alexdobin
commented
2 years ago Hi @Gump-Sun
--outFileNamePrefix SRR7014563_star should have resulted in all output files having the prefix SRR7014563_star, while you are seeing just star. If you are running these multiple files in a loop, please make sure that the --outFileNamePrefix is correct for every iteration of the loop. I would recommend also to use different --outTmpDir for each run.
Gump-Sun
I have more than 100 fastq files to run STAR to align the reads.
I didn't specify a “--outTmpdir” parameter.
For the first 16 fastq files, good aligning results came out with the complete "starAligned.out.sam" file. However, from the 17th fastq file, no aligning results came out but returned the following 5 files: "starAligned.out.sam"(0 bytes) "starLog.final.out" "starLog.out" "starLog.progress.out" "starSJ.out.tab",
I have confirmed all the fastq files are correct and proper. Would you mind heelping me to solve this problem?
And the "starLog.out" of my 17th fastq file when running STAR came with the content as follows:
STAR version=2.7.10a STAR compilation time,server,dir=2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source STAR git: On branch master ; commit ae26add7ea1724f3281ec8abedb71bcff6a4ae73 ; diff files: CHANGES.md README.md RELEASEnotes.md doc/STARmanual.pdf extras/doc-latex/STARmanual.tex extras/doc-latex/convertParDefToLatexTable.awk extras/doc-latex/parametersDefault.tex extras/docker/Dockerfile source/VERSION
Command Line:
STAR --runThreadN 40 --genomeDir /home/data/t120351/database/human/GRCh38.107.dna/index/star/ --outFileNamePrefix SRR7014563_star --readFilesCommand cat --readFilesIn /home/data/t120351/project/osteogenesis/GSE113253/data/cleandata/fastp/SRR7014563.fastp.fq
Initial USER parameters from Command Line:
outFileNamePrefix SRR7014563_star
All USER parameters from Command Line:
runThreadN 40 ~RE-DEFINED genomeDir /home/data/t120351/database/human/GRCh38.107.dna/index/star/ ~RE-DEFINED outFileNamePrefix SRR7014563_star ~RE-DEFINED readFilesCommand cat ~RE-DEFINED readFilesIn /home/data/t120351/project/osteogenesis/GSE113253/data/cleandata/fastp/SRR7014563.fastp.fq ~RE-DEFINED
Finished reading parameters from all sources
Final user re-defined parameters-----------------:
runThreadN 40 genomeDir /home/data/t120351/database/human/GRCh38.107.dna/index/star/ readFilesIn /home/data/t120351/project/osteogenesis/GSE113253/data/cleandata/fastp/SRR7014563.fastp.fq
readFilesCommand cat
outFileNamePrefix SRR7014563_star
Final effective command line:
STAR --runThreadN 40 --genomeDir /home/data/t120351/database/human/GRCh38.107.dna/index/star/ --readFilesIn /home/data/t120351/project/osteogenesis/GSE113253/data/cleandata/fastp/SRR7014563.fastp.fq --readFilesCommand cat --outFileNamePrefix SRR7014563_star
Number of fastq files for each mate = 1
Input read files for mate 1 : -rw-rw-r-- 1 t120351 t120351 1151410360 8月 3 15:34 /home/data/t120351/project/osteogenesis/GSE113253/data/cleandata/fastp/SRR7014563.fastp.fq
readsCommandsFile: exec > "SRR7014563_star_STARtmp/tmp.fifo.read1" echo FILE 0 cat "/home/data/t120351/project/osteogenesis/GSE113253/data/cleandata/fastp/SRR7014563.fastp.fq"
ParametersSolo: --soloCellFilterType CellRanger2.2 filtering parameters: 3000 0.99 10 Finished loading and checking parameters Reading genome generation parameters:
STAR --runMode genomeGenerate --runThreadN 30 --genomeDir /home/data/t120351/database/human/GRCh38.107.dna/index/star --genomeFastaFiles /home/data/t120351/database/human/GRCh38.107.dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa --sjdbGTFfile /home/data/t120351/database/human/GRCh38.107.gtf/Homo_sapiens.GRCh38.107.chr.gtf --sjdbOverhang 50
GstrandBit=32
versionGenome 2.7.4a ~RE-DEFINED genomeType Full ~RE-DEFINED genomeFastaFiles /home/data/t120351/database/human/GRCh38.107.dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa ~RE-DEFINED genomeSAindexNbases 14 ~RE-DEFINED genomeChrBinNbits 18 ~RE-DEFINED genomeSAsparseD 1 ~RE-DEFINED genomeTransformType None ~RE-DEFINED genomeTransformVCF - ~RE-DEFINED sjdbOverhang 50 ~RE-DEFINED sjdbFileChrStartEnd - ~RE-DEFINED sjdbGTFfile /home/data/t120351/database/human/GRCh38.107.gtf/Homo_sapiens.GRCh38.107.chr.gtf ~RE-DEFINED sjdbGTFchrPrefix - ~RE-DEFINED sjdbGTFfeatureExon exon ~RE-DEFINED sjdbGTFtagExonParentTranscripttranscript_id ~RE-DEFINED sjdbGTFtagExonParentGene gene_id ~RE-DEFINED sjdbInsertSave Basic ~RE-DEFINED genomeFileSizes 3178849881 genomeFileSizes 3178849881 24633756819 ~RE-DEFINED