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xargs: cat: terminated by signal 13 #154

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jhcuarta opened this issue Jul 9, 2021 · 0 comments
Open

xargs: cat: terminated by signal 13 #154

jhcuarta opened this issue Jul 9, 2021 · 0 comments

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@jhcuarta
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jhcuarta commented Jul 9, 2021

Hi
I've been trying to build a standard database, not succeded since a termination by signal 13; at first the error also displayed problems allocating some bytes, reason why i tagged the hash size as shown in next command line

(base) jason@jason:~/Documentos/Databases$ kraken-build --standard --db Kraken_db --threads 7 --jellyfish-hash-size 6400000000G

Found jellyfish v1.1.12
Skipping archaea, already completed library download
Skipping bacteria, already completed library download
Skipping viral, already completed library download
Kraken build set to minimize disk writes.
Creating k-mer set (step 1 of 6)...
Found jellyfish v1.1.12

xargs: cat: terminated by signal 13
/home/jason/Documentos/kraken-master/build_kraken_db.sh: line 96: 3786 Done find library/ -name '*.fna' -print0
3787 Exit 125 | xargs -0 cat
3788 Segmentation fault (core dumped) | jellyfish count -m $KRAKEN_KMER_LEN -s $KRAKEN_HASH_SIZE -C -t $KRAKEN_THREAD_CT -o database /dev/fd/0

I would appreaciate your colaboration, althoug i was wondering if maybe there's any repository for downloading a current kraken standard database built using kraken 1

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