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tseemann
Error reading header
Dear everyone, I used snippy to check SNP compared to reference H, pylori 26695. However, I got this error. Does anyone get same problem with me? Thank you
echo snippy 4.6.0
cd /data/Phuc/Antibiotic/Vietnam strains/Snippy
/data/Phuc/miniconda3/envs/test/bin/snippy --cpus 16 --ram 8 --R1 VN0498_1_paired.qf.fastq.gz --R2 VN0498_2_paired.qf.fastq.gz --outdir VN0498 --ref 26695.fasta
samtools faidx reference/ref.fa
bwa index reference/ref.fa
[bwa_index] Pack FASTA... 0.02 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 0.38 seconds elapse. [bwa_index] Update BWT... 0.03 sec [bwa_index] Pack forward-only FASTA... 0.01 sec [bwa_index] Construct SA from BWT and Occ... 0.23 sec [main] Version: 0.7.17-r1188 [main] CMD: bwa index reference/ref.fa [main] Real time: 0.681 sec; CPU: 0.681 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:VN0498\tSM:VN0498' -t 16 reference/ref.fa /data/Phuc/Antibiotic/Vietnam strains/Snippy/VN0498_1_paired.qf.fastq.gz /data/Phuc/Antibiotic/Vietnam strains/Snippy/VN0498_2_paired.qf.fastq.gz | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 7 -m 1000M | samtools fixmate -m --threads 7 - - | samtools sort -l 0 -T /tmp --threads 7 -m 1000M | samtools markdup -T /tmp --threads 7 -r -s - - > snps.bam
[markdup] error reading header
Hello!
I have the same exact problem, however, only on certain files. Snippy is running alright on the majority of my fasta files, but for a few I get this error in the snps.log file:
bwa mem -Y -M -R '@RG\tID:2998_FRC0473\tSM:2998_FRC0473' -t 64 reference/ref.fa /pasteur/zeus/projets/p01/Corynebacterium-ngs/ChiaraCrestani/C_ulcerans/work_paper/genomes_selected_2023-10-25/2998_FRC0473.fas | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /local/scratch/tmp --threads 31 -m 250M | samtools fixmate -m --threads 31 - - | samtools sort -l 0 -T /local/scratch/tmp --threads 31 -m 250M | samtools markdup -T /local/scratch/tmp --threads 31 -r -s - - > snps.bam
[markdup] error reading header
Has anyone found a fix? I have checked that the contigs in the fasta files only have short names. As I said this happens only with a subset of the fasta files (for which I have all the permissions).
Can someone help?
