Unable to build

[Vio]

Hi Zam

I have a bacterial genomes:
 complete asembled reference : vio1.fasta
 sample   PE 36mer : sample_R1.fastq.gz  and sample_R2.fastq.gz

Se_listRef:  

vio1.fasta

list_referencia:

vio1.fasta

pelist1:

sample_R1.fastq.gz

pelist1:

sample_R2.fastq.gz

INDEXvio1: 

 sample1    .    pelist1    pelist2

Steps and Commands:

I step:  Build binary
cortex_var_31_c1 --kmer_size 31 --mem_height 17 --mem_width 100 --se_list se_listRef --dump_binary ref.k61.ctx --sample_id vio1_ref
cortex_var_63_c1 --kmer_size 61 --mem_height 17 --mem_width 100 --se_list se_listRef --dump_binary ref.k61.ctx --sample_id vio1_ref

II step: stampy hash of reference

III step:  call run_calls.pl
run_calls.pl --first_kmer 31 --last_kmer 61 --kmer_step 30 --fastaq_index INDEXsample1 --auto_cleaning yes --bc yes --pd yes --outdir dirprueba1 --outvcf muestra --ploidy 1 --stampy_hash hashvio1 --stampy_bin /Variantes/stampy-1.0.27/stampy.py --list_ref_fasta list_referencia --refbindir indexbinarios --genome_size 4500000  --qthresh 10 --dups --mem_height 17 --mem_width 250 --vcftools_dir /Variantes/vcftools_0.1.9 --do_union yes --ref CoordinatesAndInCalling --workflow independent --logfile logfilec log.txt --apply_pop_classifier

Message error:

Unable to build /dirprueba1/binaries/uncleaned/31/sample1.unclean.kmer31.q10.ctx at /Variantes/CORTEX_release_v1.0.5.21/scripts/calling/run_calls.pl line 2097.


Logfile:

********************************************
Build uncleaned binaries:
********************************************
Build graph using quality threshold 10
/Variantes/CORTEX_release_v1.0.5.21//bin/cortex_var_31_c1 --sample_id vio1 --kmer_size 31 --mem_height 17 --mem_width 250 --dump_binary /dirprueba1/binaries/uncleaned/31/vio1.unclean.kmer31.q10.ctx  --dump_covg_distribution /dirprueba1/binaries/uncleaned/31/vio1.unclean.kmer31.q10.ctx.covg --pe_list pelist1,pelist2 --quality_score_threshold 10 --remove_pcr_duplicates > /dirprueba1/binaries/uncleaned/31/vio1.unclean.kmer31.q10.ctx.build_log 2>&1

outdir/binaries/uncleaned:

Warning: src/cortex_var/core/file_reader.c:247: Couldn't read quality scores [read: HWUSI-EAS636_0009:1:94:2532:5561#0/2; path: /Muestras/s11sequence.fastq.gz; line: 63028492]
Error: Paired-end files don't have the same number of reads
file1: /home/violeta/Documents/estanposdoc/Variantes/MuestrasAdelfo/s11sequence.fastq.gz
file2: /home/violeta/Documents/estanposdoc/Variantes/MuestrasAdelfo/s12sequence.fastq.gz

outdir/binaies/cleaned: no files
outdir/calls/: no files

I really appreciate all your attentions and help

[Zamin Iqbal]

Can I just check - do you have new-lines/carriage returns at the end of those filelists?

regards

Zam