Problem with pysam?

[minn333]

Dear: I encountered the belowing messages, and the tools stop. The output file.pytor is only 11KB. What about your suggestion on this?

error message as below:

2022-10-01 14:34:51,911 - cnvpytor.bam - INFO - File: path/to/file/file.recaled.sorted.dedup.bam successfully open 2022-10-01 14:34:51,912 - cnvpytor.bam - INFO - Detected reference genome: hg19 2022-10-01 14:34:51,916 - cnvpytor.pool - INFO - Parallel processing using 8 cores 2022-10-01 14:34:51,953 - cnvpytor.root - INFO - Reading data for chromosome chr1 with length 249250621 2022-10-01 14:34:51,953 - cnvpytor.root - INFO - Reading data for chromosome chr2 with length 243199373 2022-10-01 14:34:51,954 - cnvpytor.root - INFO - Reading data for chromosome chr3 with length 198022430 2022-10-01 14:34:51,954 - cnvpytor.root - INFO - Reading data for chromosome chr6 with length 171115067 2022-10-01 14:34:51,954 - cnvpytor.root - INFO - Reading data for chromosome chr4 with length 191154276 2022-10-01 14:34:51,954 - cnvpytor.root - INFO - Reading data for chromosome chr5 with length 180915260 2022-10-01 14:34:51,955 - cnvpytor.root - INFO - Reading data for chromosome chr7 with length 159138663 2022-10-01 14:34:51,955 - cnvpytor.root - INFO - Reading data for chromosome chr8 with length 146364022 [E::bgzf_uncompress] Inflate operation failed: 3 [E::bgzf_read] Read block operation failed with error 1 after 0 of 4 bytes 2022-10-01 14:35:00,128 - cnvpytor.bam - ERROR - Error while reading file 'path/to/file/file.recaled.sorted.dedup.bam' [E::bgzf_uncompress] Inflate operation failed: 3 [E::bgzf_read] Read block operation failed with error 1 after 0 of 4 bytes 2022-10-01 14:35:08,687 - cnvpytor.bam - ERROR - Error while reading file 'path/to/file/file.recaled.sorted.dedup.bam' [E::bgzf_uncompress] Inflate operation failed: 3 [E::bgzf_read] Read block operation failed with error 1 after 0 of 4 bytes 2022-10-01 14:35:43,699 - cnvpytor.bam - ERROR - Error while reading file 'path/to/file/file.recaled.sorted.dedup.bam' 2022-10-01 14:36:20,246 - cnvpytor.root - INFO - Reading data for chromosome chr9 with length 141213431 2022-10-01 14:36:21,315 - cnvpytor.root - INFO - Reading data for chromosome chr10 with length 135534747 2022-10-01 14:36:26,925 - cnvpytor.root - INFO - Reading data for chromosome chr11 with length 135006516 [E::bgzf_uncompress] Inflate operation failed: 3 [E::bgzf_read] Read block operation failed with error 1 after 0 of 4 bytes 2022-10-01 14:36:41,658 - cnvpytor.bam - ERROR - Error while reading file 'path/to/file/file.recaled.sorted.dedup.bam' 2022-10-01 14:37:03,905 - cnvpytor.root - INFO - Reading data for chromosome chr12 with length 133851895 2022-10-01 14:37:28,730 - cnvpytor.root - INFO - Reading data for chromosome chr13 with length 115169878 2022-10-01 14:37:42,088 - cnvpytor.root - INFO - Reading data for chromosome chr14 with length 107349540 2022-10-01 14:37:47,712 - cnvpytor.root - INFO - Reading data for chromosome chr15 with length 102531392 2022-10-01 14:38:17,383 - cnvpytor.root - INFO - Reading data for chromosome chr16 with length 90354753 2022-10-01 14:38:19,435 - cnvpytor.root - INFO - Reading data for chromosome chr17 with length 81195210 2022-10-01 14:38:31,617 - cnvpytor.root - INFO - Reading data for chromosome chr18 with length 78077248 2022-10-01 14:38:35,450 - cnvpytor.root - INFO - Reading data for chromosome chr19 with length 59128983 2022-10-01 14:39:08,147 - cnvpytor.root - INFO - Reading data for chromosome chr20 with length 63025520

[E::bgzf_uncompress] Inflate operation failed: 3 [E::bgzf_read] Read block operation failed with error 1 after 0 of 4 bytes 2022-10-01 14:39:30,154 - cnvpytor.bam - ERROR - Error while reading file path/to/file/file.recaled.sorted.dedup.bam' 2022-10-01 14:39:31,050 - cnvpytor.root - INFO - Reading data for chromosome chrY with length 59373566

while reading file.pytor as your suggestion:

Filename 'file.pytor'

File created: 2022-10-01 13:36 using CNVpytor ver 1.2.1

Chromosomes with RD signal:

Chromosomes with SNP signal:

Using reference genome: hg19 [ GC: yes, mask: yes ]

Chromosomes with RD histograms [bin sizes]: []

Chromosomes with SNP histograms [bin sizes]: []

Chromosome lengths: {}

[arpanda]

Hi, I believe there is some issue with the BAM file. You may have a look at this samtools issue. https://github.com/samtools/samtools/issues/1225

Thank You Arijit

[minn333]

sorry, you means CNVpytor also use samtools and the version matters? I thought it was the problem of pysam?

Anyway, I will check BAM files and samtools .

Thanks for your reply.

Arijit Panda @.***> 於 2022年10月2日 週日 上午1:22 寫道：

Hi, I believe there is some issue with the BAM file. You may have a look at this samtools issue. samtools/samtools#1225 https://github.com/samtools/samtools/issues/1225

Thank You Arijit

— Reply to this email directly, view it on GitHub https://github.com/abyzovlab/CNVpytor/issues/141#issuecomment-1264429311, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOUUAAITMVP2YDW32XXMJELWBBXOTANCNFSM6AAAAAAQ2MNBPA . You are receiving this because you authored the thread.Message ID: @.***>

[arpanda]

CNVpytor uses pysam only.

Some of the error/warning messages on pysam is similar to samtools (https://pysam.readthedocs.io/en/latest/index.html).

Thanks Arijit

[minn333]

Thank you.  I checked my BAM files with Picard.The error list as below: ## HISTOGRAM    java.lang.StringError Type      CountERROR:INVALID_INDEX_FILE_POINTER        1ERROR:MATE_NOT_FOUND    2055174 Do you think could I proceed the CNVpytor with these errors? Will it effect on result or processing?  Arijit Panda ***@***.***> 於 2022年10月4日 週二 上午12:32 寫道：Closed #141 as completed.—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authored the thread.Message ID: ***@***.***>