Hi,
I am trying ExpansionHunter v2.5.5 on longread data. the data is originally pacbio hifi, but then it is converted into paired end which partially worked in ExpansionHunter v4. I would like to try the same data on the earlier version of EH, since the latest version caused some issue on depth calculation on longer reads. For example, the regions which actually had a high average coverage ( >30x) did fail with a tag of LowCoverage (I did not have this error in pacbio when the read sizes were 1kb, on the other hand the error occurred on reads having size >3kb).
Anyways, for the version 2, I got the following output with an error line at the bottom. What does this error mean? Is there any way to avoid it?
Expansion Hunter v2.5.5
2021-09-09T17:28:14,[Starting Logging for NA19240_CCS.corrected_daSTRs_1000_realigned_sorted]
2021-09-09T17:28:14,[Loading AR.json]
2021-09-09T17:28:14,[Loading ATN1.json]
2021-09-09T17:28:14,[Loading ATXN1.json]
2021-09-09T17:28:14,[Loading ATXN10.json]
2021-09-09T17:28:14,[Loading ATXN2.json]
2021-09-09T17:28:14,[Input format: BAM]
2021-09-09T17:28:14,[Read length: 1000]
2021-09-09T17:28:14,[Depth: 10]
2021-09-09T17:28:14,[Analyzing chrX:67545317-67545385 GCA]
2021-09-09T17:28:14, [Caching reads]
2021-09-09T17:28:14, [Found 85 reads in target locus]
2021-09-09T17:28:14, [Filling in mates]
2021-09-09T17:28:14, [Done filling in mates]
2021-09-09T17:28:14, [Estimating short repeat sizes]
basic_string::substr: __pos (which is 18446744073709551587) > this->size() (which is 250)
Hi, I am trying ExpansionHunter v2.5.5 on longread data. the data is originally pacbio hifi, but then it is converted into paired end which partially worked in ExpansionHunter v4. I would like to try the same data on the earlier version of EH, since the latest version caused some issue on depth calculation on longer reads. For example, the regions which actually had a high average coverage ( >30x) did fail with a tag of LowCoverage (I did not have this error in pacbio when the read sizes were 1kb, on the other hand the error occurred on reads having size >3kb).
Anyways, for the version 2, I got the following output with an error line at the bottom. What does this error mean? Is there any way to avoid it?
Expansion Hunter v2.5.5 2021-09-09T17:28:14,[Starting Logging for NA19240_CCS.corrected_daSTRs_1000_realigned_sorted] 2021-09-09T17:28:14,[Loading AR.json] 2021-09-09T17:28:14,[Loading ATN1.json] 2021-09-09T17:28:14,[Loading ATXN1.json] 2021-09-09T17:28:14,[Loading ATXN10.json] 2021-09-09T17:28:14,[Loading ATXN2.json] 2021-09-09T17:28:14,[Input format: BAM] 2021-09-09T17:28:14,[Read length: 1000] 2021-09-09T17:28:14,[Depth: 10] 2021-09-09T17:28:14,[Analyzing chrX:67545317-67545385 GCA] 2021-09-09T17:28:14, [Caching reads] 2021-09-09T17:28:14, [Found 85 reads in target locus] 2021-09-09T17:28:14, [Filling in mates] 2021-09-09T17:28:14, [Done filling in mates] 2021-09-09T17:28:14, [Estimating short repeat sizes] basic_string::substr: __pos (which is 18446744073709551587) > this->size() (which is 250)