Entering edit mode
3 months ago
jiyoung
▴
20
I'm having trouble using SPAdes. I'm using SPAdes to do paired end data assembly and I'm getting an unusual stop.
error code: finished abnormally, OS return value: 28
Do you know how to resolve this issue?
Environment: conda, SPAdes genome assembler v3.15.5 WSL, ubuntu RAM: 64GB
below is the error code`
== Running: /home/default1/miniconda3/envs/spades/bin/spades-hammer /mnt/d/raw/2023nudi/01.RawData/De-metaSPAdes/0201/corrected/configs/config.info
0:00:00.000 1M / 3M INFO General (main.cpp : 75) Starting BayesHammer, built from N/A, git revision N/A
0:00:00.001 1M / 3M INFO General (main.cpp : 76) Loading config from /mnt/d/raw/2023nudi/01.RawData/De-metaSPAdes/0201/corrected/configs/config.info
0:00:00.002 1M / 3M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 16
0:00:00.002 1M / 3M INFO General (memory_limit.cpp : 54) Memory limit set to 63 Gb
0:00:00.002 1M / 3M INFO General (main.cpp : 86) Trying to determine PHRED offset
0:00:00.003 1M / 3M INFO General (main.cpp : 92) Determined value is 33
0:00:00.004 1M / 3M INFO General (hammer_tools.cpp : 38) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ]
0:00:00.004 1M / 3M INFO General (main.cpp : 113) Size of aux. kmer data 24 bytes
=== ITERATION 0 begins ===
0:00:00.004 1M / 3M INFO K-mer Counting (kmer_data.cpp : 283) Estimating k-mer count
0:00:00.157 257M / 259M INFO K-mer Counting (kmer_data.cpp : 288) Processing /mnt/d/raw/2023nudi/01.RawData/De-metaSPAdes/Nudivirus_DKDN230027457-1A_HJHVHDSX7_L1.1qc.fq
0:03:16.363 257M / 260M INFO K-mer Counting (kmer_data.cpp : 297) Processed 81274915 reads
0:03:16.364 257M / 260M INFO K-mer Counting (kmer_data.cpp : 288) Processing /mnt/d/raw/2023nudi/01.RawData/De-metaSPAdes/Nudivirus_DKDN230027457-1A_HJHVHDSX7_L1.2qc.fq
0:06:24.664 257M / 260M INFO K-mer Counting (kmer_data.cpp : 297) Processed 162549830 reads
0:06:24.665 257M / 260M INFO K-mer Counting (kmer_data.cpp : 302) Total 162549830 reads processed
0:06:24.902 257M / 260M INFO K-mer Counting (kmer_data.cpp : 305) Estimated 2283737268 distinct kmers
0:06:24.902 1M / 260M INFO K-mer Counting (kmer_data.cpp : 309) Filtering singleton k-mers
0:06:24.907 11G / 11G INFO K-mer Counting (kmer_data.cpp : 315) Processing /mnt/d/raw/2023nudi/01.RawData/De-metaSPAdes/Nudivirus_DKDN230027457-1A_HJHVHDSX7_L1.1qc.fq
0:30:45.273 11G / 11G INFO K-mer Counting (kmer_data.cpp : 324) Processed 81274915 reads
0:30:45.273 11G / 11G INFO K-mer Counting (kmer_data.cpp : 315) Processing /mnt/d/raw/2023nudi/01.RawData/De-metaSPAdes/Nudivirus_DKDN230027457-1A_HJHVHDSX7_L1.2qc.fq
0:52:44.334 11G / 11G INFO K-mer Counting (kmer_data.cpp : 324) Processed 162549830 reads
0:52:44.334 11G / 11G INFO K-mer Counting (kmer_data.cpp : 329) Total 162549830 reads processed
0:52:44.335 11G / 11G INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 16 files using 16 threads. This might take a while.
0:52:44.352 11G / 11G INFO General (file_limit.hpp : 42) Open file limit set to 1024
0:52:44.354 11G / 11G INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 1.10129 Gb
0:52:44.354 11G / 11G INFO General (kmer_splitter.hpp : 101) Using cell size of 4194304
0:52:44.355 20G / 20G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /mnt/d/raw/2023nudi/01.RawData/De-metaSPAdes/Nudivirus_DKDN230027457-1A_HJHVHDSX7_L1.1qc.fq
0:53:32.868 20G / 25G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 3735509 reads
0:54:13.891 20G / 25G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 7448398 reads
0:55:01.318 20G / 25G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 11184659 reads
0:55:42.760 20G / 25G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 14903206 reads
0:56:27.562 20G / 25G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 18622607 reads
0:57:09.621 20G / 25G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 22349705 reads
0:57:50.627 20G / 25G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 26061737 reads
0:58:31.349 20G / 25G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 29743982 reads
0:59:13.216 20G / 25G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 33449746 reads
0:59:58.255 20G / 25G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 37155147 reads
1:00:39.706 20G / 25G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 40888831 reads
1:06:24.506 20G / 25G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 70556528 reads
1:08:41.504 20G / 25G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /mnt/d/raw/2023nudi/01.RawData/De-metaSPAdes/Nudivirus_DKDN230027457-1A_HJHVHDSX7_L1.2qc.fq
1:20:18.289 20G / 25G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 137108729 reads
1:23:10.019 20G / 25G ERROR General (kmer_splitter.hpp : 150) I/O error! Incomplete write! Reason: No space left on device. Error code: 28
== Error == system call for: "['/home/default1/miniconda3/envs/spades/bin/spades-hammer', '/mnt/d/raw/2023nudi/01.RawData/De-metaSPAdes/0201/corrected/configs/config.info']" finished abnormally, OS return value: 28
None
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.
SPAdes log can be found here: /mnt/d/raw/2023nudi/01.RawData/De-metaSPAdes/0201/spades.log
