Hi
I am using Galaxy server for genome assembly using SPAdes. But there is an error occurred:
Command line: /cvmfs/main.galaxyproject.org/deps/_conda/envs/__spades@3.12.0/bin/spades.py -o /pylon5/mc48nsp/xcgalaxy/main/staging/28325065/working --disable-gzip-output --only-assembler --careful -t 7 -m 288 -k 33,55,91 --cov-cutoff auto --pe1-fr --pe1-1 fastq:/pylon5/mc48nsp/xcgalaxy/main/staging/28325065/inputs/dataset_39274260.dat --pe1-2 fastq:/pylon5/mc48nsp/xcgalaxy/main/staging/28325065/inputs/dataset_39272829.dat
System information:
SPAdes version: 3.12.0
Python version: 3.8.1
OS: Linux-3.10.0-957.27.2.el7.x86_64-x86_64-with-glibc2.10
Output dir: /pylon5/mc48nsp/xcgalaxy/main/staging/28325065/working
Mode: ONLY assembling (without read error correction)
Debug mode is turned OFF
Dataset parameters:
Multi-cell mode (you should set ‘–sc’ flag if input data was obtained with MDA (single-cell) technology or --meta flag if processing metagenomic dataset)
Reads:
Library number: 1, library type: paired-end
orientation: fr
left reads: [‘/pylon5/mc48nsp/xcgalaxy/main/staging/28325065/inputs/dataset_39274260.dat’]
right reads: [‘/pylon5/mc48nsp/xcgalaxy/main/staging/28325065/inputs/dataset_39272829.dat’]
interlaced reads: not specified
single reads: not specified
merged reads: not specified
Assembly parameters:
k: [33, 55, 91]
Repeat resolution is enabled
Mismatch careful mode is turned ON
MismatchCorrector will be used
Coverage cutoff is turned ON and threshold will be auto-detected
Other parameters:
Dir for temp files: /pylon5/mc48nsp/xcgalaxy/main/staging/28325065/working/tmp
Threads: 7
Memory limit (in Gb): 288
======= SPAdes pipeline started. Log can be found here: /pylon5/mc48nsp/xcgalaxy/main/staging/28325065/working/spades.log
===== Assembling started.
== Running assembler: K33
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /pylon5/mc48nsp/xcgalaxy/main/staging/28325065/working/K33/configs/config.info
0:00:00.001 4M / 4M INFO General (main.cpp : 74) Loaded config from /pylon5/mc48nsp/xcgalaxy/main/staging/28325065/working/K33/configs/careful_mode.info
0:00:00.002 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 288 Gb
0:00:00.002 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from N/A, git revision N/A
0:00:00.002 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128
0:00:00.002 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/pylon5/mc48nsp/xcgalaxy/main/staging/28325065/working/dataset.info) with K=33
0:00:00.003 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 7
0:00:00.003 4M / 4M INFO General (launch.hpp : 51) SPAdes started
0:00:00.003 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction
0:00:00.003 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0
0:00:00.003 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction
0:00:00.020 4M / 4M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #0 (takes a while)
0:00:00.020 4M / 4M INFO General (read_converter.hpp : 78) Converting paired reads
0:00:00.574 100M / 100M INFO General (binary_converter.hpp : 93) 16384 reads processed
0:00:00.972 116M / 116M INFO General (binary_converter.hpp : 93) 32768 reads processed
0:00:01.746 144M / 144M INFO General (binary_converter.hpp : 93) 65536 reads processed
0:00:03.283 204M / 204M INFO General (binary_converter.hpp : 93) 131072 reads processed
0:00:06.374 320M / 320M INFO General (binary_converter.hpp : 93) 262144 reads processed
0:00:12.521 548M / 548M INFO General (binary_converter.hpp : 93) 524288 reads processed
0:00:34.567 908M / 908M INFO General (binary_converter.hpp : 93) 1048576 reads processed
0:01:09.485 908M / 908M INFO General (binary_converter.hpp : 93) 2097152 reads processed
0:02:18.535 912M / 912M INFO General (binary_converter.hpp : 93) 4194304 reads processed
0:04:48.246 920M / 920M INFO General (binary_converter.hpp : 93) 8388608 reads processed
0:06:31.981 936M / 936M ERROR General (paired_readers.hpp : 58) The number of left read-pairs is larger than the number of right read-pairs
0:06:31.981 936M / 936M ERROR General (paired_readers.hpp : 60) Unequal number of read-pairs detected in the following files: /pylon5/mc48nsp/xcgalaxy/main/staging/28325065/inputs/dataset_39274260.dat /pylon5/mc48nsp/xcgalaxy/main/staging/28325065/inputs/dataset_39272829.dat
== Error == system call for: “[‘/cvmfs/main.galaxyproject.org/deps/_conda/pkgs/spades-3.12.0-1/share/spades-3.12.0-1/bin/spades-core’, ‘/pylon5/mc48nsp/xcgalaxy/main/staging/28325065/working/K33/configs/config.info’, ‘/pylon5/mc48nsp/xcgalaxy/main/staging/28325065/working/K33/configs/careful_mode.info’]” finished abnormally, err code: 255
What can I do ? Kindly help me to solve this problem.Thank You