Issue title: ERROR   General  (kmer_coverage_model.cpp   : 187) Invalid kmer coverage histogram, make sure that the coverage is indeed uniform
 Issue body: ### Description of bug

== Error ==  system call for: "['/gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/spades-core', '/gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades/K99/configs/config.info']" finished abnormally, OS return value: 21

### spades.log


== Warning ==  No assembly mode was specified! If you intend to assemble high-coverage multi-cell/isolate data, use '--isolate' option.


Command line: ./spades.py	-o	/gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades	-t	24	-m	20	-k	99,111,127	-1	/gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.S24_DKDL210000040-1a_HFL3FCCX2_L6_1_forward_paired.fq.gz.SSU.1.fq	-2	/gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.S24_DKDL210000040-1a_HFL3FCCX2_L6_1_forward_paired.fq.gz.SSU.2.fq	

System information:
  SPAdes version: 3.15.3
  Python version: 2.7.5
  OS: Linux-3.10.0-1160.45.1.el7.x86_64-x86_64-with-redhat-7.9-Nitrogen

Output dir: /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades
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: ['/gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.S24_DKDL210000040-1a_HFL3FCCX2_L6_1_forward_paired.fq.gz.SSU.1.fq']
      right reads: ['/gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.S24_DKDL210000040-1a_HFL3FCCX2_L6_1_forward_paired.fq.gz.SSU.2.fq']
      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: [99, 111, 127]
  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/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades/tmp
  Threads: 24
  Memory limit (in Gb): 20


======= SPAdes pipeline started. Log can be found here: /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades/spades.log

/gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.S24_DKDL210000040-1a_HFL3FCCX2_L6_1_forward_paired.fq.gz.SSU.2.fq: max reads length: 150
/gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.S24_DKDL210000040-1a_HFL3FCCX2_L6_1_forward_paired.fq.gz.SSU.1.fq: max reads length: 150

Reads length: 150


===== Before start started. 


===== Read error correction started. 


===== Read error correction started. 


== Running: /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/spades-hammer /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades/corrected/configs/config.info

  0:00:00.000     1M / 11M   INFO    General                 (main.cpp                  :  75)   Starting BayesHammer, built from N/A, git revision N/A
  0:00:00.004     1M / 11M   INFO    General                 (main.cpp                  :  76)   Loading config from /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades/corrected/configs/config.info
  0:00:00.008     1M / 11M   INFO    General                 (main.cpp                  :  78)   Maximum # of threads to use (adjusted due to OMP capabilities): 24
  0:00:00.011     1M / 11M   INFO    General                 (memory_limit.cpp          :  48)   Memory limit set to 20 Gb
  0:00:00.015     1M / 11M   INFO    General                 (main.cpp                  :  86)   Trying to determine PHRED offset
  0:00:00.020     1M / 11M   INFO    General                 (main.cpp                  :  92)   Determined value is 33
  0:00:00.022     1M / 11M   INFO    General                 (hammer_tools.cpp          :  38)   Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ]
  0:00:00.026     1M / 11M   INFO    General                 (main.cpp                  : 113)   Size of aux. kmer data 24 bytes
     === ITERATION 0 begins ===
  0:00:00.030     1M / 11M   INFO    General                 (kmer_index_builder.hpp    : 243)   Splitting kmer instances into 16 files using 24 threads. This might take a while.
  0:00:00.035     1M / 11M   INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 1024
  0:00:00.039     1M / 11M   INFO    General                 (kmer_splitter.hpp         :  93)   Memory available for splitting buffers: 0.277776 Gb
  0:00:00.043     1M / 11M   INFO    General                 (kmer_splitter.hpp         : 101)   Using cell size of 2330156
  0:00:00.179  7681M / 7681M INFO   K-mer Splitting          (kmer_data.cpp             :  97)   Processing /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.S24_DKDL210000040-1a_HFL3FCCX2_L6_1_forward_paired.fq.gz.SSU.1.fq
  0:00:00.214  7681M / 7681M INFO   K-mer Splitting          (kmer_data.cpp             :  97)   Processing /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.S24_DKDL210000040-1a_HFL3FCCX2_L6_1_forward_paired.fq.gz.SSU.2.fq
  0:00:00.257  7681M / 7681M INFO   K-mer Splitting          (kmer_data.cpp             : 112)   Total 3370 reads processed
  0:00:00.261     1M / 848M  INFO    General                 (kmer_index_builder.hpp    : 249)   Starting k-mer counting.
  0:00:00.289     1M / 848M  INFO    General                 (kmer_index_builder.hpp    : 260)   K-mer counting done. There are 346340 kmers in total.
  0:00:00.293     1M / 848M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 395)   Building perfect hash indices
  0:00:00.313     1M / 848M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 431)   Index built. Total 346340 kmers, 262224 bytes occupied (6.05703 bits per kmer).
  0:00:00.318     1M / 848M  INFO   K-mer Counting           (kmer_data.cpp             : 354)   Arranging kmers in hash map order
  0:00:00.339     6M / 848M  INFO    General                 (main.cpp                  : 148)   Clustering Hamming graph.
  0:00:00.469     6M / 848M  INFO    General                 (main.cpp                  : 155)   Extracting clusters:
  0:00:00.470     6M / 848M  INFO    General                 (concurrent_dsu.cpp        :  18)   Connecting to root
  0:00:00.470     6M / 848M  INFO    General                 (concurrent_dsu.cpp        :  34)   Calculating counts
  0:00:00.490    11M / 848M  INFO    General                 (concurrent_dsu.cpp        :  63)   Writing down entries
  0:00:00.527     6M / 848M  INFO    General                 (main.cpp                  : 167)   Clustering done. Total clusters: 223224
  0:00:00.528     4M / 848M  INFO   K-mer Counting           (kmer_data.cpp             : 371)   Collecting K-mer information, this takes a while.
  0:00:00.532    12M / 848M  INFO   K-mer Counting           (kmer_data.cpp             : 377)   Processing /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.S24_DKDL210000040-1a_HFL3FCCX2_L6_1_forward_paired.fq.gz.SSU.1.fq
  0:00:00.546    12M / 848M  INFO   K-mer Counting           (kmer_data.cpp             : 377)   Processing /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.S24_DKDL210000040-1a_HFL3FCCX2_L6_1_forward_paired.fq.gz.SSU.2.fq
  0:00:00.556    12M / 848M  INFO   K-mer Counting           (kmer_data.cpp             : 384)   Collection done, postprocessing.
  0:00:00.558    12M / 848M  INFO   K-mer Counting           (kmer_data.cpp             : 397)   There are 346340 kmers in total. Among them 229350 (66.2211%) are singletons.
  0:00:00.559    12M / 848M  INFO    General                 (main.cpp                  : 173)   Subclustering Hamming graph
  0:00:00.601    12M / 848M  INFO   Hamming Subclustering    (kmer_cluster.cpp          : 650)   Subclustering done. Total 61 non-read kmers were generated.
  0:00:00.601    12M / 848M  INFO   Hamming Subclustering    (kmer_cluster.cpp          : 651)   Subclustering statistics:
  0:00:00.602    12M / 848M  INFO   Hamming Subclustering    (kmer_cluster.cpp          : 652)     Total singleton hamming clusters: 195154. Among them 133930 (68.6279%) are good
  0:00:00.602    12M / 848M  INFO   Hamming Subclustering    (kmer_cluster.cpp          : 653)     Total singleton subclusters: 1131. Among them 1118 (98.8506%) are good
  0:00:00.603    12M / 848M  INFO   Hamming Subclustering    (kmer_cluster.cpp          : 654)     Total non-singleton subcluster centers: 37292. Among them 31276 (83.8679%) are good
  0:00:00.603    12M / 848M  INFO   Hamming Subclustering    (kmer_cluster.cpp          : 655)     Average size of non-trivial subcluster: 4.05575 kmers
  0:00:00.603    12M / 848M  INFO   Hamming Subclustering    (kmer_cluster.cpp          : 656)     Average number of sub-clusters per non-singleton cluster: 1.36883
  0:00:00.604    12M / 848M  INFO   Hamming Subclustering    (kmer_cluster.cpp          : 657)     Total solid k-mers: 166324
  0:00:00.604    12M / 848M  INFO   Hamming Subclustering    (kmer_cluster.cpp          : 658)     Substitution probabilities: [4,4]((0.921845,0.0226081,0.0408241,0.0147224),(0.0130674,0.933416,0.0162694,0.0372468),(0.0331917,0.0144521,0.937714,0.0146421),(0.0131874,0.0348882,0.02005,0.931874))
  0:00:00.605    12M / 848M  INFO    General                 (main.cpp                  : 178)   Finished clustering.
  0:00:00.606    12M / 848M  INFO    General                 (main.cpp                  : 197)   Starting solid k-mers expansion in 24 threads.
  0:00:00.618    12M / 848M  INFO    General                 (main.cpp                  : 218)   Solid k-mers iteration 0 produced 19858 new k-mers.
  0:00:00.629    12M / 848M  INFO    General                 (main.cpp                  : 218)   Solid k-mers iteration 1 produced 1416 new k-mers.
  0:00:00.641    12M / 848M  INFO    General                 (main.cpp                  : 218)   Solid k-mers iteration 2 produced 48 new k-mers.
  0:00:00.652    12M / 848M  INFO    General                 (main.cpp                  : 218)   Solid k-mers iteration 3 produced 25 new k-mers.
  0:00:00.664    12M / 848M  INFO    General                 (main.cpp                  : 218)   Solid k-mers iteration 4 produced 0 new k-mers.
  0:00:00.664    12M / 848M  INFO    General                 (main.cpp                  : 222)   Solid k-mers finalized
  0:00:00.665    12M / 848M  INFO    General                 (hammer_tools.cpp          : 222)   Starting read correction in 24 threads.
  0:00:00.665    12M / 848M  INFO    General                 (hammer_tools.cpp          : 235)   Correcting pair of reads: /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.S24_DKDL210000040-1a_HFL3FCCX2_L6_1_forward_paired.fq.gz.SSU.1.fq and /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.S24_DKDL210000040-1a_HFL3FCCX2_L6_1_forward_paired.fq.gz.SSU.2.fq
  0:00:00.805   534M / 848M  INFO    General                 (hammer_tools.cpp          : 170)   Prepared batch 0 of 1685 reads.
  0:00:00.830   534M / 848M  INFO    General                 (hammer_tools.cpp          : 177)   Processed batch 0
  0:00:00.840   534M / 848M  INFO    General                 (hammer_tools.cpp          : 187)   Written batch 0
  0:00:00.889    12M / 848M  INFO    General                 (hammer_tools.cpp          : 276)   Correction done. Changed 1452 bases in 900 reads.
  0:00:00.892    12M / 848M  INFO    General                 (hammer_tools.cpp          : 277)   Failed to correct 0 bases out of 481330.
  0:00:00.897     1M / 848M  INFO    General                 (main.cpp                  : 255)   Saving corrected dataset description to /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades/corrected/corrected.yaml
  0:00:00.900     1M / 848M  INFO    General                 (main.cpp                  : 262)   All done. Exiting.

===== Read error correction finished. 


===== corrected reads compression started. 


== Running: /bin/python /gpfs0/biores/users/tarun/miniconda3/envs/pf/share/spades/spades_pipeline/scripts/compress_all.py --input_file /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades/corrected/corrected.yaml --ext_python_modules_home /gpfs0/biores/users/tarun/miniconda3/envs/pf/share/spades --max_threads 24 --output_dir /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades/corrected --gzip_output

== Compressing corrected reads (with pigz)
== Files to compress: ['/gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades/corrected/S24.S24_DKDL210000040-1a_HFL3FCCX2_L6_1_forward_paired.fq.gz.SSU.2.00.0_0.cor.fastq', '/gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades/corrected/S24.S24_DKDL210000040-1a_HFL3FCCX2_L6_1_forward_paired.fq.gz.SSU._unpaired.00.0_0.cor.fastq', '/gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades/corrected/S24.S24_DKDL210000040-1a_HFL3FCCX2_L6_1_forward_paired.fq.gz.SSU.1.00.0_0.cor.fastq']
== Files compression is finished
== Dataset yaml file is updated

===== corrected reads compression finished. 


===== Read error correction finished. 


===== Assembling started. 


===== K99 started. 


== Running: /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/spades-core /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades/K99/configs/config.info

  0:00:00.000     1M / 11M   INFO    General                 (main.cpp                  :  99)   Loaded config from /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades/K99/configs/config.info
  0:00:00.002     1M / 11M   INFO    General                 (memory_limit.cpp          :  48)   Memory limit set to 20 Gb
  0:00:00.003     1M / 11M   INFO    General                 (main.cpp                  : 107)   Starting SPAdes, built from N/A, git revision N/A
  0:00:00.003     1M / 11M   INFO    General                 (main.cpp                  : 108)   Maximum k-mer length: 128
  0:00:00.004     1M / 11M   INFO    General                 (main.cpp                  : 109)   Assembling dataset (/gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades/dataset.info) with K=99
  0:00:00.004     1M / 11M   INFO    General                 (main.cpp                  : 110)   Maximum # of threads to use (adjusted due to OMP capabilities): 24
  0:00:00.004     1M / 11M   INFO    General                 (pipeline.cpp              : 212)   SPAdes started
  0:00:00.005     1M / 11M   INFO    General                 (pipeline.cpp              : 225)   Starting from stage: read_conversion
  0:00:00.005     1M / 11M   INFO    General                 (pipeline.cpp              : 231)   Two-step repeat resolution disabled
  0:00:00.005     1M / 11M   INFO   GraphCore                (graph_core.hpp            : 672)   Graph created, vertex min_id: 3, edge min_id: 3
  0:00:00.006     1M / 11M   INFO   GraphCore                (graph_core.hpp            : 673)   Vertex size: 48, edge size: 40
  0:00:00.006     1M / 11M   INFO    General                 (edge_index.hpp            : 113)   Size of edge index entries: 12/8
  0:00:00.007     1M / 11M   INFO    General                 (pipeline.cpp              : 242)   Will need read mapping, kmer mapper will be attached
  0:00:00.007     1M / 11M   INFO   StageManager             (stage.cpp                 : 185)   STAGE == Binary Read Conversion (id: read_conversion)
  0:00:00.008     1M / 11M   INFO    General                 (read_converter.cpp        :  72)   Converting reads to binary format for library #0 (takes a while)
  0:00:00.008     1M / 11M   INFO    General                 (read_converter.cpp        :  73)   Converting paired reads
  0:00:00.032    63M / 63M   INFO    General                 (binary_converter.cpp      : 111)   1616 reads written
  0:00:00.034    41M / 41M   INFO    General                 (read_converter.cpp        :  86)   Converting single reads
  0:00:00.040    71M / 71M   INFO    General                 (binary_converter.cpp      : 111)   67 reads written
  0:00:00.042    61M / 61M   INFO    General                 (read_converter.cpp        :  92)   Converting merged reads
  0:00:00.047    71M / 71M   INFO    General                 (binary_converter.cpp      : 111)   0 reads written
  0:00:00.049     1M / 23M   INFO   StageManager             (stage.cpp                 : 185)   STAGE == de Bruijn graph construction (id: construction)
  0:00:00.061     1M / 23M   INFO    General                 (construction.cpp          : 153)   Max read length 150
  0:00:00.063     1M / 23M   INFO    General                 (construction.cpp          : 159)   Average read length 144.694
  0:00:00.067     1M / 23M   INFO    General                 (stage.cpp                 : 117)   PROCEDURE == k+1-mer counting (id: construction:kpomer_counting)
  0:00:00.070     1M / 23M   INFO    General                 (kmer_index_builder.hpp    : 243)   Splitting kmer instances into 240 files using 24 threads. This might take a while.
  0:00:00.072     1M / 23M   INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 1024
  0:00:00.079     1M / 23M   INFO    General                 (kmer_splitter.hpp         :  93)   Memory available for splitting buffers: 0.277766 Gb
  0:00:00.083     1M / 23M   INFO    General                 (kmer_splitter.hpp         : 101)   Using cell size of 38834
  0:00:01.359     2M / 5830M INFO    General                 (kmer_splitters.hpp        : 131)   Used 6598 reads
  0:00:01.378     2M / 5830M INFO    General                 (kmer_index_builder.hpp    : 249)   Starting k-mer counting.
  0:00:01.530     2M / 5830M INFO    General                 (kmer_index_builder.hpp    : 260)   K-mer counting done. There are 120082 kmers in total.
  0:00:01.537     1M / 5830M INFO    General                 (stage.cpp                 : 117)   PROCEDURE == Extension index construction (id: construction:extension_index_construction)
  0:00:01.559     1M / 5830M INFO   K-mer Index Building     (kmer_index_builder.hpp    : 438)   Building kmer index
  0:00:01.563     1M / 5830M INFO    General                 (kmer_index_builder.hpp    : 243)   Splitting kmer instances into 240 files using 24 threads. This might take a while.
  0:00:01.568     2M / 5830M INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 1024
  0:00:01.574     2M / 5830M INFO    General                 (kmer_splitter.hpp         :  93)   Memory available for splitting buffers: 0.277764 Gb
  0:00:01.577     2M / 5830M INFO    General                 (kmer_splitter.hpp         : 101)   Using cell size of 38834
  0:00:02.841  8642M / 8642M INFO    General                 (kmer_splitters.hpp        : 194)   Processed 120082 kmers
  0:00:02.846  8642M / 8642M INFO    General                 (kmer_splitters.hpp        : 199)   Used 120082 kmers.
  0:00:02.850     2M / 5848M INFO    General                 (kmer_index_builder.hpp    : 249)   Starting k-mer counting.
  0:00:03.120     2M / 5848M INFO    General                 (kmer_index_builder.hpp    : 260)   K-mer counting done. There are 122062 kmers in total.
  0:00:03.122     2M / 5848M INFO   K-mer Index Building     (kmer_index_builder.hpp    : 395)   Building perfect hash indices
  0:00:03.283     3M / 5848M INFO   K-mer Index Building     (kmer_index_builder.hpp    : 431)   Index built. Total 122062 kmers, 274504 bytes occupied (17.9911 bits per kmer).
  0:00:03.286     3M / 5848M INFO    General                 (kmer_index_builder.hpp    : 169)   Merging final buckets.
  0:00:03.381     3M / 5848M INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 100)   Building k-mer extensions from k+1-mers
  0:00:03.408     3M / 5848M INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 105)   Building k-mer extensions from k+1-mers finished.
  0:00:03.421     2M / 5848M INFO    General                 (stage.cpp                 : 117)   PROCEDURE == Condensing graph (id: construction:graph_condensing)
  0:00:03.424     2M / 5848M INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 354)   Extracting unbranching paths
  0:00:03.470     2M / 5848M INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 373)   Extracting unbranching paths finished. 2768 sequences extracted
  0:00:03.483     2M / 5848M INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 309)   Collecting perfect loops
  0:00:03.495     2M / 5848M INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 342)   Collecting perfect loops finished. 0 loops collected
  0:00:03.501     2M / 5848M INFO    General                 (debruijn_graph_constructor: 487)   Total 5536 edges to create
  0:00:03.505     3M / 5848M INFO    

== Warning ==  No assembly mode was specified! If you intend to assemble high-coverage multi-cell/isolate data, use '--isolate' option.


Command line: ./spades.py	-o	/gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades	-t	24	-m	20	-k	99,111,127	-1	/gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.S24_DKDL210000040-1a_HFL3FCCX2_L6_1_forward_paired.fq.gz.SSU.1.fq	-2	/gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.S24_DKDL210000040-1a_HFL3FCCX2_L6_1_forward_paired.fq.gz.SSU.2.fq	

System information:
  SPAdes version: 3.15.3
  Python version: 2.7.5
  OS: Linux-3.10.0-1160.45.1.el7.x86_64-x86_64-with-redhat-7.9-Nitrogen

Output dir: /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades
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: ['/gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.S24_DKDL210000040-1a_HFL3FCCX2_L6_1_forward_paired.fq.gz.SSU.1.fq']
      right reads: ['/gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.S24_DKDL210000040-1a_HFL3FCCX2_L6_1_forward_paired.fq.gz.SSU.2.fq']
      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: [99, 111, 127]
  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/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades/tmp
  Threads: 24
  Memory limit (in Gb): 20


======= SPAdes pipeline started. Log can be found here: /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades/spades.log

/gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.S24_DKDL210000040-1a_HFL3FCCX2_L6_1_forward_paired.fq.gz.SSU.2.fq: max reads length: 150
/gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.S24_DKDL210000040-1a_HFL3FCCX2_L6_1_forward_paired.fq.gz.SSU.1.fq: max reads length: 150

Reads length: 150


===== Before start started. 


===== Read error correction started. 


===== Read error correction started. 


== Running: /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/spades-hammer /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades/corrected/configs/config.info

  0:00:00.000     1M / 11M   INFO    General                 (main.cpp                  :  75)   Starting BayesHammer, built from N/A, git revision N/A
  0:00:00.004     1M / 11M   INFO    General                 (main.cpp                  :  76)   Loading config from /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades/corrected/configs/config.info
  0:00:00.008     1M / 11M   INFO    General                 (main.cpp                  :  78)   Maximum # of threads to use (adjusted due to OMP capabilities): 24
  0:00:00.011     1M / 11M   INFO    General                 (memory_limit.cpp          :  48)   Memory limit set to 20 Gb
  0:00:00.015     1M / 11M   INFO    General                 (main.cpp                  :  86)   Trying to determine PHRED offset
  0:00:00.020     1M / 11M   INFO    General                 (main.cpp                  :  92)   Determined value is 33
  0:00:00.022     1M / 11M   INFO    General                 (hammer_tools.cpp          :  38)   Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ]
  0:00:00.026     1M / 11M   INFO    General                 (main.cpp                  : 113)   Size of aux. kmer data 24 bytes
     === ITERATION 0 begins ===
  0:00:00.030     1M / 11M   INFO    General                 (kmer_index_builder.hpp    : 243)   Splitting kmer instances into 16 files using 24 threads. This might take a while.
  0:00:00.035     1M / 11M   INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 1024
  0:00:00.039     1M / 11M   INFO    General                 (kmer_splitter.hpp         :  93)   Memory available for splitting buffers: 0.277776 Gb
  0:00:00.043     1M / 11M   INFO    General                 (kmer_splitter.hpp         : 101)   Using cell size of 2330156
  0:00:00.179  7681M / 7681M INFO   K-mer Splitting          (kmer_data.cpp             :  97)   Processing /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.S24_DKDL210000040-1a_HFL3FCCX2_L6_1_forward_paired.fq.gz.SSU.1.fq
  0:00:00.214  7681M / 7681M INFO   K-mer Splitting          (kmer_data.cpp             :  97)   Processing /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.S24_DKDL210000040-1a_HFL3FCCX2_L6_1_forward_paired.fq.gz.SSU.2.fq
  0:00:00.257  7681M / 7681M INFO   K-mer Splitting          (kmer_data.cpp             : 112)   Total 3370 reads processed
  0:00:00.261     1M / 848M  INFO    General                 (kmer_index_builder.hpp    : 249)   Starting k-mer counting.
  0:00:00.289     1M / 848M  INFO    General                 (kmer_index_builder.hpp    : 260)   K-mer counting done. There are 346340 kmers in total.
  0:00:00.293     1M / 848M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 395)   Building perfect hash indices
  0:00:00.313     1M / 848M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 431)   Index built. Total 346340 kmers, 262224 bytes occupied (6.05703 bits per kmer).
  0:00:00.318     1M / 848M  INFO   K-mer Counting           (kmer_data.cpp             : 354)   Arranging kmers in hash map order
  0:00:00.339     6M / 848M  INFO    General                 (main.cpp                  : 148)   Clustering Hamming graph.
  0:00:00.469     6M / 848M  INFO    General                 (main.cpp                  : 155)   Extracting clusters:
  0:00:00.470     6M / 848M  INFO    General                 (concurrent_dsu.cpp        :  18)   Connecting to root
  0:00:00.470     6M / 848M  INFO    General                 (concurrent_dsu.cpp        :  34)   Calculating counts
  0:00:00.490    11M / 848M  INFO    General                 (concurrent_dsu.cpp        :  63)   Writing down entries
  0:00:00.527     6M / 848M  INFO    General                 (main.cpp                  : 167)   Clustering done. Total clusters: 223224
  0:00:00.528     4M / 848M  INFO   K-mer Counting           (kmer_data.cpp             : 371)   Collecting K-mer information, this takes a while.
  0:00:00.532    12M / 848M  INFO   K-mer Counting           (kmer_data.cpp             : 377)   Processing /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.S24_DKDL210000040-1a_HFL3FCCX2_L6_1_forward_paired.fq.gz.SSU.1.fq
  0:00:00.546    12M / 848M  INFO   K-mer Counting           (kmer_data.cpp             : 377)   Processing /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.S24_DKDL210000040-1a_HFL3FCCX2_L6_1_forward_paired.fq.gz.SSU.2.fq
  0:00:00.556    12M / 848M  INFO   K-mer Counting           (kmer_data.cpp             : 384)   Collection done, postprocessing.
  0:00:00.558    12M / 848M  INFO   K-mer Counting           (kmer_data.cpp             : 397)   There are 346340 kmers in total. Among them 229350 (66.2211%) are singletons.
  0:00:00.559    12M / 848M  INFO    General                 (main.cpp                  : 173)   Subclustering Hamming graph
  0:00:00.601    12M / 848M  INFO   Hamming Subclustering    (kmer_cluster.cpp          : 650)   Subclustering done. Total 61 non-read kmers were generated.
  0:00:00.601    12M / 848M  INFO   Hamming Subclustering    (kmer_cluster.cpp          : 651)   Subclustering statistics:
  0:00:00.602    12M / 848M  INFO   Hamming Subclustering    (kmer_cluster.cpp          : 652)     Total singleton hamming clusters: 195154. Among them 133930 (68.6279%) are good
  0:00:00.602    12M / 848M  INFO   Hamming Subclustering    (kmer_cluster.cpp          : 653)     Total singleton subclusters: 1131. Among them 1118 (98.8506%) are good
  0:00:00.603    12M / 848M  INFO   Hamming Subclustering    (kmer_cluster.cpp          : 654)     Total non-singleton subcluster centers: 37292. Among them 31276 (83.8679%) are good
  0:00:00.603    12M / 848M  INFO   Hamming Subclustering    (kmer_cluster.cpp          : 655)     Average size of non-trivial subcluster: 4.05575 kmers
  0:00:00.603    12M / 848M  INFO   Hamming Subclustering    (kmer_cluster.cpp          : 656)     Average number of sub-clusters per non-singleton cluster: 1.36883
  0:00:00.604    12M / 848M  INFO   Hamming Subclustering    (kmer_cluster.cpp          : 657)     Total solid k-mers: 166324
  0:00:00.604    12M / 848M  INFO   Hamming Subclustering    (kmer_cluster.cpp          : 658)     Substitution probabilities: [4,4]((0.921845,0.0226081,0.0408241,0.0147224),(0.0130674,0.933416,0.0162694,0.0372468),(0.0331917,0.0144521,0.937714,0.0146421),(0.0131874,0.0348882,0.02005,0.931874))
  0:00:00.605    12M / 848M  INFO    General                 (main.cpp                  : 178)   Finished clustering.
  0:00:00.606    12M / 848M  INFO    General                 (main.cpp                  : 197)   Starting solid k-mers expansion in 24 threads.
  0:00:00.618    12M / 848M  INFO    General                 (main.cpp                  : 218)   Solid k-mers iteration 0 produced 19858 new k-mers.
  0:00:00.629    12M / 848M  INFO    General                 (main.cpp                  : 218)   Solid k-mers iteration 1 produced 1416 new k-mers.
  0:00:00.641    12M / 848M  INFO    General                 (main.cpp                  : 218)   Solid k-mers iteration 2 produced 48 new k-mers.
  0:00:00.652    12M / 848M  INFO    General                 (main.cpp                  : 218)   Solid k-mers iteration 3 produced 25 new k-mers.
  0:00:00.664    12M / 848M  INFO    General                 (main.cpp                  : 218)   Solid k-mers iteration 4 produced 0 new k-mers.
  0:00:00.664    12M / 848M  INFO    General                 (main.cpp                  : 222)   Solid k-mers finalized
  0:00:00.665    12M / 848M  INFO    General                 (hammer_tools.cpp          : 222)   Starting read correction in 24 threads.
  0:00:00.665    12M / 848M  INFO    General                 (hammer_tools.cpp          : 235)   Correcting pair of reads: /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.S24_DKDL210000040-1a_HFL3FCCX2_L6_1_forward_paired.fq.gz.SSU.1.fq and /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.S24_DKDL210000040-1a_HFL3FCCX2_L6_1_forward_paired.fq.gz.SSU.2.fq
  0:00:00.805   534M / 848M  INFO    General                 (hammer_tools.cpp          : 170)   Prepared batch 0 of 1685 reads.
  0:00:00.830   534M / 848M  INFO    General                 (hammer_tools.cpp          : 177)   Processed batch 0
  0:00:00.840   534M / 848M  INFO    General                 (hammer_tools.cpp          : 187)   Written batch 0
  0:00:00.889    12M / 848M  INFO    General                 (hammer_tools.cpp          : 276)   Correction done. Changed 1452 bases in 900 reads.
  0:00:00.892    12M / 848M  INFO    General                 (hammer_tools.cpp          : 277)   Failed to correct 0 bases out of 481330.
  0:00:00.897     1M / 848M  INFO    General                 (main.cpp                  : 255)   Saving corrected dataset description to /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades/corrected/corrected.yaml
  0:00:00.900     1M / 848M  INFO    General                 (main.cpp                  : 262)   All done. Exiting.

===== Read error correction finished. 


===== corrected reads compression started. 


== Running: /bin/python /gpfs0/biores/users/tarun/miniconda3/envs/pf/share/spades/spades_pipeline/scripts/compress_all.py --input_file /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades/corrected/corrected.yaml --ext_python_modules_home /gpfs0/biores/users/tarun/miniconda3/envs/pf/share/spades --max_threads 24 --output_dir /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades/corrected --gzip_output

== Compressing corrected reads (with pigz)
== Files to compress: ['/gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades/corrected/S24.S24_DKDL210000040-1a_HFL3FCCX2_L6_1_forward_paired.fq.gz.SSU.2.00.0_0.cor.fastq', '/gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades/corrected/S24.S24_DKDL210000040-1a_HFL3FCCX2_L6_1_forward_paired.fq.gz.SSU._unpaired.00.0_0.cor.fastq', '/gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades/corrected/S24.S24_DKDL210000040-1a_HFL3FCCX2_L6_1_forward_paired.fq.gz.SSU.1.00.0_0.cor.fastq']
== Files compression is finished
== Dataset yaml file is updated

===== corrected reads compression finished. 


===== Read error correction finished. 


===== Assembling started. 


===== K99 started. 


== Running: /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/spades-core /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades/K99/configs/config.info

  0:00:00.000     1M / 11M   INFO    General                 (main.cpp                  :  99)   Loaded config from /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades/K99/configs/config.info
  0:00:00.002     1M / 11M   INFO    General                 (memory_limit.cpp          :  48)   Memory limit set to 20 Gb
  0:00:00.003     1M / 11M   INFO    General                 (main.cpp                  : 107)   Starting SPAdes, built from N/A, git revision N/A
  0:00:00.003     1M / 11M   INFO    General                 (main.cpp                  : 108)   Maximum k-mer length: 128
  0:00:00.004     1M / 11M   INFO    General                 (main.cpp                  : 109)   Assembling dataset (/gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades/dataset.info) with K=99
  0:00:00.004     1M / 11M   INFO    General                 (main.cpp                  : 110)   Maximum # of threads to use (adjusted due to OMP capabilities): 24
  0:00:00.004     1M / 11M   INFO    General                 (pipeline.cpp              : 212)   SPAdes started
  0:00:00.005     1M / 11M   INFO    General                 (pipeline.cpp              : 225)   Starting from stage: read_conversion
  0:00:00.005     1M / 11M   INFO    General                 (pipeline.cpp              : 231)   Two-step repeat resolution disabled
  0:00:00.005     1M / 11M   INFO   GraphCore                (graph_core.hpp            : 672)   Graph created, vertex min_id: 3, edge min_id: 3
  0:00:00.006     1M / 11M   INFO   GraphCore                (graph_core.hpp            : 673)   Vertex size: 48, edge size: 40
  0:00:00.006     1M / 11M   INFO    General                 (edge_index.hpp            : 113)   Size of edge index entries: 12/8
  0:00:00.007     1M / 11M   INFO    General                 (pipeline.cpp              : 242)   Will need read mapping, kmer mapper will be attached
  0:00:00.007     1M / 11M   INFO   StageManager             (stage.cpp                 : 185)   STAGE == Binary Read Conversion (id: read_conversion)
  0:00:00.008     1M / 11M   INFO    General                 (read_converter.cpp        :  72)   Converting reads to binary format for library #0 (takes a while)
  0:00:00.008     1M / 11M   INFO    General                 (read_converter.cpp        :  73)   Converting paired reads
  0:00:00.032    63M / 63M   INFO    General                 (binary_converter.cpp      : 111)   1616 reads written
  0:00:00.034    41M / 41M   INFO    General                 (read_converter.cpp        :  86)   Converting single reads
  0:00:00.040    71M / 71M   INFO    General                 (binary_converter.cpp      : 111)   67 reads written
  0:00:00.042    61M / 61M   INFO    General                 (read_converter.cpp        :  92)   Converting merged reads
  0:00:00.047    71M / 71M   INFO    General                 (binary_converter.cpp      : 111)   0 reads written
  0:00:00.049     1M / 23M   INFO   StageManager             (stage.cpp                 : 185)   STAGE == de Bruijn graph construction (id: construction)
  0:00:00.061     1M / 23M   INFO    General                 (construction.cpp          : 153)   Max read length 150
  0:00:00.063     1M / 23M   INFO    General                 (construction.cpp          : 159)   Average read length 144.694
  0:00:00.067     1M / 23M   INFO    General                 (stage.cpp                 : 117)   PROCEDURE == k+1-mer counting (id: construction:kpomer_counting)
  0:00:00.070     1M / 23M   INFO    General                 (kmer_index_builder.hpp    : 243)   Splitting kmer instances into 240 files using 24 threads. This might take a while.
  0:00:00.072     1M / 23M   INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 1024
  0:00:00.079     1M / 23M   INFO    General                 (kmer_splitter.hpp         :  93)   Memory available for splitting buffers: 0.277766 Gb
  0:00:00.083     1M / 23M   INFO    General                 (kmer_splitter.hpp         : 101)   Using cell size of 38834
  0:00:01.359     2M / 5830M INFO    General                 (kmer_splitters.hpp        : 131)   Used 6598 reads
  0:00:01.378     2M / 5830M INFO    General                 (kmer_index_builder.hpp    : 249)   Starting k-mer counting.
  0:00:01.530     2M / 5830M INFO    General                 (kmer_index_builder.hpp    : 260)   K-mer counting done. There are 120082 kmers in total.
  0:00:01.537     1M / 5830M INFO    General                 (stage.cpp                 : 117)   PROCEDURE == Extension index construction (id: construction:extension_index_construction)
  0:00:01.559     1M / 5830M INFO   K-mer Index Building     (kmer_index_builder.hpp    : 438)   Building kmer index
  0:00:01.563     1M / 5830M INFO    General                 (kmer_index_builder.hpp    : 243)   Splitting kmer instances into 240 files using 24 threads. This might take a while.
  0:00:01.568     2M / 5830M INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 1024
  0:00:01.574     2M / 5830M INFO    General                 (kmer_splitter.hpp         :  93)   Memory available for splitting buffers: 0.277764 Gb
  0:00:01.577     2M / 5830M INFO    General                 (kmer_splitter.hpp         : 101)   Using cell size of 38834
  0:00:02.841  8642M / 8642M INFO    General                 (kmer_splitters.hpp        : 194)   Processed 120082 kmers
  0:00:02.846  8642M / 8642M INFO    General                 (kmer_splitters.hpp        : 199)   Used 120082 kmers.
  0:00:02.850     2M / 5848M INFO    General                 (kmer_index_builder.hpp    : 249)   Starting k-mer counting.
  0:00:03.120     2M / 5848M INFO    General                 (kmer_index_builder.hpp    : 260)   K-mer counting done. There are 122062 kmers in total.
  0:00:03.122     2M / 5848M INFO   K-mer Index Building     (kmer_index_builder.hpp    : 395)   Building perfect hash indices
  0:00:03.283     3M / 5848M INFO   K-mer Index Building     (kmer_index_builder.hpp    : 431)   Index built. Total 122062 kmers, 274504 bytes occupied (17.9911 bits per kmer).
  0:00:03.286     3M / 5848M INFO    General                 (kmer_index_builder.hpp    : 169)   Merging final buckets.
  0:00:03.381     3M / 5848M INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 100)   Building k-mer extensions from k+1-mers
  0:00:03.408     3M / 5848M INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 105)   Building k-mer extensions from k+1-mers finished.
  0:00:03.421     2M / 5848M INFO    General                 (stage.cpp                 : 117)   PROCEDURE == Condensing graph (id: construction:graph_condensing)
  0:00:03.424     2M / 5848M INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 354)   Extracting unbranching paths
  0:00:03.470     2M / 5848M INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 373)   Extracting unbranching paths finished. 2768 sequences extracted
  0:00:03.483     2M / 5848M INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 309)   Collecting perfect loops
  0:00:03.495     2M / 5848M INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 342)   Collecting perfect loops finished. 0 loops collected
  0:00:03.501     2M / 5848M INFO    General                 (debruijn_graph_constructor: 487)   Total 5536 edges to create
  0:00:03.505     3M / 5848M INFO    General                 (debruijn_graph_constructor: 489)   Collecting link records
  0:00:03.517     3M / 5848M INFO    General                 (debruijn_graph_constructor: 491)   Ordering link records
  0:00:03.534     3M / 5848M INFO    General                 (debruijn_graph_constructor: 493)   Sorting done
  0:00:03.537     3M / 5848M INFO    General                 (debruijn_graph_constructor: 503)   Total 4748 vertices to create
  0:00:03.537     3M / 5848M INFO    General                 (debruijn_graph_constructor: 506)   Connecting the graph
  0:00:03.543     3M / 5848M INFO    General                 (stage.cpp                 : 117)   PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm)
  0:00:03.543     3M / 5848M INFO   K-mer Index Building     (kmer_index_builder.hpp    : 395)   Building perfect hash indices
  0:00:03.667     4M / 5848M INFO   K-mer Index Building     (kmer_index_builder.hpp    : 431)   Index built. Total 120082 kmers, 272728 bytes occupied (18.1695 bits per kmer).
  0:00:03.673     4M / 5848M INFO    General                 (coverage_hash_map_builder.:  47)   Collecting k-mer coverage information from reads, this takes a while.
  0:00:03.685     4M / 5848M INFO    General                 (construction.cpp          : 430)   Filling coverage and flanking coverage from PHM
  0:00:03.693     4M / 5848M INFO    General                 (coverage_filling.hpp      :  82)   Processed 5536 edges
  0:00:03.745     1M / 5848M INFO   StageManager             (stage.cpp                 : 185)   STAGE == EC Threshold Finding (id: ec_threshold_finder)
  0:00:03.750     1M / 5848M ERROR   General                 (kmer_coverage_model.cpp   : 187)   Invalid kmer coverage histogram, make sure that the coverage is indeed uniform


== Error ==  system call for: "['/gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/spades-core', '/gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades/K99/configs/config.info']" finished abnormally, OS return value: 21
None

In case you have troubles running SPAdes, you can write to jacobthomas@example.org
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: /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades/spades.log

Thank you for using SPAdes!General                 (debruijn_graph_constructor: 489)   Collecting link records
  0:00:03.517     3M / 5848M INFO    General                 (debruijn_graph_constructor: 491)   Ordering link records
  0:00:03.534     3M / 5848M INFO    General                 (debruijn_graph_constructor: 493)   Sorting done
  0:00:03.537     3M / 5848M INFO    General                 (debruijn_graph_constructor: 503)   Total 4748 vertices to create
  0:00:03.537     3M / 5848M INFO    General                 (debruijn_graph_constructor: 506)   Connecting the graph
  0:00:03.543     3M / 5848M INFO    General                 (stage.cpp                 : 117)   PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm)
  0:00:03.543     3M / 5848M INFO   K-mer Index Building     (kmer_index_builder.hpp    : 395)   Building perfect hash indices
  0:00:03.667     4M / 5848M INFO   K-mer Index Building     (kmer_index_builder.hpp    : 431)   Index built. Total 120082 kmers, 272728 bytes occupied (18.1695 bits per kmer).
  0:00:03.673     4M / 5848M INFO    General                 (coverage_hash_map_builder.:  47)   Collecting k-mer coverage information from reads, this takes a while.
  0:00:03.685     4M / 5848M INFO    General                 (construction.cpp          : 430)   Filling coverage and flanking coverage from PHM
  0:00:03.693     4M / 5848M INFO    General                 (coverage_filling.hpp      :  82)   Processed 5536 edges
  0:00:03.745     1M / 5848M INFO   StageManager             (stage.cpp                 : 185)   STAGE == EC Threshold Finding (id: ec_threshold_finder)
  0:00:03.750     1M / 5848M ERROR   General                 (kmer_coverage_model.cpp   : 187)   Invalid kmer coverage histogram, make sure that the coverage is indeed uniform


== Error ==  system call for: "['/gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/spades-core', '/gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades/K99/configs/config.info']" finished abnormally, OS return value: 21
None

In case you have troubles running SPAdes, you can write to jacobthomas@example.org
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: /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades/spades.log

Thank you for using SPAdes!

### params.txt

Command line: ./spades.py	-o	/gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades	-t	24	-m	20	-k	99,111,127	-1	/gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.S24_DKDL210000040-1a_HFL3FCCX2_L6_1_forward_paired.fq.gz.SSU.1.fq	-2	/gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.S24_DKDL210000040-1a_HFL3FCCX2_L6_1_forward_paired.fq.gz.SSU.2.fq	

System information:
  SPAdes version: 3.15.3
  Python version: 2.7.5
  OS: Linux-3.10.0-1160.45.1.el7.x86_64-x86_64-with-redhat-7.9-Nitrogen

Output dir: /gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades
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: ['/gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.S24_DKDL210000040-1a_HFL3FCCX2_L6_1_forward_paired.fq.gz.SSU.1.fq']
      right reads: ['/gpfs0/biores/users/tarun/miniconda3/envs/pf/bin/S24.S24_DKDL210000040-1a_HFL3FCCX2_L6_1_forward_paired.fq.gz.SSU.2.fq']
      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: [99, 111, 127]
  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/biores/users/tarun/miniconda3/envs/pf/bin/S24.spades/tmp
  Threads: 24
  Memory limit (in Gb): 20

### SPAdes version

  SPAdes version: 3.15.3

### Operating System

  OS: Linux-3.10.0-1160.45.1.el7.x86_64-x86_64-with-redhat-7.9-Nitrogen

### Python Version

Python version: 2.7.5

### Method of SPAdes installation

conda

### No errors reported in spades.log

- [X] Yes
 Comments: 
 Comment 0: The log reads:

```
0:00:03.750 1M / 5848M ERROR General (kmer_coverage_model.cpp : 187) Invalid kmer coverage histogram, make sure that the coverage is indeed uniform
```

Your data does not seem to be a normal microbial isolate dataset
{'source': 'GithubIssues', 'repo_name_with_owner': 'ablab/spades', 'issue_id': 1112749316, 'repo_stars': 480.0}