Hello,
I run below command for joint calling which binds several bin file
cat ../AD_WGS_batch1-7_STRling.txt | xargs -L 2000 strling merge -f ../../resources/chm13v2.0.fa --output-prefix ~/WGS/AD_STR/outputs/joint_bin/ > ~/WGS/AD_STR/outputs/joint_bin/str_joint_log.txt 2>&1
The command finished with logs below.
More than 65535 reads in cluster with first read:(tid: 3, position: 169960672, repeat: ['G', '\x00', '\x00', '\x00', '\x00', '\x00'], flag: PAIRED,READ2,DUP, split: right, mapping_quality: 47, repeat_count: 70, align_length: 70, qname: "20") skipping
More than 65535 reads in cluster with first read:(tid: 24, position: 10263, repeat: ['G', '\x00', '\x00', '\x00', '\x00', '\x00'], flag: PAIRED,MREVERSE,READ2, split: none, mapping_quality: 43, repeat_count: 150, align_length: 150, qname: "428") skipping
More than 65535 reads in cluster with first read:(tid: 24, position: 15757, repeat: ['G', '\x00', '\x00', '\x00', '\x00', '\x00'], flag: PAIRED,MREVERSE,READ2, split: none, mapping_quality: 60, repeat_count: 150, align_length: 150, qname: "113") skipping
More than 65535 reads in cluster with first read:(tid: 1, position: 181396416, repeat: ['A', '\x00', '\x00', '\x00', '\x00', '\x00'], flag: PAIRED,READ2, split: none_right, mapping_quality: 0, repeat_count: 124, align_length: 150, qname: "49") skipping
More than 65535 reads in cluster with first read:(tid: 3, position: 169960503, repeat: ['A', '\x00', '\x00', '\x00', '\x00', '\x00'], flag: PAIRED,PROPER_PAIR,MREVERSE,READ1, split: none, mapping_quality: 54, repeat_count: 128, align_length: 150, qname: "1138") skipping
More than 65535 reads in cluster with first read:(tid: 22, position: 149830784, repeat: ['G', '\x00', '\x00', '\x00', '\x00', '\x00'], flag: PAIRED,PROPER_PAIR,REVERSE,READ1, split: none, mapping_quality: 60, repeat_count: 142, align_length: 150, qname: "754") skipping
More than 65535 reads in cluster with first read:(tid: 6, position: 86499722, repeat: ['G', '\x00', '\x00', '\x00', '\x00', '\x00'], flag: PAIRED,MREVERSE,READ2, split: none, mapping_quality: 57, repeat_count: 144, align_length: 150, qname: "233") skipping
More than 65535 reads in cluster with first read:(tid: 24, position: 15398, repeat: ['C', '\x00', '\x00', '\x00', '\x00', '\x00'], flag: PAIRED,READ2, split: none, mapping_quality: 60, repeat_count: 150, align_length: 150, qname: "97") skipping
More than 65535 reads in cluster with first read:(tid: 24, position: 15965, repeat: ['C', '\x00', '\x00', '\x00', '\x00', '\x00'], flag: PAIRED,READ2, split: none, mapping_quality: 60, repeat_count: 150, align_length: 150, qname: "71") skipping
More than 65535 reads in cluster with first read:(tid: 6, position: 86500001, repeat: ['C', '\x00', '\x00', '\x00', '\x00', '\x00'], flag: PAIRED,READ2, split: none, mapping_quality: 60, repeat_count: 122, align_length: 150, qname: "1715") skipping
I'm asking if it is okay to continue the skipping warning, or should I check other options to solve this problem.
I used 1,824 samples with strling.
Thank you for providing a great tool.
Best regards,
Chan
[log]
strling version: 0.5.2
[strling] read 815645 STR reads from file: WGS_0001.bin
[strling] read 501777 STR reads from file: WGS_0002.bin
...
[strling] read 102666 STR reads from file: WGS_1836.bin
[strling] read 113928 STR reads from file: WGS_1837.bin
[strling] read 123117 STR reads from file: WGS_1838.bin
More than 65535 reads in cluster with first read:(tid: 3, position: 169960672, repeat: ['G', '\x00', '\x00', '\x00', '\x00', '\x00'], flag: PAIRED,READ2,DUP, split: right, mapping_quality: 47, repeat_count: 70, align_length: 70, qname: "20") skipping
More than 65535 reads in cluster with first read:(tid: 24, position: 10263, repeat: ['G', '\x00', '\x00', '\x00', '\x00', '\x00'], flag: PAIRED,MREVERSE,READ2, split: none, mapping_quality: 43, repeat_count: 150, align_length: 150, qname: "428") skipping
More than 65535 reads in cluster with first read:(tid: 24, position: 15757, repeat: ['G', '\x00', '\x00', '\x00', '\x00', '\x00'], flag: PAIRED,MREVERSE,READ2, split: none, mapping_quality: 60, repeat_count: 150, align_length: 150, qname: "113") skipping
More than 65535 reads in cluster with first read:(tid: 1, position: 181396416, repeat: ['A', '\x00', '\x00', '\x00', '\x00', '\x00'], flag: PAIRED,READ2, split: none_right, mapping_quality: 0, repeat_count: 124, align_length: 150, qname: "49") skipping
More than 65535 reads in cluster with first read:(tid: 3, position: 169960503, repeat: ['A', '\x00', '\x00', '\x00', '\x00', '\x00'], flag: PAIRED,PROPER_PAIR,MREVERSE,READ1, split: none, mapping_quality: 54, repeat_count: 128, align_length: 150, qname: "1138") skipping
More than 65535 reads in cluster with first read:(tid: 22, position: 149830784, repeat: ['G', '\x00', '\x00', '\x00', '\x00', '\x00'], flag: PAIRED,PROPER_PAIR,REVERSE,READ1, split: none, mapping_quality: 60, repeat_count: 142, align_length: 150, qname: "754") skipping
More than 65535 reads in cluster with first read:(tid: 6, position: 86499722, repeat: ['G', '\x00', '\x00', '\x00', '\x00', '\x00'], flag: PAIRED,MREVERSE,READ2, split: none, mapping_quality: 57, repeat_count: 144, align_length: 150, qname: "233") skipping
More than 65535 reads in cluster with first read:(tid: 24, position: 15398, repeat: ['C', '\x00', '\x00', '\x00', '\x00', '\x00'], flag: PAIRED,READ2, split: none, mapping_quality: 60, repeat_count: 150, align_length: 150, qname: "97") skipping
More than 65535 reads in cluster with first read:(tid: 24, position: 15965, repeat: ['C', '\x00', '\x00', '\x00', '\x00', '\x00'], flag: PAIRED,READ2, split: none, mapping_quality: 60, repeat_count: 150, align_length: 150, qname: "71") skipping
More than 65535 reads in cluster with first read:(tid: 6, position: 86500001, repeat: ['C', '\x00', '\x00', '\x00', '\x00', '\x00'], flag: PAIRED,READ2, split: none, mapping_quality: 60, repeat_count: 122, align_length: 150, qname: "1715") skipping