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NGS Log File

Last updated on 13-Mar-2018 by Thomas P. Boesen
Thomas P. Boesen

Founder
boesen@scifeon.com

The logfile for the NGS application example can be downloaded here:

The NGS-27544 logfiles looks like this:

Info: ScifCall 3.9-a7

Input samples:
- SCIF722
- SCIF723
- SCIF724
- SCIF725

NGS reads:
- SCIF722-2
  /ngs/scif722-2/scif722-2-R1.fastq.gz
  /ngs/scif722-2/scif722-2-R2.fastq.gz
- SCIF723-1
  /ngs/scif723-1/scif723-1-R1.fastq.gz
- SCIF724-1
  /ngs/scif724-1/scif724-1-R1.fastq.gz
- SCIF725-1
  /ngs/scif725-1/scif725-1-R1.fastq.gz

Step: Mapping
Info: vcftools: /pro/NGSutils/vcftools_0.1.13/bin/vcftools
Info: Starting a round of 2 mappings to the reference genome
Info: RefGenome: refgenome-hg19-20160512
Info: Mapping input: SCIF722-2
Info: Mapping result: SCIF722-2-A
Info: Mapping input: SCIF723-1
Info: Mapping result: SCIF723-1-A
Info: Mapping input: SCIF724-1
Info: Mapping result: SCIF724-1-A
Info: Mapping input: SCIF725-1
Info: Mapping result: SCIF725-1-A

Step: VarCall

/pro/NGSutils/vcftools_0.1.13/bin/vcftools --vcf VARCALL/scif722-2-a.vcf --diff VARCALL/refgenome-hg19-20160824.vcf --diff-site --chr chr1 --stdout | /bin/grep -v CHROM >> VARCALL/scif722-2-a-1.sites

Hit: chr17,NG_027730,CCL3,17,12
Hit: chr3,NM_001168298,CXCR2,2,22
Hit: chr6,BC013615,IL-8,1,352
Info: scifcall finished OK

/pro/NGSutils/vcftools_0.1.13/bin/vcftools --vcf VARCALL/scif723-1-a.vcf --diff VARCALL/refgenome-hg19-20160824.vcf --diff-site --chr chr1 --stdout | /bin/grep -v CHROM >> VARCALL/scif723-1-a-1.sites

Hit: chr17,NG_027730,CCL3,17,25
Hit: chr3,NM_001168298,CXCR2,2,23
Hit: chr6,BC013615,IL-8,1,152
Info: scifcall finished OK

/pro/NGSutils/vcftools_0.1.13/bin/vcftools --vcf VARCALL/scif724-1-a.vcf --diff VARCALL/refgenome-hg19-20160824.vcf --diff-site --chr chr1 --stdout | /bin/grep -v CHROM >> VARCALL/scif724-1-a-1.sites

Hit: chr17,NG_027730,CCL3,17,26
Hit: chr3,NM_001168298,CXCR2,2,21
Hit: chr6,BC013615,IL-8,1,345
Info: scifcall finished OK

/pro/NGSutils/vcftools_0.1.13/bin/vcftools --vcf VARCALL/scif725-1-a.vcf --diff VARCALL/refgenome-hg19-20160824.vcf --diff-site --chr chr1 --stdout | /bin/grep -v CHROM >> VARCALL/scif725-1-a-1.sites

Hit: chr17,NG_027730,CCL3,17,11
Hit: chr3,NM_001168298,CXCR2,2,24
Hit: chr6,BC013615,IL-8,1,342
Info: scifcall finished OK
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