[markdup] error reading header

[charlescongxu]

I have a simple header reading error from markdup that caused my snippy to fail... I've pasted the log file below.

### cd /lustre06/project/6000186/congxu/snippy/A.rubrum

### /home/congxu/0_def-barrett_project_congxu/snippy/bin/snippy --cpus 16 --outdir /home/congxu/scratch/A.rubrum_Aug9_G7_snps --ref GCA_900156265.1_IMG-taxon_2681812815_annotated_assembly_genomic.gbff --ctgs /home/congxu/scratch/Aug9_G7_mapped_contigs.fa

### samtools faidx reference/ref.fa


### bwa index reference/ref.fa

[bwa_index] Pack FASTA... 0.03 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.73 seconds elapse.
[bwa_index] Update BWT... 0.02 sec
[bwa_index] Pack forward-only FASTA... 0.03 sec
[bwa_index] Construct SA from BWT and Occ... 0.26 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index reference/ref.fa
[main] Real time: 2.344 sec; CPU: 1.073 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


### snpEff build -c reference/snpeff.config -dataDir . -gff3 ref

Picked up JAVA_TOOL_OPTIONS: -Xmx2g
WARNING: All frames are zero! This seems rather odd, please check that 'frame' information in your 'genes' file is accurate.

### bwa mem  -Y -M -R '@RG\tID:A.rubrum_Aug9_G7_snps\tSM:A.rubrum_Aug9_G7_snps' -t 16 reference/ref.fa fake_reads.fq | 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

[zhichusun]

Hello, I also encountered the same problem, how did you solve it, thank you very much

[KEACER]

I've solved the markdup error. Solution: The running memory is greater than 8G