IndexError: list index out of range

[Hufflepuff1012]

Hi!

I am trying to test LazyB on my Illumina + nanopore reads to achieve an hybrid genome assembly. So far, I observe some error reported when I try to run the software.

The command I used:

sh ./MuCHSALSA-develop/pipeline/pipeline.sh 50 90 LazyB-hybrid-Calhyp14 ../Calhyp_14_R1.fastq.gz ../Calhyp_14_R2.fastq.gz ../merged.trimmed.fastq.gz ./LazyB-Run1

And here is the error message reported:

>>>> K-mer Filtering of Illumina Reads
terminate called after throwing an instance of 'std::runtime_error'
  what():  Unsupported format
./MuCHSALSA-develop/pipeline/pipeline.sh: line 30: 94682 Aborted                 (core dumped) jellyfish count -m $K_MER_JELLY -s 100M -t $CORES -C $ILLUMINA_RAW_1 $ILLUMINA_RAW_2 -o ${TMP}/"jelly_count_k${K_MER_JELLY}.jf"
Failed to open input file '/proj/uppstore2018098/nobackup/marvin/Calanus_hyperboreus/Assembly_Chyp14/HybridAssembly/LazyB/./LazyB-Run1/tmp.nLTLFxpLag/jelly_count_k50.jf'
Traceback (most recent call last):
  File "/crex/proj/uppstore2018098/nobackup/marvin/Calanus_hyperboreus/Assembly_Chyp14/HybridAssembly/LazyB/MuCHSALSA-develop/pipeline/setAbundanceThresholdFromHisto.py", line 12, in <module>
    total_non_unique_k_mers = int(sys.argv[2])
IndexError: list index out of range
Invalid uint64_t '/proj/uppstore2018098/nobackup/marvin/Calanus_hyperboreus/Assembly_Chyp14/HybridAssembly/LazyB/./LazyB-Run1/tmp.nLTLFxpLag/jelly_count_k50.jf' for [-L, --lower-count=uint64]: Invalid unsigned int string
java -ea -Xmx272229m -Xms272229m -cp /proj/uppstore2018098/nobackup/marvin/Calanus_hyperboreus/Assembly_Chyp14/HybridAssembly/LazyB/bbmap/current/ jgi.BBDuk in1=../Calhyp_14_R1.fastq.gz in2=../Calhyp_14_R2.fastq.gz out1=/proj/uppstore2018098/nobackup/marvin/Calanus_hyperboreus/Assembly_Chyp14/HybridAssembly/LazyB/./LazyB-Run1/tmp.nLTLFxpLag/illu_filtered.1.fastq out2=/proj/uppstore2018098/nobackup/marvin/Calanus_hyperboreus/Assembly_Chyp14/HybridAssembly/LazyB/./LazyB-Run1/tmp.nLTLFxpLag/illu_filtered.2.fastq ref=/proj/uppstore2018098/nobackup/marvin/Calanus_hyperboreus/Assembly_Chyp14/HybridAssembly/LazyB/./LazyB-Run1/tmp.nLTLFxpLag/filtered_kmers_50_.fa k=50 hdist=0
Executing jgi.BBDuk [in1=../Calhyp_14_R1.fastq.gz, in2=../Calhyp_14_R2.fastq.gz, out1=/proj/uppstore2018098/nobackup/marvin/Calanus_hyperboreus/Assembly_Chyp14/HybridAssembly/LazyB/./LazyB-Run1/tmp.nLTLFxpLag/illu_filtered.1.fastq, out2=/proj/uppstore2018098/nobackup/marvin/Calanus_hyperboreus/Assembly_Chyp14/HybridAssembly/LazyB/./LazyB-Run1/tmp.nLTLFxpLag/illu_filtered.2.fastq, ref=/proj/uppstore2018098/nobackup/marvin/Calanus_hyperboreus/Assembly_Chyp14/HybridAssembly/LazyB/./LazyB-Run1/tmp.nLTLFxpLag/filtered_kmers_50_.fa, k=50, hdist=0]
Version 39.01

maskMiddle was disabled because kbig>k

Any help will be appreciated! Thanks a lot :)

[0x002A]

Hey,

thanks for using MuCHSALSA. The error message suggests that the format you are using (.fastq.gz) is not supported by jellyfish (which we run as the first step of the pipeline) and thus intermediate results can not be calculated and the execution aborts. Please try again with uncompressed input files.

[Hufflepuff1012]

Oh! Yes, you are right, now it does not complain anymore when using uncompressed files. Thank you for your prompt answer :)