Unicycler: SPAdes crash without log file

[gaferguz]

Hi Everyone! This is my first time with SPAdes and Unicycler so I am not familiarised with any of these tools. I'm running Unicycler to perform a hybrid assembly using long and short reads in Mac Os Catalina, and I'm facing the following issue with SPAdes:

Command: /Users/Comms/.local/bin/unicycler -1 IKER_ENSAMBLAJES/Raw_reads_B25-B2021-B2017/103-IKER-Raw_Data/B2017_S4_R1_001.fastq -2 IKER_ENSAMBLAJES/Raw_reads_B25-B2021-B2017/103-IKER-Raw_Data/B2017_S4_R2_001.fastq -l MINION_31_7_20/qcat_demultiplexed/barcode02.fastq -o Unicycler/ -t 4

Unicycler version: v0.4.9b
Using 4 threads

The output directory already exists and files may be reused or overwritten:
  /Users/Comms/Desktop/GENOMAAT/Unicycler

Dependencies:
  Program         Version   Status  
  spades.py       3.13.0    good    
  racon           1.4.17    good    
  makeblastdb     2.10.1+   good    
  tblastn         2.10.1+   good    
  bowtie2-build   2.3.5.1   good    
  bowtie2         2.3.5.1   good    
  samtools        1.10      good    
  java            14.0.2    good    
  pilon           1.23      good    
  bcftools                  not used

SPAdes read error correction (2020-09-15 09:47:55)
    Unicycler uses the SPAdes read error correction module to reduce the number
of errors in the short read before SPAdes assembly. This can make the assembly
faster and simplify the assembly graph structure.

Error: SPAdes crashed! Please view spades.log for more information.

Since my reads have already reported sufficient quality for an assembly, I decided to skip the read error correction mode to see if SPAdes would take it from there, but It still crashing:

Command: /Users/Comms/.local/bin/unicycler -1 IKER_ENSAMBLAJES/Raw_reads_B25-B2021-B2017/103-IKER-Raw_Data/B2017_S4_R1_001.fastq -2 IKER_ENSAMBLAJES/Raw_reads_B25-B2021-B2017/103-IKER-Raw_Data/B2017_S4_R2_001.fastq -l MINION_31_7_20/qcat_demultiplexed/barcode03.fastq -o Unicycler/ --no_correct -t 4

Unicycler version: v0.4.9b
Using 4 threads

The output directory already exists and files may be reused or overwritten:
  /Users/Comms/Desktop/GENOMAAT/Unicycler

Choosing k-mer range for assembly (2020-09-15 10:07:03)
    Unicycler chooses a k-mer range for SPAdes based on the length of the input reads. It uses a wide range of many k-mer sizes to maximise the
chance of finding an ideal assembly.

K-mer range already exists:
  /Users/Comms/Desktop/GENOMAAT/Unicycler/spades_assembly/kmer_range

Will use this existing range:
  27, 47, 63, 77, 89, 99, 107, 115, 121, 127

SPAdes assemblies (2020-09-15 10:07:03)
    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.

Error: SPAdes failed to produce assemblies. See spades_assembly/assembly/spades.log for more info.

The main problem that I have is that the referred path do not contain any spades.log file at all. I think it may be related to the computer itself because I've run the exact same commands from Ubuntu 18.04 and It worked fine.

I would appreciate any help or orientation on what should I do without any log file.

Thanks in advance.

[kohe167cm]

I'm facing the same problem. But, some fastq datasets was passed analysis with no problem in same condition. So, I think it's due to dataset.

[yananzh]

I'm facing the same problem. I just changed the names of input files and then it works! For example change "xxx.fq.clean.gz" to "xxx.fq.gz".

[FengjuanjuanCMS]

I'm facing the same problem. I changed the name of the folder where the data was stored and removed the Chinese characters.