Killed trimming process

[Jaoquien]

Hi everyone,

I usually apply Porechop after Albacore Basecalling.

porechop -i ./albacore/ -b ./porechop/

Now I am working with a run where 12 Staphylococcus pseudintermedius strains were sequenced with Rapid Barcoding Kit (SQK-RBK004). I don't know why the process dies at Trimming Adapters step:

Trimming adapters from read ends
  Rapid_adapter: GTTTTCGCATTTATCGTGAAACGCTTTCGCGTTTTTCGTGCGCCGCTTCA
       BC02_rev: ACAGACGACTACAAACGGAATCGA
           BC02: TCGATTCCGTTTGTAGTCGTCTGT
       BC03_rev: CCTGGTAACTGGGACACAAGACTC
           BC03: GAGTCTTGTGTCCCAGTTACCAGG
       BC10_rev: GAGAGGACAAAGGTTTCAACGCTT
           BC10: AAGCGTTGAAACCTTTGTCCTCTC
       BC11_rev: TCCATTCCCTCCGATAGATGAAAC
           BC11: GTTTCATCTATCGGAGGGAATGGA
           BC01: AAGAAAGTTGTCGGTGTCTTTGTG
       BC01_rev: CACAAAGACACCGACAACTTTCTT
           BC02: TCGATTCCGTTTGTAGTCGTCTGT
       BC02_rev: ACAGACGACTACAAACGGAATCGA
           BC03: GAGTCTTGTGTCCCAGTTACCAGG
       BC03_rev: CCTGGTAACTGGGACACAAGACTC
           BC04: TTCGGATTCTATCGTGTTTCCCTA
       BC04_rev: TAGGGAAACACGATAGAATCCGAA
           BC05: CTTGTCCAGGGTTTGTGTAACCTT
       BC05_rev: AAGGTTACACAAACCCTGGACAAG
           BC06: TTCTCGCAAAGGCAGAAAGTAGTC
       BC06_rev: GACTACTTTCTGCCTTTGCGAGAA
           BC07: GTGTTACCGTGGGAATGAATCCTT
       BC07_rev: AAGGATTCATTCCCACGGTAACAC
           BC08: TTCAGGGAACAAACCAAGTTACGT
       BC08_rev: ACGTAACTTGGTTTGTTCCCTGAA
           BC09: AACTAGGCACAGCGAGTCTTGGTT
       BC09_rev: AACCAAGACTCGCTGTGCCTAGTT
           BC10: AAGCGTTGAAACCTTTGTCCTCTC
       BC10_rev: GAGAGGACAAAGGTTTCAACGCTT
           BC11: GTTTCATCTATCGGAGGGAATGGA
       BC11_rev: TCCATTCCCTCCGATAGATGAAAC
           BC12: CAGGTAGAAAGAAGCAGAATCGGA
       BC12_rev: TCCGATTCTGCTTCTTTCTACCTG
2,480,060 / 3,406,426 (72.8%)Killed
(porechop-0.2.3) [jvinyes@node010 GABRI_1]$

Could someone help me?

Thank you,

Quim

[benno77]

Hi Quim,

I have just had the same issue, did you ever work out what was going wrong?

Cheers,

Ben

[XueyiDong]

Hi Quim and @benno77 ,
I have had the same issue too. I think it's because the server was running out of memory. I am running it again and it has already used more than 200GB memory.
Cheers,
Xueyi

[mbhall88]

Yes, this is likely a memory problem. I have had lots of problems with porechop's memory usage. By default it actually tries to get all the threads available, and the memory usage seems to scale with the number of threads. So if you have a big fastq file I would suggest just using a small number of threads (<=4). It will take longer than say 8 threads, but will use less memory.
How big is your fastq file out of interest?

[XueyiDong]

I divided my fastq file into 10 parts and ran them separately. Finally it ran successfully.