Fatal error running v2

[jwitch]

I ran the following:

$ AdapterRemoval --file1 SNJW007_S2_L002_R1_001.fastq --file2 SNJW007_S2_L002_R2_001.fastq --gzip --basename AR_demux --barcode-list CCS6_barcodes_forAR.txt

And got this error:

Read 15 barcodes / barcode pairs from 'CCS6_barcodes_forAR.txt'... Trimming paired end reads ...

FATAL ERROR: Debug assertion failed in 'src/demultiplex.cc', line 105: child != -1

This should not happen! Please file a bug-report at https://github.com/MikkelSchubert/adapterremoval/issues/new Abort trap: 6

I had some trouble adding C++11, could that be the issue?

[MikkelSchubert]

Hey jwitch, Sorry about that, it is most likely caused by a mistake on my part. If possible, could you attach your 'CCS6_barcodes_forAR.txt' file, so that I can try to replicate the problem? Alternatively, if you'd prefer not posting it in public, you can also email it to MSchubert@snm.ku.dk

Hopefully this shouldn't have anything to do with C++11, as this code did not change in the transition. However, if you have made any changes to AR to get it to work, then it would be helpful if you could also attach / email these to me.

Cheers, Mikkel

[jwitch]

Here's the barcode file. I didn't change anything about AdapterRemoval. I even reinstalled it after updating my computer (Mac running Mavericks so had to install older XCode 6 version) because I got this fatal error.

On Thu, Aug 18, 2016 at 11:17 PM, Mikkel Schubert notifications@github.com wrote:

Hey jwitch, Sorry about that, it is most likely caused by a mistake on my part. If possible, could you attach your 'CCS6_barcodes_forAR.txt' file, so that I can try to replicate the problem? Alternatively, if you'd prefer not posting it in public, you can also email it to MSchubert@snm.ku.dk

Hopefully this shouldn't have anything to do with C++11, as this code did not change in the transition. However, if you have made any changes to AR to get it to work, then it would be helpful if you could also attach / email these to me.

Cheers, Mikkel

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/MikkelSchubert/adapterremoval/issues/11#issuecomment-240937377, or mute the thread https://github.com/notifications/unsubscribe-auth/AFOE4UaykcWE1HQ3kGOWeV9ne4nfg4NIks5qhUqKgaJpZM4JoE5I .

Jessica Witchley PhD candidate, Tetrad graduate program Laboratory of Dr. Suzanne Noble Department of Microbiology & Immunology University of California, San Francisco 513 Parnassus Ave., Room HSE451, Box 0414 San Francisco, CA 94143-0414 Phone: 415-476-8992

BC1_BC4 CAGTGGCGTCAATTTTACGCAGACTATCTTTCTAGGG GTTATGAAGGCC BC1_BC5 CAGTGGCGTCAATTTTACGCAGACTATCTTTCTAGGG ATCACTTAAGCC BC1_BC6 CAGTGGCGTCAATTTTACGCAGACTATCTTTCTAGGG ATAGCTCAGACC BC1_BC7 CAGTGGCGTCAATTTTACGCAGACTATCTTTCTAGGG ACCAAAAAACCC BC1_BC8 CAGTGGCGTCAATTTTACGCAGACTATCTTTCTAGGG GACGGGGGTGCC BC2_BC4 TGACAGCGTCAATTTTACGCAGACTATCTTTCTAGGG GTTATGAAGGCC BC2_BC5 TGACAGCGTCAATTTTACGCAGACTATCTTTCTAGGG ATCACTTAAGCC BC2_BC6 TGACAGCGTCAATTTTACGCAGACTATCTTTCTAGGG ATAGCTCAGACC BC2_BC7 TGACAGCGTCAATTTTACGCAGACTATCTTTCTAGGG ACCAAAAAACCC BC2_BC8 TGACAGCGTCAATTTTACGCAGACTATCTTTCTAGGG GACGGGGGTGCC BC3_BC4 GTCATGCGTCAATTTTACGCAGACTATCTTTCTAGGG GTTATGAAGGCC BC3_BC5 GTCATGCGTCAATTTTACGCAGACTATCTTTCTAGGG ATCACTTAAGCC BC3_BC6 GTCATGCGTCAATTTTACGCAGACTATCTTTCTAGGG ATAGCTCAGACC BC3_BC7 GTCATGCGTCAATTTTACGCAGACTATCTTTCTAGGG ACCAAAAAACCC BC3_BC8 GTCATGCGTCAATTTTACGCAGACTATCTTTCTAGGG GACGGGGGTGCC

[MikkelSchubert]

Thank you very much! The problem was indeed my fault, since I had incorrectly assumed that barcodes would always be short (< 10 bp). I've reworked the relevant code, and it should now be able to handle barcodes of any length, including of course your list of barcodes.

I'd greatly appreciate it if you could try to build the latest version of AdapterRemoval, and let me know if that fixes it for you, too.

Cheers

[jwitch]

It did not throw a fatal error this time but it's going to take a while to run. This issue has resolved. Thanks!

On Fri, Aug 19, 2016 at 11:29 AM, Mikkel Schubert notifications@github.com wrote:

Thank you very much! The problem was indeed my fault, since I had incorrectly assumed that barcodes would always be short (< 10 bp). I've reworked the relevant code, and it should now be able to handle barcodes of any length, including of course your list of barcodes.

I'd greatly appreciate it if you could try to build the latest version of AdapterRemoval, and let me know if that fixes it for you, too.

Cheers

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/MikkelSchubert/adapterremoval/issues/11#issuecomment-241097945, or mute the thread https://github.com/notifications/unsubscribe-auth/AFOE4YPBBBAOl3GpT6eqEHx3BPRmSBgwks5qhfYngaJpZM4JoE5I .

Jessica Witchley PhD candidate, Tetrad graduate program Laboratory of Dr. Suzanne Noble Department of Microbiology & Immunology University of California, San Francisco 513 Parnassus Ave., Room HSE451, Box 0414 San Francisco, CA 94143-0414 Phone: 415-476-8992

[MikkelSchubert]

Thanks! Something I forgot to mention though, since you are using long barcodes: It may be worthwhile for you to experiment with allowing some number of mismatches in the barcode sequence, since there is probably a non-negliable chance that there will be a sequencing error. But, by default, AdapterRemoval requires perfect matches for the barcodes. You could, for example, allow a single mismatch in either of the two barcodes using '--barcode-mm 1', or you could allow a single mismatch in just the (long) mate 1 barcode, like so: '--barcode-mm-r1 1'.

Don't hesitate to write again if you run into other problems.

Cheers