Got broken pipeline when running freebayes-parallel

[buihoangphuc412]

I got this error like this. Does anyone can help to fix?? I run command on HPC: snippy --R1 $p_trim/VN0467_1_paired.fastq.gz --R2 $p_trim/VN0467_2_paired.fastq.gz --outdir /lustre7/home/buihoangphuc412/Projects/GWAS/variant/VN0467 --prefix VN0467 --ref $p_ref/genome/CHC97.fasta --report --cpus 4 --ram 2 --basequal 15 VN0467.log

echo snippy 4.6.0

cd /lustre7/home/buihoangphuc412

/home/buihoangphuc412/miniconda3/envs/pyseer/bin/snippy --R1 /lustre7/home/buihoangphuc412/Projects/GWAS/trim/VN0467_1_paired.fastq.gz --R2 /lustre7/home/buihoangphuc412/Projects/GWAS/trim/VN0467_2_paired.fastq.gz --outdir /lustre7/home/buihoangphuc412/Projects/GWAS/variant/VN0467 --prefix VN0467 --ref /lustre7/home/buihoangphuc412/Projects/GWAS/ref/genome/CHC97.fasta --report --cpus 4 --ram 2 --basequal 15

samtools faidx reference/ref.fa

bwa index reference/ref.fa

[bwa_index] Pack FASTA... 0.00 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 0.25 seconds elapse. [bwa_index] Update BWT... 0.02 sec [bwa_index] Pack forward-only FASTA... 0.00 sec [bwa_index] Construct SA from BWT and Occ... 0.09 sec [main] Version: 0.7.17-r1188 [main] CMD: bwa index reference/ref.fa [main] Real time: 0.420 sec; CPU: 0.368 sec

mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa

ln -sf reference/ref.fa .

ln -sf reference/ref.fa.fai .

mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz

bwa mem -Y -M -R '@RG\tID:VN0467\tSM:VN0467' -t 4 reference/ref.fa /lustre7/home/buihoangphuc412/Projects/GWAS/trim/VN0467_1_paired.fastq.gz /lustre7/home/buihoangphuc412/Projects/GWAS/trim/VN0467_2_paired.fastq.gz | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 1 -m 1000M | samtools fixmate -m --threads 1 - - | samtools sort -l 0 -T /tmp --threads 1 -m 1000M | samtools markdup -T /tmp --threads 1 -r -s - - > VN0467.bam

COMMAND: samtools markdup -T /tmp --threads 1 -r -s - - READ: 907222 WRITTEN: 895475 EXCLUDED: 106405 EXAMINED: 800817 PAIRED: 752182 SINGLE: 48635 DUPLICATE PAIR: 1168 DUPLICATE SINGLE: 10579 DUPLICATE PAIR OPTICAL: 0 DUPLICATE SINGLE OPTICAL: 0 DUPLICATE NON PRIMARY: 0 DUPLICATE NON PRIMARY OPTICAL: 0 DUPLICATE PRIMARY TOTAL: 11747 DUPLICATE TOTAL: 11747 ESTIMATED_LIBRARY_SIZE: 120974295

samtools index VN0467.bam

fasta_generate_regions.py reference/ref.fa.fai 237553 > reference/ref.txt

freebayes-parallel reference/ref.txt 4 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 15 -m 60 --strict-vcf -f reference/ref.fa VN0467.bam > VN0467.raw.vcf

vcfstreamsort: symbol lookup error: /lustre7/home/buihoangphuc412/miniconda3/envs/pyseer/bin/../lib/libvcflib.so.1: undefined symbol: wavefront_align vcfuniq: symbol lookup error: /lustre7/home/buihoangphuc412/miniconda3/envs/pyseer/bin/../lib/libvcflib.so.1: undefined symbol: wavefront_align Traceback (most recent call last): File "/lustre7/home/buihoangphuc412/miniconda3/envs/pyseer/bin/vcffirstheader", line 17, in print(line.strip()) BrokenPipeError: [Errno 32] Broken pipe