segmentation fault issue

[hddesai]

I get a "segmentation fault" issue when executing this command:

dragen-os -r /work3/vca3/hash_ref -1 mrna-alpha-x1_S1_L001_R1_001.dmx.fastq.gz -2 mrna-alpha-x1_S1_L001_R2_001.dmx.fastq.gz > test.sam

Please assist. I downloaded dragmap version 1.2 from conda. It works on other files but not this one.

[hddesai]

Hello, the issue is with the reference. After I remove a repetitive region with many A, the alignment works. Is there a command line feature or option you can advise on using so that an alignment with repetitive region does not fail? Thank you. Below is the region that resulted in segmentation fault.

[rizkg]

Hi, we have fixed a few bugs in the last release 1.3.0, would you be able to update dragmap and retry?
Version 1.3.0 is not yet available in conda, so you would have to install from source.

[hddesai]

Hello, sure I will try to download from source and give it a shot.

[georgiiprovisor]

I had the same issue. When I removed reads with lengths less than 100 bp problem is solved, maybe this could help.

[rizkg]

Hi, thanks for the information. I am looking into it.
Is there any chance you could share the data that leads to the crash ?

[georgiiprovisor]

Hi, thanks for the information. I am looking into it. Is there any chance you could share the data that leads to the crash ?

Is it a question for me?:)
Sorry, it's confidential data (GDPR and this stuff). I could try to recreate the problem on some open-source data and give feedback on how it's going.

[Rohit-Satyam]

I am facing the same error.

dragen-os -r results/00_indexes/dragmapidx/ -1 Test_sample_L001_R1_001.fastq.gz -2 Test_sample_L001_R2_001.fastq.gz >  result.sam
2022-08-10 16:12:06 	[151459a79740]	Version: 1.3.0
2022-08-10 16:12:06 	[151459a79740]	argc: 7 argv: dragen-os -r results/00_indexes/dragmapidx/ -1 Test_sample_L001_R1_001.fastq.gz -2 Test_sample_L001_R2_001.fastq.gz
decompHashTableCtxInit...
  0.000 seconds
decompHashTableHeader...
  0.003 seconds
decompHashTableLiterals...
  0.006 seconds
decompHashTableExtIndex...
  0.000 seconds
decompHashTableAutoHits...
  0.009 seconds
decompHashTableSetFlags...
  0.023 seconds
finished decompress
Running dual fastq workflow on 112 threads. System supports 112 threads.
0	249	0	0	0	0	10000	1	40000	1	1000	0	0	0	6	
0	250	0	0	0	0	10000	1	40000	1	1000	0	0	0	5	
0	251	0	0	0	0	10000	1	40000	1	1000	0	0	0	4	
0	252	0	0	0	0	10000	1	40000	1	1000	0	0	0	3	
0	253	0	0	0	0	10000	1	40000	1	1000	0	0	0	2	
0	254	0	0	0	0	10000	1	40000	1	1000	0	0	0	1	
Segmentation fault (core dumped)

I tried even after removing the polyA tail but facing the same error. I installed dragmap via conda if that helps.

[nservant]

Same issue here with dragmap 1.3.0. Any news on the topic ?
It run smoothly with dragmap 1.2.1, but after building the new indexes and aligning the same data with the 1.3.0, we have a segmentation fault.
Thanks

[mikecuoco]

Having the same issue here. I installed 1.3.0 with conda and have been testing on chr20

[sri-jumpcode]

Trying dragen-os (installed using conda). I seem to run into this issue of Segmentation fault. Help will be highly appreciated.

[cmatKhan]

I have also run into this problem using both 1.2.1 and 1.3.0.

The data I'm using is 69M -- larger than the 25M limit to attach here -- so it is in this repo

https://github.com/cmatKhan/dragon_seg_fault_cneoformans

[gambalab]

if someone is still interested, i made a docker/singularity image that works. You can find it HERE