileup] 1 samples in 1 input files [2020-04-21 13:34:34,322] general_functions WARNING GGPSResources.general_functions.remove_files Failed To Remove 21-04-2020-17.cnf [2020-04-21 13:34:34,323] general_functions WARNING GGPSResources.general_functions.remove_files Failed To Remove 21-04-2020-17.cnf Traceback (most recent call last): File "Tools/EditingIndex/A2IEditingIndex.py", line 1341, in
File "Tools/EditingIndex/A2IEditingIndex.py", line 1166, in main
File "Tools/EditingIndex/DataConverters/RefSeqGenesCoverter.py", line 101, in load_refseq_bed
ValueError: too many values to unpack
[182468] Failed to execute script A2IEditingIndex