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2.2 years ago
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I've been running metaspades on 83 different samples. For 81 of them it has ran fine, but for 2 the same issue is occuring. This is the command I am running;
spades.py --meta --pe1-1 CUH022T2_unclassified_paired_R1.fastq --pe1-2 CUH022T2_unclassified_paired_R2.fastq -o /backup/user_data/ciara/COVIDbiome/metaspades/CUH022T2
And here is the log;
======= SPAdes pipeline started. Log can be found here: /backup/user_data/ciara/COVIDbiome/metaspades/CUH022T2/spades.log
===== Read error correction started.
== Running read error correction tool: /usr/local/src/SPAdes-3.13.0-Linux/bin/spades-hammer /backup/user_data/ciara/COVIDbiome/metaspades/CUH022T2/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
0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /backup/user_data/ciara/COVIDbiome/metaspades/CUH022T2/corrected/configs/config.info
0:00:00.001 4M / 4M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 16
0:00:00.001 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 250 Gb
0:00:00.001 4M / 4M INFO General (main.cpp : 86) Trying to determine PHRED offset
0:00:00.024 4M / 4M INFO General (main.cpp : 92) Determined value is 33
0:00:00.024 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ]
0:00:00.024 4M / 4M INFO General (main.cpp : 113) Size of aux. kmer data 24 bytes
=== ITERATION 0 begins ===
0:00:00.024 4M / 4M INFO K-mer Counting (kmer_data.cpp : 280) Estimating k-mer count
0:00:00.176 260M / 260M INFO K-mer Counting (kmer_data.cpp : 285) Processing
/backup/user_data/ciara/COVIDbiome/kraken/temp_repeat/CUH022T2_unclassified_paired_R1.fastq
0:00:23.948 320M / 320M INFO K-mer Counting (kmer_data.cpp : 294) Processed 9223592 reads
0:00:23.948 320M / 320M INFO K-mer Counting (kmer_data.cpp : 285) Processing
/backup/user_data/ciara/COVIDbiome/kraken/temp_repeat/CUH022T2_unclassified_paired_R2.fastq
0:00:44.232 320M / 320M INFO K-mer Counting (kmer_data.cpp : 294) Processed 18447184 reads
0:00:44.232 320M / 320M INFO K-mer Counting (kmer_data.cpp : 299) Total 18447184 reads processed
0:00:45.972 320M / 320M INFO K-mer Counting (kmer_data.cpp : 306) Estimated 508800847 distinct kmers
0:00:45.986 64M / 320M INFO K-mer Counting (kmer_data.cpp : 311) Filtering singleton k-mers
38 8 0
nslots: 1073741824
bits per slot: 8 range: 0000004000000000
0:00:45.986 1G / 1G INFO K-mer Counting (kmer_data.cpp : 317) Processing
/backup/user_data/ciara/COVIDbiome/kraken/temp_repeat/CUH022T2_unclassified_paired_R1.fastq
0:09:43.722 1G / 1G INFO K-mer Counting (kmer_data.cpp : 326) Processed 9223592 reads
0:09:43.722 1G / 1G INFO K-mer Counting (kmer_data.cpp : 317) Processing
/backup/user_data/ciara/COVIDbiome/kraken/temp_repeat/CUH022T2_unclassified_paired_R2.fastq
It is the same spot that the run is getting stuck for both samples. No error ever comes up but I've let it run for over 30 hours and it does not proceed. I've also checked if the size of the files between forward and reverse reads are different or if the reverse read is of poorer quality than the forward read, but everything looks fine.
Has anyone ever encountered this before and have any solutions?
