Starting Unicycler (2019-12-19 13:20:37)
    Welcome to Unicycler, an assembly pipeline for bacterial genomes. Since you
provided both short and long reads, Unicycler will perform a hybrid assembly.
It will first use SPAdes to make a short-read assembly graph, and then it will
use various methods to scaffold that graph with the long reads.
    For more information, please see https://github.com/rrwick/Unicycler

Command: /proj/04_programs/Unicycler/Unicycler/unicycler-runner.py -l ../02_trimmed+corrected-reads/fastq_runid_1d2f069b4156b0bfdc46e8cd5825a3419de1a39d_ALL.fq.gz.qcat-len100.fq.gz.canu-corr.fasta.gz -1 /tmp/slurm-6561352/pe12.fq.gz -2 /tmp/slurm-6561352/pe22.fq.gz --out unicycler-hybrid_1385_A_all_R1.fq.gz.trim+corr.fq.gz-paired_fastq_runid_1d2f069b4156b0bfdc46e8cd5825a3419de1a39d_ALL.fq.gz.qcat-len100.fq.gz.canu-corr.fasta.gz_flag-meta_mode-normal_kmers-21,33,55,77-_6561352 -t 8 --mode normal --spades_tmp_dir /tmp/slurm-6561352 --kmers 21,33,55,77 --no_correct

Unicycler version: v0.4.8
Using 8 threads

Making output directory:
  /scratch/mg_ton_2019-12-17/03_assembly_ill-corr_ont-corr/unicycler-hybrid_1385_A_all_R1.fq.gz.trim+corr.fq.gz-paired_fastq_runid_1d2f069b4156b0bfdc46e8cd5825a3419de1a39d_ALL.fq.gz.qcat-len100.fq.gz.canu-corr.fasta.gz_flag-meta_mode-normal_kmers-21,33,55,77-_6561352

Dependencies:
  Program         Version     Status  
  spades.py       3.13.1      good    
  racon           1.4.3       good    
  makeblastdb     2.8.1+      good    
  tblastn         2.8.1+      good    
  bowtie2-build   2.3.5.1     good    
  bowtie2         2.3.5.1     good    
  samtools        1.9         good    
  java            1.8.0_152   good    
  pilon           1.22        good    
  bcftools                    not used


SPAdes assemblies (2019-12-19 13:24:19)
    Unicycler now uses SPAdes to assemble the short reads. It scores the
assembly graph for each k-mer using the number of contigs (fewer is better) and
the number of dead ends (fewer is better). The score function is 1/(c*(d+2)),
where c is the contig count and d is the dead end count.

K-mer   Contigs   Dead ends   Score   
   21                           failed
   33                           failed
   55                           failed
   77    79,986      18,176   6.88e-10 ← best

Read depth filter: removed 102385 contigs totalling 27191794 bp
Deleting /scratch/mg_ton_2019-12-17/03_assembly_ill-corr_ont-corr/unicycler-hybrid_1385_A_all_R1.fq.gz.trim+corr.fq.gz-paired_fastq_runid_1d2f069b4156b0bfdc46e8cd5825a3419de1a39d_ALL.fq.gz.qcat-len100.fq.gz.canu-corr.fasta.gz_flag-meta_mode-normal_kmers-21,33,55,77-_6561352/spades_assembly/
Deleting /tmp/slurm-6561352/


Determining graph multiplicity (2019-12-19 20:25:29)
    Multiplicity is the number of times a sequence occurs in the underlying
sequence. Single-copy contigs (those with a multiplicity of one, occurring only
once in the underlying sequence) are particularly useful.
Traceback (most recent call last):
  File "/proj/04_programs/Unicycler/Unicycler/unicycler-runner.py", line 21, in <module>
    main()
  File "/proj/04_programs/Unicycler/Unicycler/unicycler/unicycler.py", line 89, in main
    determine_copy_depth(graph)
  File "/proj/04_programs/Unicycler/Unicycler/unicycler/assembly_graph_copy_depth.py", line 74, in determine_copy_depth
    determine_copy_depth_part_2(graph, settings.COPY_PROPAGATION_TOLERANCE, copy_depth_table)
  File "/proj/04_programs/Unicycler/Unicycler/unicycler/assembly_graph_copy_depth.py", line 104, in determine_copy_depth_part_2
    determine_copy_depth_part_2(graph, tolerance, copy_depth_table)
  File "/proj/04_programs/Unicycler/Unicycler/unicycler/assembly_graph_copy_depth.py", line 104, in determine_copy_depth_part_2
    determine_copy_depth_part_2(graph, tolerance, copy_depth_table)
  File "/proj/04_programs/Unicycler/Unicycler/unicycler/assembly_graph_copy_depth.py", line 104, in determine_copy_depth_part_2
    determine_copy_depth_part_2(graph, tolerance, copy_depth_table)
  [Previous line repeated 982 more times]
  File "/proj/04_programs/Unicycler/Unicycler/unicycler/assembly_graph_copy_depth.py", line 103, in determine_copy_depth_part_2
    if redistribute_copy_depths(graph, tolerance, copy_depth_table):
  File "/proj/04_programs/Unicycler/Unicycler/unicycler/assembly_graph_copy_depth.py", line 240, in redistribute_copy_depths
    arrangements = shuffle_into_bins(copy_depths, bins, targets)
  File "/proj/04_programs/Unicycler/Unicycler/unicycler/assembly_graph_copy_depth.py", line 459, in shuffle_into_bins
    arrangements += shuffle_into_bins(items[1:], bins_copy, targets)
  File "/proj/04_programs/Unicycler/Unicycler/unicycler/assembly_graph_copy_depth.py", line 459, in shuffle_into_bins
    arrangements += shuffle_into_bins(items[1:], bins_copy, targets)
  File "/proj/04_programs/Unicycler/Unicycler/unicycler/assembly_graph_copy_depth.py", line 459, in shuffle_into_bins
    arrangements += shuffle_into_bins(items[1:], bins_copy, targets)
  [Previous line repeated 3 more times]
  File "/proj/04_programs/Unicycler/Unicycler/unicycler/assembly_graph_copy_depth.py", line 463, in shuffle_into_bins
    elif all(x for x in bins) and \
RecursionError: maximum recursion depth exceeded