Entering edit mode
6.2 years ago
imdad.ce07buet
•
0
I ran the folowing command for assembly in Spades and having the error:
/home/mdimdadi/Downloads/SPAdes-3.11.1-Linux/bin/spades.py -1 14777x5_S1_L001_R1_001_prinseq_good_rHpg.fastq -2 147
77x5_S1_L001_R2_001_prinseq_good_Yy8G.fastq -s 14777x5_singletons_merged.fastq --meta -o 14777x5_assembly1 -t 32 -m 300 &
Command line: /home/mdimdadi/Downloads/SPAdes-3.11.1-Linux/bin/spades.py -1 /home/mdimdadi/14777R/FastQ/Passed_Reads/14777x5/14777x5_S1_L001_R1_001_prinseq_good_rHpg.fastq -2 /home/mdimdadi/14777R/FastQ/Passed_Reads/14777x5/14777x5_S1_L001_R2_001_prinseq_good_Yy8G.fastq -s /home/mdimdadi/14777R/FastQ/Passed_Reads/14777x5/14777x5_singletons_merged.fastq --meta -o /home/mdimdadi/14777R/FastQ/Passed_Reads/14777x5/14777x5_assembly1 -t 32 -m 300
System information:
SPAdes version: 3.11.1
Python version: 2.7.5
OS: Linux-3.10.0-514.6.1.el7.x86_64-x86_64-with-centos-7.3.1611-Core
Output dir: /home/mdimdadi/14777R/FastQ/Passed_Reads/14777x5/14777x5_assembly1
Mode: read error correction and assembling
Debug mode is turned OFF
Dataset parameters:
Metagenomic mode
Reads:
Library number: 1, library type: paired-end
orientation: fr
left reads: ['/home/mdimdadi/14777R/FastQ/Passed_Reads/14777x5/14777x5_S1_L001_R1_001_prinseq_good_rHpg.fastq']
right reads: ['/home/mdimdadi/14777R/FastQ/Passed_Reads/14777x5/14777x5_S1_L001_R2_001_prinseq_good_Yy8G.fastq']
interlaced reads: not specified
single reads: ['/home/mdimdadi/14777R/FastQ/Passed_Reads/14777x5/14777x5_singletons_merged.fastq']
Read error correction parameters:
Iterations: 1
PHRED offset will be auto-detected
Corrected reads will be compressed (with gzip)
Assembly parameters:
k: [21, 33, 55]
Repeat resolution is enabled
Mismatch careful mode is turned OFF
MismatchCorrector will be SKIPPED
Coverage cutoff is turned OFF
Other parameters:
Dir for temp files: /home/mdimdadi/14777R/FastQ/Passed_Reads/14777x5/14777x5_assembly1/tmp
Threads: 32
Memory limit (in Gb): 300
=== Stack Trace ===
[0x40c26a]
[0x6805d0]
[0x7a3989]
[0x7ac52d]
[0x7ee5d9]
Verification of expression 'f' failed in function 'void utils::KMerSortingSplitter<Seq>::DumpBuffers(const files_t&) [with Seq = RuntimeSeq<128ul>; fs::files_t = std::vector<std::basic_string<char> >]'. In file '/spades/src/common/utils/kmer_mph/kmer_splitters.hpp' on line 126. Message 'Cannot open temporary file to write'.
Verification of expression 'f' failed in function 'void utils::KMerSortingSplitter<Seq>::DumpBuffers(const files_t&) [with Seq = RuntimeSeq<128ul>; fs::files_t = std::vector<std::basic_string<char> >]'. In file '/spades/src/common/utils/kmer_mph/kmer_splitters.hpp' on line 126. Message 'Cannot open temporary file to write'.
spades: /spades/src/common/utils/kmer_mph/kmer_splitters.hpp:126: void utils::KMerSortingSplitter<Seq>::DumpBuffers(const files_t&) [with Seq = RuntimeSeq<128ul>; fs::files_t = std::vector<std::basic_string<char> >]: Assertion `f' failed.
== Error == system call for: "['/home/mdimdadi/Downloads/SPAdes-3.11.1-Linux/bin/spades', '/home/mdimdadi/14777R/FastQ/Passed_Reads/14777x5/14777x5_assembly1/K21/configs/config.info', '/home/mdimdadi/14777R/FastQ/Passed_Reads/14777x5/14777x5_assembly1/K21/configs/mda_mode.info', '/home/mdimdadi/14777R/FastQ/Passed_Reads/14777x5/14777x5_assembly1/K21/configs/meta_mode.info']" finished abnormally, err code: -6
In case you have troubles running SPAdes, you can write to spades.support@cab.spbu.ru
or report an issue on our GitHub repository github.com/ablab/spades
Please provide us with params.txt and spades.log files from the output directory.
I would start there and debug. Looks like you can't write to
/home/mdimdadi/14777R/FastQ/Passed_Reads/14777x5/14777x5_assembly1/
this directory from the account you are using to runSPAdes
.