finished abnormally, Err code: -15 (running as script did not help)

[swiesenfeld0]

Hi, I'm trying to run SPAdes for the first time, and I'm getting these parameters & spades log.
I saw that there was a previous thread with err code -15, but the solution posted did not fix my problem. Also, running the toy data set does work on my computer.

#319

If anyone knows what the problem is, I would greatly appreciate the help! Any ideas of things I could try to troubleshoot this would also be appreciated.

params.txt
`Command line: /n/home05/swiesenfeld/miniconda3/bin/spades.py --pe1-1 /n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/output_3118_R1_paired.fq.gz --pe1-2 /n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/output_3118_R2_paired.fq.gz --pe1-s /n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/output_3118_R1_unpaired.fq.gz --pe1-s /n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/output_3118_R2_unpaired.fq.gz --careful -t 10 -o /n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/assembled_3318_2I

System information:
SPAdes version: 3.13.0
Python version: 3.9.12
OS: Linux-3.10.0-1160.36.2.el7.x86_64-x86_64-with-glibc2.17

Output dir: /n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/assembled_3318_2I
Mode: read error correction and assembling
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: ['/n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/output_3118_R1_paired.fq.gz']
right reads: ['/n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/output_3118_R2_paired.fq.gz']
interlaced reads: not specified
single reads: ['/n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/output_3118_R1_unpaired.fq.gz', '/n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/output_3118_R2_unpaired.fq.gz']
merged reads: not specified
Read error correction parameters:
Iterations: 1
PHRED offset will be auto-detected
Corrected reads will be compressed
Assembly parameters:
k: automatic selection based on read length
Repeat resolution is enabled
Mismatch careful mode is turned ON
MismatchCorrector will be used
Coverage cutoff is turned OFF
Other parameters:
Dir for temp files: /n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/assembled_3318_2I/tmp
Threads: 10
Memory limit (in Gb): 92
`

spades.log
`Command line: /n/home05/swiesenfeld/miniconda3/bin/spades.py --pe1-1 /n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/output_3118_R1_paired.fq.gz --pe1-2 /n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/output_3118_R2_paired.fq.gz --pe1-s /n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/output_3118_R1_unpaired.fq.gz --pe1-s /n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/output_3118_R2_unpaired.fq.gz --careful -t 10 -o /n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/assembled_3318_2I

System information:
SPAdes version: 3.13.0
Python version: 3.9.12
OS: Linux-3.10.0-1160.36.2.el7.x86_64-x86_64-with-glibc2.17

Output dir: /n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/assembled_3318_2I
Mode: read error correction and assembling
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: ['/n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/output_3118_R1_paired.fq.gz']
right reads: ['/n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/output_3118_R2_paired.fq.gz']
interlaced reads: not specified
single reads: ['/n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/output_3118_R1_unpaired.fq.gz', '/n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/output_3118_R2_unpaired.fq.gz']
merged reads: not specified
Read error correction parameters:
Iterations: 1
PHRED offset will be auto-detected
Corrected reads will be compressed
Assembly parameters:
k: automatic selection based on read length
Repeat resolution is enabled
Mismatch careful mode is turned ON
MismatchCorrector will be used
Coverage cutoff is turned OFF
Other parameters:
Dir for temp files: /n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/assembled_3318_2I/tmp
Threads: 10
Memory limit (in Gb): 92

======= SPAdes pipeline started. Log can be found here: /n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/assembled_3318_2I/spades.log

===== Read error correction started.

== Running read error correction tool: /n/home05/swiesenfeld/miniconda3/share/spades-3.13.0-0/bin/spades-hammer /n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/assembled_3318_2I/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 8ea4665
0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/assembled_3318_2I/corrected/configs/config.info
0:00:00.039 4M / 4M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 1
0:00:00.039 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 92 Gb
0:00:00.039 4M / 4M INFO General (main.cpp : 86) Trying to determine PHRED offset
0:00:00.059 4M / 4M INFO General (main.cpp : 92) Determined value is 33
0:00:00.059 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ]
0:00:00.059 4M / 4M INFO General (main.cpp : 113) Size of aux. kmer data 24 bytes
=== ITERATION 0 begins ===
0:00:00.147 4M / 4M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
0:00:00.148 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 16 files using 1 threads. This might take a while.
0:00:00.167 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 100000
0:00:00.167 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 30.6654 Gb
0:00:00.167 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 4194304
0:00:00.168 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 97) Processing /n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/output_3118_R1_paired.fq.gz
0:00:16.176 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 107) Processed 325080 reads
0:00:29.704 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 107) Processed 650062 reads
0:00:43.166 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 107) Processed 975358 reads
0:00:56.377 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 107) Processed 1300611 reads
0:01:09.393 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 107) Processed 1626193 reads
0:01:22.574 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 107) Processed 1951499 reads
0:01:35.774 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 107) Processed 2276804 reads
0:02:55.039 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 107) Processed 4228352 reads
0:03:07.095 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 97) Processing /n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/output_3118_R2_paired.fq.gz
0:05:46.403 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 107) Processed 8395129 reads
0:06:11.665 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 97) Processing /n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/output_3118_R1_unpaired.fq.gz
0:06:12.994 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 97) Processing /n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/output_3118_R2_unpaired.fq.gz
0:06:14.361 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 112) Total 9002796 reads processed
0:06:14.363 4M / 616M INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
0:06:34.326 4M / 616M INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 47380452 kmers in total.
0:06:34.326 4M / 616M INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
0:06:37.831 4M / 616M INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
0:06:48.676 24M / 616M INFO General (kmer_index_builder.hpp : 150) Merging final buckets.
0:06:50.607 24M / 616M INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 21978792 bytes occupied (3.71103 bits per kmer).
0:06:50.724 24M / 616M INFO K-mer Counting (kmer_data.cpp : 356) Arranging kmers in hash map order
0:06:55.333 752M / 752M INFO General (main.cpp : 148) Clustering Hamming graph.
0:11:44.191 752M / 752M INFO General (main.cpp : 155) Extracting clusters
0:11:57.650 752M / 2G INFO General (main.cpp : 167) Clustering done. Total clusters: 24092170
0:11:57.651 388M / 2G INFO K-mer Counting (kmer_data.cpp : 376) Collecting K-mer information, this takes a while.
0:11:57.966 1G / 2G INFO K-mer Counting (kmer_data.cpp : 382) Processing /n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/output_3118_R1_paired.fq.gz

== Error == system call for: "['/n/home05/swiesenfeld/miniconda3/share/spades-3.13.0-0/bin/spades-hammer', '/n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/assembled_3318_2I/corrected/configs/config.info']" finished abnormally, err code: -15

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.`

[asl]

Does the problem reproduce with the latest SPAdes 3.15.5?

[swiesenfeld0]

Hi @asl ! I updated SPAdes to 3.15.5 and now this is the error message (--continue does not allow it to pass this unfortunately

== Error == system call for: "['/n/home05/swiesenfeld/miniconda3/envs/assembler/bin/spades-hammer', '/n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/assembled_3318_2I/corrected/configs/config.info']" finished abnormally, OS return value: -15 None

New params.txt:
`Command line: /n/home05/swiesenfeld/miniconda3/envs/assembler/bin/spades.py --pe1-1 /n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/output_3118_R1_paired.fq.gz --pe1-2 /n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/output_3118_R2_paired.fq.gz --pe1-s /n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/output_3118_R1_unpaired.fq.gz --pe1-s /n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/output_3118_R2_unpaired.fq.gz --careful
-t 10 -o /n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/assembled_3318_2I

System information:
SPAdes version: 3.15.5
Python version: 3.8.13
OS: Linux-3.10.0-1160.36.2.el7.x86_64-x86_64-with-glibc2.10

Output dir: /n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/assembled_3318_2I
Mode: read error correction and assembling
Debug mode is turned OFF

Dataset parameters:
Standard mode
For multi-cell/isolate data we recommend to use '--isolate' option; for single-cell MDA data use '--sc'; for metagenomic data use '--meta'; for RNA-Seq use '--rna'.
Reads:
Library number: 1, library type: paired-end
orientation: fr
left reads: ['/n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/output_3118_R1_paired.fq.gz']
right reads: ['/n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/output_3118_R2_paired.fq.gz']
interlaced reads: not specified
single reads: ['/n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/output_3118_R1_unpaired.fq.gz', '/n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/output_3118_R2_unpaired.fq.gz']
merged reads: not specified
Read error correction parameters:
Iterations: 1
PHRED offset will be auto-detected
Corrected reads will be compressed
Assembly parameters:
k: automatic selection based on read length
Repeat resolution is enabled
Mismatch careful mode is turned ON
MismatchCorrector will be used
Coverage cutoff is turned OFF
Other parameters:
Dir for temp files: /n/holylfs05/LABS/hanage_lab/Lab/holyscratch01/sophia/merged_reads3118/assembled_3318_2I/tmp
Threads: 10
Memory limit (in Gb): 92`

[asl]

Will you please attach a complete spades.log file?

[swiesenfeld0]

@asl Yes, here it is! Thank you for helping

spades.log

[asl]

I'm seeing lots of strange things in the log. First of all you're running only using 1 threads:

  0:00:00.012     1M / 29M   INFO    General                 (main.cpp                  :  78)   Maximum # of threads to use (adjusted due to OMP capabilities): 1

You might want to talk with your system administrator to ask how one could properly specify # of OpenMP threads as it seems you're running on some kind of cluster environment.

Next, it seems like the SPAdes job was killed from outside. You could probably check for your cluster / system log for more clues. E.g. whether some disk / cpu / time quota was exceeded or something similar.

[swiesenfeld0]

That was the issue, everything is running fine now. I was having trouble setting the number of threads, but now things assemble very quickly and very well. Thank you!!!