hxj5
commented
2 years ago Hi, seems the bam file is corrupted. It could be caused by errors during downloading, alignment or post-processing. You could check the status of the bam file by samtools quickcheck (for quick check) or bgzip -t sample.bam (for a more thorough check). If the file is indeed corrupted, you may have to re-download or re-align the file. More details in samtools issue 1225.
Hi, CellSNP-lite works well for most of my data except this bam file where it throws the following error. Please let me know what is causing this error and how to resolve it. I have posted the last few lines of log file here. Thank you! ... I::csp_fetch_core][Thread-22] 98.00% SNPs processed. [I::csp_fetch_core][Thread-17] 98.00% SNPs processed. [I::csp_fetch_core][Thread-27] 86.00% SNPs processed. [I::csp_fetch_core][Thread-29] 86.00% SNPs processed. [I::csp_fetch_core][Thread-19] 90.00% SNPs processed. [I::csp_fetch_core][Thread-10] 56.00% SNPs processed. [I::csp_fetch_core][Thread-16] 94.00% SNPs processed. [I::csp_fetch_core][Thread-13] 86.00% SNPs processed. [I::csp_fetch_core][Thread-28] 66.00% SNPs processed. [I::csp_fetch_core][Thread-8] 54.00% SNPs processed. [I::csp_fetch_core][Thread-10] 58.00% SNPs processed. [E::bgzf_uncompress] Inflate operation failed: 3 [E::bgzf_read] Read block operation failed with error 1 after 0 of 4 bytes [E::csp_fetch_core] failed to pileup snp (18:9772213) [E::main] running mode 1 failed. [E::main] Quiting... [I::main] end time: 2021-11-17 16:55:05 [I::main] time spent: 2861 seconds.