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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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hammer err code: 6 #91

Closed parkjongbin closed 6 years ago

parkjongbin commented 6 years ago

Hello, I've sequenced one bacteria genome using HiSeq platform (2x150bp). Sequencing depths are good (almost 330-fold). I typed the commands like in the below, but some error reported and spades is not working. Those anyone help that problems?

Command /home/ebkim/BioSW/SPAdes-3.11.1-Linux/bin/spades.py \ -t 48 -k 21 --careful \ -o spades_output \ -1 Adaptor_Filtered_Reads/JB8_AS1D0I0_97perc_over90bp_64cutoff_F_pair.fastq \ -2 Adaptor_Filtered_Reads/JB8_AS1D0I0_97perc_over90bp_64cutoff_R_pair.fastq \ -s Adaptor_Filtered_Reads/JB8_AS1D0I0_97perc_over90bp_64cutoff_single.fastq

=== Stack Trace === [0x407a6a] [0x409561] [0x40c79b] [0x40129a] [0x5442b0] [0x40620d] Verification of expression '(intptr_t) MappedRegion != -1L' failed in function 'void MMappedWriter::reserve(size_t)'. In file '/spades/src/common/io/kmers/mmapped_writer.hpp' on line 94. Message 'mmap(2) failed. Reason: Invalid argument. Error code: 22'. Verification of expression '(intptr_t) MappedRegion != -1L' failed in function 'void MMappedWriter::reserve(size_t)'. In file '/spades/src/common/io/kmers/mmapped_writer.hpp' on line 94. Message 'mmap(2) failed. Reason: Invalid argument. Error code: 22'. hammer: /spades/src/common/io/kmers/mmapped_writer.hpp:94: void MMappedWriter::reserve(size_t): Assertion `(intptr_t) MappedRegion != -1L' failed.

== Error == system call for: "['/home/ebkim/BioSW/SPAdes-3.11.1-Linux/bin/hammer', '/home/ebkim/share/180319_EfaeciumJB00008_HiSeq/Adaptor_Filtered_Reads/JB8_AS1D0I0_97perc_over90bp_64cutoff_17mer/corrected/configs/config.info']" finished abnormally, err code: -6

params.txt spades.log

Sincerely, Department of Animal Life System, Kangwon National University (KNU), Chuncheon, Republic of Korea. Lab of Microbial Genomics and Big Data, College of Animal Life Sciences. Jongbin Park

asl commented 6 years ago

Are you running SPAdes inside a VM?

parkjongbin commented 6 years ago

Yes, my linux (Lubuntu 17.04) was installed in the Oracle VM VirtualBox. Previous results are good (i've already assembled many genomes using VM), but i don't know why theses commands are shown.

asl commented 6 years ago

VirtualBox has a broken implementation of memory mapped files on top of its shared folders. So, you cannot have SPAdes scratch directory located inside VirtualBox shared folder. "Normal" folder inside VM is ok. Input / output files could be located on shared folder. You can use --tmp-dir option to specify the location of scratch folder.

parkjongbin commented 6 years ago

Okay, I will try. Thank you very much for your kind explanation.