STAR quits halfway through mapping NO ERRORS!!

[Abhishek Choudhary]

Hi Alex,

I'm running into a weird issue where STAR alignment step quits before the alignment is complete, and doesn't even give any error. At first I thought it's because of CPU/memory issue, but despite trying with much higher compute resources, it behaves exactly the same. Do you have an idea why it's doing that?

Log.out file is attached here.

Thank you!

[Alexander Dobin]

Hi @abhich,

This is a complex diploid genome run with a lot of non-trivial parameters...

The error is probably a seg-fault, which should be captured in stderr.

I did not test STAR-diploid with --peOverlap* parameters, please try to run without them.

If it does not work, could you share a minimalistic example that reproduces the error?

[Abhishek Choudhary]

Hi Alex,

Thank you for your response! I confirmed that it's indeed a segmentation fault issue with the message "Command terminated by signal 11".

Attaching the Log.out file again, after running with the minimal parameters set as:

STAR --runThreadN 36 --genomeDir genome_index_folder 

--readFilesIn sample_1.fastq.gz sample_2.fastq.gz --readFilesCommand zcat

--outSAMattrRGline ID:7316-2192  LB:1242270  PL:illumina SM:BS_AAV1YVCH 

--outSAMattributes NH HI AS nM NM MD ha

--outSAMtype BAM Unsorted

--outSAMunmapped Within 

--quantMode TranscriptomeSAM GeneCounts

--genomeTransformOutput SAM SJ Quant

I ran the same command also with standard genome index (and w/o genomeTransformOutput, 'MD ha' in outSAMattributes) which ran successfully.

Couple of other differences in the two runs: 

1. "File system inputs: 0" for standard vs. "File system inputs: 122855528" for diploid, and
2. for diploid run, /var/log/messages file also showed
   

            kernel: [12372.219518] show_signal_msg: 21 callbacks suppressed
            kernel: [12372.219520] STAR[4365]: segfault at 108 ip 00007fa95431e4b7 sp 00007f99037ece48 error 4 in libc-2.31.so[7fa9541e0000+159000]
            kernel: [12372.236033] Code: c7 80 00 00 00 48 81 fa 80 00 00 00 77 bc c5 fe 7f 29 c5 fe 7f 71 e0 c5 fe 7f 79 c0 c5 7e 7f 41 a0 c4 c1 7e 7f 23 c5 f8 77 c3 <c5> fe 6f 26 c5 fe 6f 6e 20 c5 fe 6f 76 40 c5 fe 6f 7e 60 c5 7e 6f

I would greatly appreciate any insight into this issue, or suggestions of parameters I could try..

Thank you!

[Abhishek Choudhary]

Additionally, from the Log.out files, I noticed that it always breaks for me after line:

       "Created thread # ${runThreadN}-1"

While the next line (in a successful run) is:

       "Thread #.. end of input stream, nextChar=-1"

       ...

indicating input stream is not ending correctly (?!) when personal genome is used..

Regards,

Abhishek

[Alexander Dobin]

Hi Abhishek,

could you please try the new patch:

https://github.com/dobinlab/STAR_pre_releases/releases/tag/2.7.11b_alpha_2024-02-09

If this does not help, I will try to reproduce the error - if you could send me the minimal FASTQ that cause the error.

[Abhishek Choudhary]

Hi Alex,

The patch did not work for me.

I subsetted the original fastq to one with only a few reads which doesn't work (attached here). I can't promise all the other reads (which are not in this subset) from original fastq are fine, but one or more reads in this subset causes the same behavior (i.e. shows no error and quits).

Aligning command I'm running is same as above but I'll put it here again for your convenience:

STAR \

--runThreadN 8 \

--genomeDir genome_dir_loc/ \

--readFilesIn sub1.fastq sub2.fastq \

--outSAMattrRGline ID:7316-2192 LB:1242270 PL:illumina SM:BS_AAV1YVCH \

--outSAMattributes NH HI AS nM NM MD ha \

--outSAMtype BAM Unsorted \

--outSAMunmapped Within \

--quantMode TranscriptomeSAM GeneCounts \

--genomeTransformOutput SAM SJ Quant

Thank you!

Abhishek