Open yzhzu opened 4 years ago
I have subscribed, as I have the same error message:
[bam_sort_core] merging from 0 files and 7 in-memory blocks... samtools sort: couldn't allocate memory for bam_mem [15:37:11] Error running command, check mysnps/snps.log
snps.log copied below: `
[bwa_index] Pack FASTA... 0.04 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 1.98 seconds elapse. [bwa_index] Update BWT... 0.03 sec [bwa_index] Pack forward-only FASTA... 0.03 sec [bwa_index] Construct SA from BWT and Occ... 0.67 sec [main] Version: 0.7.17-r1188 [main] CMD: bwa index reference/ref.fa [main] Real time: 3.120 sec; CPU: 2.765 sec
WARNING: All frames are zero! This seems rather odd, please check that 'frame' information in your 'genes' file is accurate.
[markdup] error reading header`
I also had a similar error as above:
snpEff build -c reference/snpeff.config -dataDir . -gff3 ref
WARNING: All frames are zero! This seems rather odd, please check that 'frame' information in your 'genes' file is accurate.
[markdup] error reading header`
Did you have any luck sorting it out?
I have the same error when running:
snippy --cpus 8 --outdir AcisSNPs --ref BW25113.fasta --R1 NG-30008_Acies_lib593532_8049_2_1.fastq --R2 NG-30008_Acies_lib593532_8049_2_2.fastq
Error message in snps.log:
[bwa_index] Pack FASTA... 0.03 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 1.08 seconds elapse. [bwa_index] Update BWT... 0.02 sec [bwa_index] Pack forward-only FASTA... 0.02 sec [bwa_index] Construct SA from BWT and Occ... 0.37 sec [main] Version: 0.7.17-r1188 [main] CMD: bwa index reference/ref.fa [main] Real time: 1.551 sec; CPU: 1.516 sec
[markdup] error reading header
How did you manage to solve it? I have the same error:
echo snippy 4.6.0 cd /home/uoc/prueba /home/uoc/snippy/bin/snippy --cpus 2 --ref pseudomonas.fna --R1 1pio_R1.fastq.gz --R2 1pio_R2.fastq.gz --outdir /home/uoc/variant samtools faidx reference/ref.fa bwa index reference/ref.fa [bwa_index] Pack FASTA... 0.08 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 1.79 seconds elapse. [bwa_index] Update BWT... 0.04 sec [bwa_index] Pack forward-only FASTA... 0.03 sec [bwa_index] Construct SA from BWT and Occ... 0.77 sec [main] Version: 0.7.17-r1188 [main] CMD: bwa index reference/ref.fa [main] Real time: 2.796 sec; CPU: 2.715 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:variant\tSM:variant' -t 2 reference/ref.fa /home/uoc/prueba/1pio_R1.fastq.gz /home/uoc/prueba/1pio_R2.fastq.gz | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 8000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 8000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam markdup: invalid option -- 'T'
Usage: samtools markdup
Option: -r Remove duplicate reads -l Max read length (default 300 bases) -s Report stats. --input-fmt-option OPT[=VAL] Specify a single input file format option in the form of OPTION or OPTION=VALUE -O, --output-fmt FORMAT[,OPT[=VAL]]... Specify output format (SAM, BAM, CRAM) --output-fmt-option OPT[=VAL] Specify a single output file format option in the form of OPTION or OPTION=VALUE --reference FILE Reference sequence FASTA FILE [null] -@, --threads INT Number of additional threads to use [0]
The input file must be coordinate sorted and must have gone through fixmates with the mate scoring option on.
Can you help me? I try `--cpus 1--ram 3
but nothing.
Thank you!!!
Hi, After update snippy, I used snippy again, the error happened.
the error information:
snpEff build -c reference/snpeff.config -dataDir . -gff3 ref
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:New\tSM:New' -t 8 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools
sort -n -l 0 -T /tmp --threads 3 -m 2000M | samtools fixmate -m --threads 3 - - | samtools sort -l 0 -T /tmp --threads 3 -m 2000M | sam tools markdup -T /tmp --threads 3 -r -s - - > d5BvsDSM.bam
[markdup] warning: unable to calculate estimated library size. Read pairs 0 should be greater than duplicate pairs 0, which should both be non zero.
can anyone help me deal with the error? Thanks yzhzhu