Open yunkaig opened 6 months ago
Hi Yunkai,
Thank you for reporting the issue. As you pointed out, I have made some recent changes to address the issue. There are other ongoing items I am working on, so I have not made a new release that includes the commit.
Seems like this issue is blocking your analysis at the BQSR step? If that's the case, building the software from the main
branch might help.
Thanks for the quick reply! The issue occurs after the BQSR step was completed, but I will try the main
branch to see if it solves the issue.
Hi @milkschen,
I have rerun lift over the version built from the main
branch. Now instead of the previous error, ValidateSamFile presents me with these errors:
ERROR::MISMATCH_MATE_ALIGNMENT_START:Record 1, Read name ST-E00106:225:HHM22CCXX:7:1118:9557:28558, Mate alignment does not match alignment start of mate
ERROR::MISMATCH_FLAG_MATE_NEG_STRAND:Record 1, Read name ST-E00106:225:HHM22CCXX:7:1118:9557:28558, Mate negative strand flag does not match read negative strand flag of mate
ERROR::MISMATCH_FLAG_MATE_UNMAPPED:Record 1, Read name ST-E00106:225:HHM22CCXX:7:1118:9557:28558, Mate unmapped flag does not match read unmapped flag of mate
ERROR::MISMATCH_MATE_CIGAR_STRING:Record 1, Read name ST-E00106:225:HHM22CCXX:7:1118:9557:28558, Mate CIGAR string does not match CIGAR string of mate
Other reads also at least 3 out of these 4 errors. Again it halts after encountering 100 errors.
Not sure if it helps but here is the read pair where these errors came from:
ST-E00106:225:HHM22CCXX:7:1118:9557:28558 99 chr1 260895 0 150M = 261280 535 ATCCCAGAACAGAATGCATCATGTGAAAAAGAATTTATGCTACAAATTACTATGGTTTGGATGTGGTTTGTCCCCGCAAAAACTCATGTTGAAATTTGACCCCCAATGTGGCAGTGTGGGGCGGTGGGGCCTAGTGGATGGTGTTTGGGT ????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????5??????????5?????? XA:Z:chr6,-172119695,150M,1;chr19,+205336,150M,4; MC:Z:78M1I70M MD:Z:7G7A34G24A24T4C4T27C11 RF:Z:source RG:Z:HHM22CCXX-7-1EBCC218 NM:i:8 LO:Z:L_L UQ:i:42 AS:i:145 XS:i:145
ST-E00106:225:HHM22CCXX:7:1118:9557:28558 133 chr1 260895 0 * = 260895 0 ACCATTTTCCCTCCACCTTCAGTGAGTTTTTACCTACATTTGTGTCTTAGTCCATCTTGTGCTTCTGTAAACAGAATACCTGAGGCTGGGTAATTTATAAGTAAAAAAGATTCATTTGGCTCACAATACTGGTAGCTGGAATGGCCGAC ????????????????????????????????????????????????????????????????????????5?????????????????????????????????+?????????????????????555+?+5??5????5+55%5% XA:Z:chr6,+172119311,68M1I80M,3; MC:Z:150M MD:Z:0c4a142 RF:Z:source RG:Z:HHM22CCXX-7-1EBCC218 NM:i:3 LO:Z:UM_L UQ:i:18 AS:i:135 XS:i:135
Many thanks
Hi there,
I have been trying to adapt leviosam2 to out pipeline. This is the process I ran through:
These are the parameters I used to run leviosam2:
And the error messages from ValidateSamFile:
It seems to me that no one has brought up that issue, but I did found a commit to remove
MC:z
tags for unmapped reads.Is there anything I have missed?
Thanks in advance, Yunkai