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ylab-hi / ScanNeo

A pipeline for identifying indel derived neoantigens using RNA-Seq data
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No .bwa.bam generated #7

Closed Mt-cn closed 3 years ago

Mt-cn commented 3 years ago

Hi@dolittle007, thanks for the great work, I am new to python and I met an error in step 1 ,

`INFO 2021-05-02 21:04:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2021-05-02 21:04:45 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2021-05-02 21:04:45 SortingCollection Creating merging iterator from 7 files INFO 2021-05-02 21:04:58 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2021-05-02 21:04:58 SortingCollection Creating merging iterator from 14 files INFO 2021-05-02 21:05:17 MarkDuplicates Sorting list of duplicate records. INFO 2021-05-02 21:05:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 527485280; totalMemory: 806354944; maxMemory: 1073741824 INFO 2021-05-02 21:05:19 MarkDuplicates Marking 16683374 records as duplicates. INFO 2021-05-02 21:05:19 MarkDuplicates Found 351931 optical duplicate clusters. INFO 2021-05-02 21:05:19 MarkDuplicates Reads are assumed to be ordered by: unsorted [Sun May 02 21:05:19 CST 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 6.72 minutes. Runtime.totalMemory()=806354944 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Exception in thread "main" picard.PicardException: This program requires input that are either coordinate or query sorted (according to the header, or at least ASSUME_SORT_ORDER and the content.) Found ASSUME_SORT_ORDER=null and header sortorder=unsorted at picard.sam.markduplicates.MarkDuplicates.doWork(MarkDuplicates.java:294) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:295) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)

Error: No cz4434523.bwa.bam generated! `

I would really appreciate it if you can give me some suggestions on fixing this problem. Thanks.

dolittle007 commented 3 years ago

Hi@Mt-cn, "Found ASSUME_SORT_ORDER=null and header sortorder=unsorted" It seems that your input an unsorted RNA-Seq BAM file, please use SamTools to sort it before feed it to ScanNeo.

Mt-cn commented 3 years ago

Hi@Mt-cn, "Found ASSUME_SORT_ORDER=null and header sortorder=unsorted" It seems that your input an unsorted RNA-Seq BAM file, please use SamTools to sort it before feed it to ScanNeo.

Thank you so much!