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a2iEditing / RNAEditingIndexer

A tool for the calculation of RNA-editing index for RNA seq data
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Cannot run test data #34

Open ryrl9703 opened 2 years ago

ryrl9703 commented 2 years ago

../RNAEditingIndex -d ../TestResources/BAMs/BAMs --genome hg38 -f _sampled_with_0.1.Aligned.sortedByCoord.out.bam.AluChr1Only.bam

Error: Unable to open file ../TestResources/BAMs/BAMs/SRR5962217/SRR5962217_sampled_with_0.1.Aligned.sortedByCoord.out.bam.AluChr1Only.bam. Exiting. samtools sort: failed to read header from "-" [2021-09-15 15:45:57,824] EIPipelineManger ERROR Process: Editing_Index_Pipline_SRR5962217; Going To Error Step: Step_1_backup Error: Unable to open file ../TestResources/BAMs/BAMs/SRR5962219/SRR5962219_sampled_with_0.1.Aligned.sortedByCoord.out.bam.AluChr1Only.bam. Exiting. samtools sort: failed to read header from "-" [2021-09-15 15:45:57,865] EIPipelineManger ERROR Process: Editing_Index_Pipline_SRR5962219; Going To Error Step: Step_1_backup Error: Unable to open file ../TestResources/BAMs/BAMs/SRR5962209/SRR5962209_sampled_with_0.1.Aligned.sortedByCoord.out.bam.AluChr1Only.bam. Exiting. samtools sort: failed to read header from "-" [2021-09-15 15:45:57,906] EIPipelineManger ERROR Process: Editing_Index_Pipline_SRR5962209; Going To Error Step: Step_1_backup Error: Unable to open file ../TestResources/BAMs/BAMs/SRR5962201/SRR5962201_sampled_with_0.1.Aligned.sortedByCoord.out.bam.AluChr1Only.bam. Exiting. samtools sort: failed to read header from "-" [2021-09-15 15:45:57,948] EIPipelineManger ERROR Process: Editing_Index_Pipline_SRR5962201; Going To Error Step: Step_1_backup [2021-09-15 15:45:57,950] general_functions WARNING GGPSResources.general_functions.remove_files Failed To Remove 15-09-2021-07.cnf [2021-09-15 15:45:57,950] general_functions WARNING GGPSResources.general_functions.remove_files Failed To Remove 15-09-2021-07.cnf [2021-09-15 15:48:48,076] A2IEditingIndex ERROR Failed Loading Coverage Data of SRR5962201! (Won't Delete cmpileup) Traceback (most recent call last): File "Tools/EditingIndex/A2IEditingIndex.py", line 856, in get_strands_and_counts File "Tools/EditingIndex/DataConverters/CountPileupCoverter.py", line 69, in parse_count_pileup IOError: [Errno 2] No such file or directory: './SRR5962201/SRR5962201/SRR5962201_ucscHg38Alu.bed.gz_mpileup.cmpileup' [2021-09-15 15:48:48,426] A2IEditingIndex ERROR Failed Loading Coverage Data of SRR5962219! (Won't Delete cmpileup) Traceback (most recent call last): File "Tools/EditingIndex/A2IEditingIndex.py", line 856, in get_strands_and_counts File "Tools/EditingIndex/DataConverters/CountPileupCoverter.py", line 69, in parse_count_pileup IOError: [Errno 2] No such file or directory: './SRR5962219/SRR5962219/SRR5962219_ucscHg38Alu.bed.gz_mpileup.cmpileup' [2021-09-15 15:48:48,774] A2IEditingIndex ERROR Failed Loading Coverage Data of SRR5962217! (Won't Delete cmpileup) Traceback (most recent call last): File "Tools/EditingIndex/A2IEditingIndex.py", line 856, in get_strands_and_counts File "Tools/EditingIndex/DataConverters/CountPileupCoverter.py", line 69, in parse_count_pileup IOError: [Errno 2] No such file or directory: './SRR5962217/SRR5962217/SRR5962217_ucscHg38Alu.bed.gz_mpileup.cmpileup' [2021-09-15 15:48:49,121] A2IEditingIndex ERROR Failed Loading Coverage Data of SRR5962209! (Won't Delete cmpileup) Traceback (most recent call last): File "Tools/EditingIndex/A2IEditingIndex.py", line 856, in get_strands_and_counts File "Tools/EditingIndex/DataConverters/CountPileupCoverter.py", line 69, in parse_count_pileup IOError: [Errno 2] No such file or directory: './SRR5962209/SRR5962209/SRR5962209_ucscHg38Alu.bed.gz_mpileup.cmpileup' [2021-09-15 15:48:49,327] general_functions WARNING GGPSResources.general_functions.remove_files Failed To Remove ./SRR5962219/SRR5962219/SRR5962219_ucscHg38Alu.bed.gz_mpileup.cmpileup [2021-09-15 15:48:49,327] general_functions WARNING GGPSResources.general_functions.remove_files Failed To Remove ./SRR5962201/SRR5962201/SRR5962201_ucscHg38Alu.bed.gz_mpileup.cmpileup [2021-09-15 15:48:49,328] general_functions WARNING GGPSResources.general_functions.remove_files Failed To Remove ./SRR5962209/SRR5962209/SRR5962209_ucscHg38Alu.bed.gz_mpileup.cmpileup [2021-09-15 15:48:49,328] general_functions WARNING GGPSResources.general_functions.remove_files Failed To Remove ./ucscHg38Genome.fa.GenomeIndex.jsd [2021-09-15 15:48:49,328] general_functions WARNING GGPSResources.general_functions.remove_files Failed To Remove ./SRR5962217/SRR5962217/SRR5962217_ucscHg38Alu.bed.gz_mpileup.cmpileup

How should I solve this problem?

izengyx commented 4 weeks ago

same problem.