Hello guys
Recently, when i used IpdSummary tool of smrtlink v11.0 to get some methylated site information of virus genomes. i have performed the step about samtools sort and index and pbindex for my bam file, which generated by pbmm2. here is my error information
[INFO] 2024-11-22 01:50:04,609Z [kineticsTools.ipdSummary _pacbio_main_runner 160] Using pbcommand v2.3.2
[INFO] 2024-11-22 01:50:04,610Z [kineticsTools.ipdSummary _pacbio_main_runner 161] completed setting up logger with <function setup_log at 0x7f9595bf7b80>
[INFO] 2024-11-22 01:50:04,610Z [kineticsTools.ipdSummary _pacbio_main_runner 164] log opts {'level': 20, 'file_name': None}
[INFO] 2024-11-22 01:50:04,611Z [kineticsTools.loader getResourcePathSpec 59] found SMRT_CHEMISTRY_BUNDLE_DIR, prepending to default paramsPath
[INFO] 2024-11-22 01:50:04,612Z [root loadSharedAlignmentSet 475] Reading AlignmentSet: /home/wuzhongzi2019/cz/meth/BMXV01.align.bam
[INFO] 2024-11-22 01:50:04,612Z [root loadSharedAlignmentSet 476] reference: /home/wuzhongzi2019/cz/meth/Mash_filtered_ref.fasta
invalid literal for int() with base 16: 'default'
Traceback (most recent call last):
File "/home/wuzhongzi2019/cz/software/smrtlink/install/smrtlink-release_11.0.0.146107/bundles/smrttools/install/smrttools-release_11.0.0.146107/private/th
return_code = exe_main_func(*args, **kwargs)
File "/home/wuzhongzi2019/cz/software/smrtlink/install/smrtlink-release_11.0.0.146107/bundles/smrttools/install/smrttools-release_11.0.0.146107/private/th
return kt.start()
File "/home/wuzhongzi2019/cz/software/smrtlink/install/smrtlink-release_11.0.0.146107/bundles/smrttools/install/smrttools-release_11.0.0.146107/private/th
return self.run()
File "/home/wuzhongzi2019/cz/software/smrtlink/install/smrtlink-release_11.0.0.146107/bundles/smrttools/install/smrttools-release_11.0.0.146107/private/th
ret = self._mainLoop()
File "/home/wuzhongzi2019/cz/software/smrtlink/install/smrtlink-release_11.0.0.146107/bundles/smrttools/install/smrttools-release_11.0.0.146107/private/th
self.loadSharedAlignmentSet(self.args.alignment_set)
File "/home/wuzhongzi2019/cz/software/smrtlink/install/smrtlink-release_11.0.0.146107/bundles/smrttools/install/smrttools-release_11.0.0.146107/private/th
self.alignments = AlignmentSet(alignmentFilename,
It seems like something wrong with my bam file, such as the "RG id". here is part of bam file
@SQ SN:SWMM05m547946 LN:34454
@SQ SN:SWMM05m1097158 LN:44380
@RG ID:default PL:PACBIO DS:READTYPE=UNKNOWN PU:default SM:BMXV01 PM:SEQUEL
@PG ID:pbmm2 PN:pbmm2 VN:1.16.0 (commit v1.16.0) CL:pbmm2 align -j 40 -J 8 /gxn/zhechen/phagesv/pacbiosample/BMXV01/Mash_filtered_ref.fasta /gxn/zhechen/DNA_virus/all_HIFI/0.CCS/0.virus/BMXV01/BMXV01.CCS.fasta BMXV01.align.bam --sort --preset CCS --sample BMXV01
Hello guys Recently, when i used IpdSummary tool of smrtlink v11.0 to get some methylated site information of virus genomes. i have performed the step about samtools sort and index and pbindex for my bam file, which generated by pbmm2. here is my error information [INFO] 2024-11-22 01:50:04,609Z [kineticsTools.ipdSummary _pacbio_main_runner 160] Using pbcommand v2.3.2 [INFO] 2024-11-22 01:50:04,610Z [kineticsTools.ipdSummary _pacbio_main_runner 161] completed setting up logger with <function setup_log at 0x7f9595bf7b80> [INFO] 2024-11-22 01:50:04,610Z [kineticsTools.ipdSummary _pacbio_main_runner 164] log opts {'level': 20, 'file_name': None} [INFO] 2024-11-22 01:50:04,611Z [kineticsTools.loader getResourcePathSpec 59] found SMRT_CHEMISTRY_BUNDLE_DIR, prepending to default paramsPath [INFO] 2024-11-22 01:50:04,612Z [root loadSharedAlignmentSet 475] Reading AlignmentSet: /home/wuzhongzi2019/cz/meth/BMXV01.align.bam [INFO] 2024-11-22 01:50:04,612Z [root loadSharedAlignmentSet 476] reference: /home/wuzhongzi2019/cz/meth/Mash_filtered_ref.fasta invalid literal for int() with base 16: 'default' Traceback (most recent call last): File "/home/wuzhongzi2019/cz/software/smrtlink/install/smrtlink-release_11.0.0.146107/bundles/smrttools/install/smrttools-release_11.0.0.146107/private/th return_code = exe_main_func(*args, **kwargs) File "/home/wuzhongzi2019/cz/software/smrtlink/install/smrtlink-release_11.0.0.146107/bundles/smrttools/install/smrttools-release_11.0.0.146107/private/th return kt.start() File "/home/wuzhongzi2019/cz/software/smrtlink/install/smrtlink-release_11.0.0.146107/bundles/smrttools/install/smrttools-release_11.0.0.146107/private/th return self.run() File "/home/wuzhongzi2019/cz/software/smrtlink/install/smrtlink-release_11.0.0.146107/bundles/smrttools/install/smrttools-release_11.0.0.146107/private/th ret = self._mainLoop() File "/home/wuzhongzi2019/cz/software/smrtlink/install/smrtlink-release_11.0.0.146107/bundles/smrttools/install/smrttools-release_11.0.0.146107/private/th self.loadSharedAlignmentSet(self.args.alignment_set) File "/home/wuzhongzi2019/cz/software/smrtlink/install/smrtlink-release_11.0.0.146107/bundles/smrttools/install/smrttools-release_11.0.0.146107/private/th self.alignments = AlignmentSet(alignmentFilename,
It seems like something wrong with my bam file, such as the "RG id". here is part of bam file @SQ SN:SWMM05m547946 LN:34454 @SQ SN:SWMM05m1097158 LN:44380 @RG ID:default PL:PACBIO DS:READTYPE=UNKNOWN PU:default SM:BMXV01 PM:SEQUEL @PG ID:pbmm2 PN:pbmm2 VN:1.16.0 (commit v1.16.0) CL:pbmm2 align -j 40 -J 8 /gxn/zhechen/phagesv/pacbiosample/BMXV01/Mash_filtered_ref.fasta /gxn/zhechen/DNA_virus/all_HIFI/0.CCS/0.virus/BMXV01/BMXV01.CCS.fasta BMXV01.align.bam --sort --preset CCS --sample BMXV01
So what should I do, appreciated it L