Command line: /usr/local/bin/spades.py --rna --threads 12 --memory 72 -1 /omics/groups/OE0436/data/kurilov/nikolas/de_novo_rna/work/93/3f41134417b204e9852823c85beb69/pooled_reads_1.merged.fastq.gz -2 /omics/groups/OE0436/data/kurilov/nikolas/de_novo_rna/work/93/3f41134417b204e9852823c85beb69/pooled_reads_2.merged.fastq.gz -o /omics/groups/OE0436/data/kurilov/nikolas/de_novo_rna/work/93/3f41134417b204e9852823c85beb69 System information: SPAdes version: 4.0.0 Python version: 3.12.3 OS: Linux-3.10.0-1160.90.1.el7.x86_64-x86_64-with-glibc2.36 Output dir: /omics/groups/OE0436/data/kurilov/nikolas/de_novo_rna/work/93/3f41134417b204e9852823c85beb69 Debug mode is turned OFF Dataset parameters: RNA-seq mode Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/omics/groups/OE0436/data/kurilov/nikolas/de_novo_rna/work/93/3f41134417b204e9852823c85beb69/pooled_reads_1.merged.fastq.gz'] right reads: ['/omics/groups/OE0436/data/kurilov/nikolas/de_novo_rna/work/93/3f41134417b204e9852823c85beb69/pooled_reads_2.merged.fastq.gz'] interlaced reads: not specified single reads: not specified merged reads: not specified Assembly parameters: k: automatic selection based on read length Repeat resolution is enabled Mismatch careful mode is turned OFF MismatchCorrector will be SKIPPED Coverage cutoff is turned OFF Assembly graph output will use GFA v1.2 format Other parameters: Dir for temp files: /omics/groups/OE0436/data/kurilov/nikolas/de_novo_rna/work/93/3f41134417b204e9852823c85beb69/tmp Threads: 12 Memory limit (in Gb): 72 ======= SPAdes pipeline started. Log can be found here: /omics/groups/OE0436/data/kurilov/nikolas/de_novo_rna/work/93/3f41134417b204e9852823c85beb69/spades.log /omics/groups/OE0436/data/kurilov/nikolas/de_novo_rna/work/93/3f41134417b204e9852823c85beb69/pooled_reads_1.merged.fastq.gz: max reads length: 150 /omics/groups/OE0436/data/kurilov/nikolas/de_novo_rna/work/93/3f41134417b204e9852823c85beb69/pooled_reads_2.merged.fastq.gz: max reads length: 150 Reads length: 150 K values to be used: [49, 73] ===== Before start started. ===== Assembling started. ===== K49 started. == Running: /usr/local/bin/spades-core /omics/groups/OE0436/data/kurilov/nikolas/de_novo_rna/work/93/3f41134417b204e9852823c85beb69/K49/configs/config.info /omics/groups/OE0436/data/kurilov/nikolas/de_novo_rna/work/93/3f41134417b204e9852823c85beb69/K49/configs/mda_mode.info /omics/groups/OE0436/data/kurilov/nikolas/de_novo_rna/work/93/3f41134417b204e9852823c85beb69/K49/configs/rna_mode.info 0:00:00.000 1M / 18M INFO General (main.cpp : 94) Loaded config from "/omics/groups/OE0436/data/kurilov/nikolas/de_novo_rna/work/93/3f41134417b204e9852823c85beb69/K49/configs/config.info" 0:00:00.001 1M / 18M INFO General (main.cpp : 94) Loaded config from "/omics/groups/OE0436/data/kurilov/nikolas/de_novo_rna/work/93/3f41134417b204e9852823c85beb69/K49/configs/mda_mode.info" 0:00:00.001 1M / 18M INFO General (main.cpp : 94) Loaded config from "/omics/groups/OE0436/data/kurilov/nikolas/de_novo_rna/work/93/3f41134417b204e9852823c85beb69/K49/configs/rna_mode.info" 0:00:00.001 1M / 18M INFO General (memory_limit.cpp : 55) Memory limit set to 72 Gb 0:00:00.002 1M / 18M INFO General (main.cpp : 102) Starting SPAdes, built from N/A, git revision N/A 0:00:00.002 1M / 18M INFO General (main.cpp : 103) Maximum k-mer length: 128 0:00:00.002 1M / 18M INFO General (main.cpp : 104) Assembling dataset ("/omics/groups/OE0436/data/kurilov/nikolas/de_novo_rna/work/93/3f41134417b204e9852823c85beb69/dataset.info") with K=49 0:00:00.002 1M / 18M INFO General (main.cpp : 105) Maximum # of threads to use (adjusted due to OMP capabilities): 12 0:00:00.002 1M / 18M INFO General (pipeline.cpp : 212) SPAdes started 0:00:00.002 1M / 18M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion 0:00:00.002 1M / 18M INFO General (pipeline.cpp : 234) Two-step repeat resolution disabled 0:00:00.006 1M / 18M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 0:00:00.006 1M / 18M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 0:00:00.010 1M / 18M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 0:00:00.013 1M / 18M INFO StageManager (stage.cpp : 189) STAGE == Binary Read Conversion (id: read_conversion) 0:00:00.294 1M / 18M INFO General (read_converter.cpp : 78) Converting reads to binary format for library #0 (takes a while) 0:00:00.294 1M / 18M INFO General (read_converter.cpp : 99) Converting paired reads 0:00:01.200 82M / 116M INFO General (binary_converter.cpp : 127) 16384 reads processed 0:00:01.206 82M / 117M INFO General (binary_converter.cpp : 127) 32768 reads processed 0:00:01.218 82M / 118M INFO General (binary_converter.cpp : 127) 65536 reads processed 0:00:01.360 82M / 158M INFO General (binary_converter.cpp : 127) 131072 reads processed 0:00:01.855 52M / 187M INFO General (binary_converter.cpp : 127) 262144 reads processed 0:00:02.447 0M / 237M INFO General (binary_converter.cpp : 127) 524288 reads processed 0:00:08.346 0M / 315M INFO General (binary_converter.cpp : 127) 1048576 reads processed 0:00:11.990 0M / 360M INFO General (binary_converter.cpp : 127) 2097152 reads processed 0:00:18.688 0M / 407M INFO General (binary_converter.cpp : 127) 4194304 reads processed 0:00:38.248 0M / 522M INFO General (binary_converter.cpp : 127) 8388608 reads processed 0:01:09.930 0M / 568M INFO General (binary_converter.cpp : 127) 16777216 reads processed 0:02:15.520 0M / 568M INFO General (binary_converter.cpp : 127) 33554432 reads processed 0:03:37.323 0M / 657M INFO General (binary_converter.cpp : 127) 67108864 reads processed 0:06:19.181 0M / 657M INFO General (binary_converter.cpp : 127) 134217728 reads processed 0:11:19.682 0M / 669M INFO General (binary_converter.cpp : 127) 268435456 reads processed 0:20:45.523 0M / 669M INFO General (binary_converter.cpp : 127) 536870912 reads processed 0:39:39.248 0M / 669M INFO General (binary_converter.cpp : 127) 1073741824 reads processed 1:17:30.590 0M / 690M INFO General (binary_converter.cpp : 127) 2147483648 reads processed 1:53:42.915 0M / 719M INFO General (binary_converter.cpp : 143) 3160970116 reads written 1:53:42.934 0M / 719M INFO General (read_converter.cpp : 113) Converting single reads 1:53:42.956 0M / 719M INFO General (binary_converter.cpp : 143) 0 reads written 1:53:42.956 0M / 719M INFO General (read_converter.cpp : 119) Converting merged reads 1:53:42.962 0M / 719M INFO General (binary_converter.cpp : 143) 0 reads written 1:53:43.942 1M / 719M INFO StageManager (stage.cpp : 189) STAGE == de Bruijn graph construction (id: construction) 1:53:44.061 1M / 719M INFO General (construction.cpp : 150) Max read length 150 1:53:44.064 1M / 719M INFO General (construction.cpp : 156) Average read length 140.073 1:53:44.064 1M / 719M INFO General (stage.cpp : 121) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting) 1:53:44.064 1M / 719M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 120 files using 12 threads. This might take a while. 1:53:44.071 1M / 719M INFO General (file_limit.hpp : 43) Open file limit set to 131072 1:53:44.071 1M / 719M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 1.99998 Gb 1:53:44.071 1M / 719M INFO General (kmer_splitter.hpp : 102) Using cell size of 279620 1:53:59.844 6841M / 6841M INFO General (kmer_splitters.hpp : 128) Processed 8387372 reads 1:54:08.003 6841M / 6841M INFO General (kmer_splitters.hpp : 128) Processed 16783304 reads 1:54:17.696 6841M / 6841M INFO General (kmer_splitters.hpp : 128) Processed 25174193 reads 1:54:25.825 6841M / 6841M INFO General (kmer_splitters.hpp : 128) Processed 33569157 reads 1:54:36.099 6841M / 6841M INFO General (kmer_splitters.hpp : 128) Processed 41966348 reads 1:54:44.628 6841M / 6841M INFO General (kmer_splitters.hpp : 128) Processed 50347613 reads 1:54:53.058 6841M / 6841M INFO General (kmer_splitters.hpp : 128) Processed 58743197 reads 1:55:02.936 6841M / 6841M INFO General (kmer_splitters.hpp : 128) Processed 67132870 reads 1:55:12.325 6841M / 6841M INFO General (kmer_splitters.hpp : 128) Processed 75530046 reads 1:55:21.522 6841M / 6841M INFO General (kmer_splitters.hpp : 128) Processed 83908733 reads 1:55:31.152 6841M / 6841M INFO General (kmer_splitters.hpp : 128) Processed 92265171 reads 1:55:39.568 6841M / 6841M INFO General (kmer_splitters.hpp : 128) Processed 100632124 reads 1:56:29.181 6841M / 6841M INFO General (kmer_splitters.hpp : 128) Processed 142414231 reads 1:58:57.696 6841M / 6841M INFO General (kmer_splitters.hpp : 128) Processed 276013418 reads 2:03:49.040 6841M / 6841M INFO General (kmer_splitters.hpp : 128) Processed 543218563 reads 2:14:04.296 6841M / 6841M INFO General (kmer_splitters.hpp : 128) Processed 1079126126 reads 2:34:23.717 6841M / 6841M INFO General (kmer_splitters.hpp : 128) Processed 2148117392 reads 3:21:32.195 6841M / 6841M INFO General (kmer_splitters.hpp : 128) Processed 4300239430 reads 4:40:22.115 6841M / 6841M INFO General (kmer_splitters.hpp : 128) Processed 8595740436 reads 5:50:23.486 1M / 6611M INFO General (kmer_splitters.hpp : 134) Used 12643880464 reads 5:50:23.741 1M / 6611M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 5:50:25.919 1M / 6611M ERROR General (mmapped_reader.hpp : 52) mmap(2) failed. Reason: Cannot allocate memory. Error code: 12 5:50:25.919 1M / 6611M ERROR General (mmapped_reader.hpp : 52) mmap(2) failed. Reason: Cannot allocate memory. Error code: 12 5:50:25.919 1M / 6611M ERROR General (mmapped_reader.hpp : 52) mmap(2) failed. Reason: Cannot allocate memory. Error code: 12 5:50:25.919 1M / 6611M ERROR General (mmapped_reader.hpp : 52) mmap(2) failed. Reason: Cannot allocate memory. Error code: 12=== Stack Trace === === Stack Trace === 5:50:25.919 1M / 6611M ERROR General (mmapped_reader.hpp : 52) mmap(2) failed. Reason: Cannot allocate memory. Error code: 12 5:50:25.919 1M / 6611M ERROR General (mmapped_reader.hpp : 52) mmap(2) failed. Reason: Cannot allocate memory. Error code: 12 === Stack Trace ====== Stack Trace === === Stack Trace ====== Stack Trace === /usr/local/bin/spades-core(+0x61a97) [0x56415c685a97] /usr/local/bin/spades-core(+0x7cae0) [0x56415c6a0ae0] /usr/local/bin/spades-core(+0x2888cd) [0x56415c8ac8cd] /usr/local/bin/spades-core(+0x28a781) [0x56415c8ae781] /usr/local/bin/../lib/libgomp.so.1(+0x186d9) [0x2b55787df6d9] /lib/x86_64-linux-gnu/libc.so.6(+0x89134) [0x2b5578b76134] /lib/x86_64-linux-gnu/libc.so.6(__clone+0x40) [0x2b5578bf5a40] /usr/local/bin/spades-core(+0x61a97) [0x56415c685a97] /usr/local/bin/spades-core(+0x7cae0) [0x56415c6a0ae0] /usr/local/bin/spades-core(+0x2888cd) [0x56415c8ac8cd] /usr/local/bin/spades-core(+0x28a781) [0x56415c8ae781] /usr/local/bin/../lib/libgomp.so.1(+0x186d9) [0x2b55787df6d9] /lib/x86_64-linux-gnu/libc.so.6(+0x89134) [0x2b5578b76134] /lib/x86_64-linux-gnu/libc.so.6(__clone+0x40) [0x2b5578bf5a40] /usr/local/bin/spades-core(+0x61a97) [0x56415c685a97] /usr/local/bin/spades-core(+0x7cae0) [0x56415c6a0ae0] /usr/local/bin/spades-core(+0x2888cd) [0x56415c8ac8cd] /usr/local/bin/spades-core(+0x28a781) [0x56415c8ae781] /usr/local/bin/../lib/libgomp.so.1(+0x186d9) [0x2b55787df6d9] /lib/x86_64-linux-gnu/libc.so.6(+0x89134) [0x2b5578b76134] /lib/x86_64-linux-gnu/libc.so.6(__clone+0x40) [0x2b5578bf5a40] /usr/local/bin/spades-core(+0x61a97) [0x56415c685a97] /usr/local/bin/spades-core(+0x7cae0) [0x56415c6a0ae0] /usr/local/bin/spades-core(+0x2888cd) [0x56415c8ac8cd] /usr/local/bin/spades-core(+0x28a781) [0x56415c8ae781] /usr/local/bin/../lib/libgomp.so.1(+0x186d9) [0x2b55787df6d9] /lib/x86_64-linux-gnu/libc.so.6(+0x89134) [0x2b5578b76134] /lib/x86_64-linux-gnu/libc.so.6(__clone+0x40) [0x2b5578bf5a40] == Error == system call for: "['/usr/local/bin/spades-core', '/omics/groups/OE0436/data/kurilov/nikolas/de_novo_rna/work/93/3f41134417b204e9852823c85beb69/K49/configs/config.info', '/omics/groups/OE0436/data/kurilov/nikolas/de_novo_rna/work/93/3f41134417b204e9852823c85beb69/K49/configs/mda_mode.info', '/omics/groups/OE0436/data/kurilov/nikolas/de_novo_rna/work/93/3f41134417b204e9852823c85beb69/K49/configs/rna_mode.info']" finished abnormally, OS return value: -11 In case you have troubles running SPAdes, you can 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: /omics/groups/OE0436/data/kurilov/nikolas/de_novo_rna/work/93/3f41134417b204e9852823c85beb69/spades.log Thank you for using rnaSPAdes! If you use it in your research, please cite: Bushmanova, E., Antipov, D., Lapidus, A. and Prjibelski, A.D., 2019. rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data. GigaScience, 8(9), p.giz100. doi.org/10.1093/gigascience/giz100