Entering edit mode
5.3 years ago
Ming
▴
110
Hello there,
I was trying to run a meta-assembly on my Hi-Seq samples and I came across this error:
Command line: /scratch/shiming/tools/SPAdes-3.13.0-Linux/bin/spades.py -o /gpfs0/scratch/shiming/trimmed_sequences/fastq/Assembly-Spades/CFC280618_metaspades --meta -t 16 -k 21,33,55,77 --pe1-1 /gpfs0/scratch/shiming/trimmed_sequences/fastq/CFC280618_S3_R1.normalised.fastq --pe1-2 /gpfs0/scratch/shiming/trimmed_sequences/fastq/CFC280618_S3_R2.normalised.fastq
System information:
SPAdes version: 3.13.0
Python version: 3.6.3
OS: Linux-2.6.32-696.6.3.el6.x86_64-x86_64-with-centos-6.9-Final
Output dir: /gpfs0/scratch/shiming/trimmed_sequences/fastq/Assembly-Spades/CFC280618_metaspades
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: ['/gpfs0/scratch/shiming/trimmed_sequences/fastq/CFC280618_S3_R1.normalised.fastq']
right reads: ['/gpfs0/scratch/shiming/trimmed_sequences/fastq/CFC280618_S3_R2.normalised.fastq']
interlaced reads: not specified
single reads: not specified
merged reads: not specified
Read error correction parameters:
Iterations: 1
PHRED offset will be auto-detected
Corrected reads will be compressed
Assembly parameters:
k: [21, 33, 55, 77]
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: /gpfs0/scratch/shiming/trimmed_sequences/fastq/Assembly-Spades/CFC280618_metaspades/tmp
Threads: 16
Memory limit (in Gb): 250
======= SPAdes pipeline started. Log can be found here: /gpfs0/scratch/shiming/trimmed_sequences/fastq/Assembly-Spades/CFC280618_metaspades/spades.log
===== Read error correction started.
== Running read error correction tool: /gpfs0/scratch/shiming/tools/SPAdes-3.13.0-Linux/bin/spades-hammer /gpfs0/scratch/shiming/trimmed_sequences/fastq/Assembly-Spades/CFC280618_metaspades/corrected/configs/config.info
0:00:00.000 4M / 4M INFO General (main.cpp : 75) Starting BayesHammer, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b
0:00:00.001 4M / 4M INFO General (main.cpp : 76) Loading config from /gpfs0/scratch/shiming/trimmed_sequences/fastq/Assembly-Spades/CFC280618_metaspades/corrected/configs/config.info
0:00:00.004 4M / 4M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 16
0:00:00.004 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 250 Gb
0:00:00.004 4M / 4M INFO General (main.cpp : 86) Trying to determine PHRED offset
0:00:00.057 4M / 4M INFO General (main.cpp : 92) Determined value is 33
0:00:00.058 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ]
0:00:00.058 4M / 4M INFO General (main.cpp : 113) Size of aux. kmer data 24 bytes
=== ITERATION 0 begins ===
0:00:00.058 4M / 4M INFO K-mer Counting (kmer_data.cpp : 280) Estimating k-mer count
0:00:00.334 260M / 260M INFO K-mer Counting (kmer_data.cpp : 285) Processing /gpfs0/scratch/shiming/trimmed_sequences/fastq/CFC280618_S3_R1.normalised.fastq
0:06:06.950 320M / 320M INFO K-mer Counting (kmer_data.cpp : 294) Processed 43334790 reads
0:06:06.950 320M / 320M INFO K-mer Counting (kmer_data.cpp : 285) Processing /gpfs0/scratch/shiming/trimmed_sequences/fastq/CFC280618_S3_R2.normalised.fastq
0:12:37.626 320M / 320M INFO K-mer Counting (kmer_data.cpp : 294) Processed 88493589 reads
0:12:37.626 320M / 320M INFO K-mer Counting (kmer_data.cpp : 299) Total 88493589 reads processed
0:12:39.123 320M / 320M INFO K-mer Counting (kmer_data.cpp : 306) Estimated 21912863491 distinct kmers
0:12:39.125 64M / 320M INFO K-mer Counting (kmer_data.cpp : 311) Filtering singleton k-mers
44 8 0
nslots: 68719476736
bits per slot: 8 range: 0000100000000000
0:12:39.125 81G / 81G INFO K-mer Counting (kmer_data.cpp : 317) Processing /gpfs0/scratch/shiming/trimmed_sequences/fastq/CFC280618_S3_R1.normalised.fastq
2:31:31.587 81G / 81G INFO K-mer Counting (kmer_data.cpp : 326) Processed 43334790 reads
2:31:31.593 81G / 81G INFO K-mer Counting (kmer_data.cpp : 317) Processing /gpfs0/scratch/shiming/trimmed_sequences/fastq/CFC280618_S3_R2.normalised.fastq
4:49:11.327 81G / 81G INFO K-mer Counting (kmer_data.cpp : 326) Processed 88493589 reads
4:49:11.328 81G / 81G INFO K-mer Counting (kmer_data.cpp : 331) Total 88493589 reads processed
4:49:11.383 81G / 81G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
4:49:11.383 81G / 81G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while.
4:49:11.397 81G / 81G INFO General (file_limit.hpp : 32) Open file limit set to 4224
4:49:11.398 81G / 81G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 3.51807 Gb
4:49:11.398 81G / 81G INFO General (kmer_splitters.hpp : 97) Using cell size of 262144
4:53:08.802 89G / 89G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /gpfs0/scratch/shiming/trimmed_sequences/fastq/CFC280618_S3_R1.normalised.fastq
4:56:01.077 89G / 90G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 5011320 reads
4:57:07.415 89G / 90G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 9116411 reads
4:58:10.764 89G / 90G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 13645695 reads
4:59:25.548 89G / 90G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 17907661 reads
5:00:28.031 89G / 90G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 22229606 reads
5:01:36.956 89G / 90G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 26788200 reads
5:02:41.890 89G / 90G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 31331777 reads
5:04:21.561 89G / 90G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 36002288 reads
5:05:49.361 89G / 90G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 40579473 reads
5:06:34.607 89G / 90G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 43334790 reads
5:06:34.607 89G / 90G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /gpfs0/scratch/shiming/trimmed_sequences/fastq/CFC280618_S3_R2.normalised.fastq
5:07:54.456 89G / 90G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 48404389 reads
5:13:26.306 89G / 90G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 67817903 reads
5:18:38.920 89G / 90G INFO K-mer Splitting (kmer_data.cpp : 112) Total 88493589 reads processed
5:18:44.154 81G / 90G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
5:28:04.207 81G / 90G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 5845832720 kmers in total.
5:28:04.207 81G / 90G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
5:32:39.909 81G / 90G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
5:44:19.128 83G / 90G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.
5:45:52.933 83G / 90G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2710741562 bytes occupied (3.70964 bits per kmer).
5:45:53.698 2G / 90G INFO K-mer Counting (kmer_data.cpp : 356) Arranging kmers in hash map order
8:40:07.610 89G / 90G INFO General (main.cpp : 148) Clustering Hamming graph.
12:16:01.420 89G / 90G INFO General (main.cpp : 155) Extracting clusters
== Error == system call for: "['/gpfs0/scratch/shiming/tools/SPAdes-3.13.0-Linux/bin/spades-hammer', '/gpfs0/scratch/shiming/trimmed_sequences/fastq/Assembly-Spades/CFC280618_metaspades/corrected/configs/config.info']" finished abnormally, err code: -9
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.
Will anyone be kind enough to advice on how to resolve this?
Thank You
Thank you very much!