I've been troubleshooting for a while and I can't seem to figure out this issue. I installed from source using bamutil 1.0.14, samtools 1.8, bedtools 2.26, JDK 8, and python 2.7. No errors reported during compilation or configuration. However, when I run the example dataset or any of my own datasets there seem to be issues with reading bam files. For example:
./RNAEditingIndex -d ~/bin/RNAEditingIndexer/TestResources/BAMs -f _sampled_with_0.1.Aligned.sortedByCoord.out.bam.AluChr1Only.bam -l ~/bin/RNAEditingIndexer/test/log -o ~/bin/RNAEditingIndexer/test/out -os ~/bin/RNAEditingIndexer/test/summary --genome hg38 -rb ~/bin/RNAEditingIndexer/TestResources/AnnotationAndRegions/ucscHg38Alu.OnlyChr1.bed.gz --refseq ~/bin/RNAEditingIndexer/TestResources/AnnotationAndRegions/ucscHg38RefSeqCurated.OnlyChr1.bed.gz --snps ~/bin/RNAEditingIndexer/TestResources/AnnotationAndRegions/ucscHg38CommonGenomicSNPs150.OnlyChr1.bed.gz --genes_expression ~/bin/RNAEditingIndexer/TestResources/AnnotationAndRegions/ucscHg38GTExGeneExpression.OnlyChr1.bed.gz --verbose --stranded --paired --keep_cmpileup
Arguments in effect:
Input file : <redacted>/bin/RNAEditingIndexer/test/out/BAMs/SRR5962217/SRR5962217/SRR5962217_region_ucscHg38Alu.OnlyChr1.bed.gz_alignments_strand_1.bam
Output file : <redacted>/bin/RNAEditingIndexer/test/out/BAMs/SRR5962217/SRR5962217/SRR5962217_region_ucscHg38Alu.OnlyChr1.bed.gz_alignments_strand_1.bam.trimmed_5.bam
#Bases to trim from each side : 5
Number of records read = 0
Number of records written = 0
Arguments in effect:
Input file : <redacted>/bin/RNAEditingIndexer/test/out/BAMs/SRR5962217/SRR5962217/SRR5962217_region_ucscHg38Alu.OnlyChr1.bed.gz_alignments_strand_2.bam
Output file : <redacted>/bin/RNAEditingIndexer/test/out/BAMs/SRR5962217/SRR5962217/SRR5962217_region_ucscHg38Alu.OnlyChr1.bed.gz_alignments_strand_2.bam.trimmed_5.bam
#Bases to trim from each side : 5
So it looks like something is happening where the trimming step is not finding any records? Strangely, this doesn't trigger any warnings and it appears like the program finished. But when I look at the results the AEI and other metrics in the summary is 0 for all samples.
If it gives you any clues, I also consistently get this error:
[2020-12-30 04:46:50,884] general_functions WARNING GGPSResources.general_functions.remove_files Failed To Remove 30-12-2020-09.cnf
[2020-12-30 04:46:50,884] general_functions WARNING GGPSResources.general_functions.remove_files Failed To Remove 30-12-2020-09.cnf
Let me know if there is any other information that could help you. I can also send the full log files by email if you'd like. I hope to use this software, so I hope we can figure this out. Thanks in advance for your help!
Hello,
I've been troubleshooting for a while and I can't seem to figure out this issue. I installed from source using bamutil 1.0.14, samtools 1.8, bedtools 2.26, JDK 8, and python 2.7. No errors reported during compilation or configuration. However, when I run the example dataset or any of my own datasets there seem to be issues with reading bam files. For example:
So it looks like something is happening where the trimming step is not finding any records? Strangely, this doesn't trigger any warnings and it appears like the program finished. But when I look at the results the AEI and other metrics in the summary is 0 for all samples.
If it gives you any clues, I also consistently get this error:
Let me know if there is any other information that could help you. I can also send the full log files by email if you'd like. I hope to use this software, so I hope we can figure this out. Thanks in advance for your help!