No Chimeric.out.junction file generated
Mirable8me opened this issue · comments
Hi,
I ran STAR using this command:
STAR --runThreadN 12
--genomeDir
ref_genome.fa.star.idx
--readFilesIn R1_val_1.fq.gz R2_val_2.fq.gz
--outReadsUnmapped None
--twopassMode Basic
--readFilesCommand "gunzip -c"
--outSAMstrandField intronMotif \
--outSAMunmapped Within
--chimOutType Junctions
--chimSegmentMin 12 \
--chimJunctionOverhangMin 8
--chimOutJunctionFormat 1 \
--alignSJDBoverhangMin 10
--alignMatesGapMax 100000 \
--alignIntronMax 100000
--alignSJstitchMismatchNmax 5 -1 5 5 \
--outSAMattrRGline ID:GRPundef
--chimMultimapScoreRange 3
--chimScoreJunctionNonGTAG -4
--chimMultimapNmax 20
--chimNonchimScoreDropMin 10
--peOverlapNbasesMin 12
--peOverlapMMp 0.1
--alignInsertionFlush Right
--alignSplicedMateMapLminOverLmate 0
--alignSplicedMateMapLmin 30
I want to get Chimeric.out.junction file to run STAR-Fusion. However, the output I only get is sam and Log.final.out. Tell me, what am I doing wrong?
Hi @Mirable8me
Please check the Log.out file to see if your command options were read correctly by STAR.
Hi @Mirable8me
Please check the Log.out file to see if your command options were read correctly by STAR.
Everything seems to be fine in the file.
STAR version=2.7.9a
STAR compilation time,server,dir=2021-05-04T09:43:56-0400 vega:/home/dobin/data/STAR/STARcode/STAR.master/source
Command Line:
STAR --runThreadN 12 --genomeDir /mnt/cancerproject/tools/STAR-Fusion.v0.13.0/GRCh38_gencode_v44_CTAT_lib_Oct292023.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx --readFilesIn /mnt/singlecellproject/our_data/syncrip/fastq-trim/Shv196_R1_val_1.fq.gz /mnt/singlecellproject/our_data/syncrip/fastq-trim/Shv196_R2_val_2.fq.gz --outReadsUnmapped None --twopassMode Basic --readFilesCommand "gunzip -c" --outSAMstrandField intronMotif " "
Initial USER parameters from Command Line:
All USER parameters from Command Line:
runThreadN 12 ~RE-DEFINED
genomeDir /mnt/cancerproject/tools/STAR-Fusion.v0.13.0/GRCh38_gencode_v44_CTAT_lib_Oct292023.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx ~RE-DEFINED
readFilesIn /mnt/singlecellproject/our_data/syncrip/fastq-trim/Shv196_R1_val_1.fq.gz /mnt/singlecellproject/our_data/syncrip/fastq-trim/Shv196_R2_val_2.fq.gz ~RE-DEFINED
outReadsUnmapped None ~RE-DEFINED
twopassMode Basic ~RE-DEFINED
readFilesCommand "gunzip -c" ~RE-DEFINED
outSAMstrandField intronMotif ~RE-DEFINED
Finished reading parameters from all sources
Final user re-defined parameters-----------------:
runThreadN 12
genomeDir /mnt/cancerproject/tools/STAR-Fusion.v0.13.0/GRCh38_gencode_v44_CTAT_lib_Oct292023.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx
readFilesIn /mnt/singlecellproject/our_data/syncrip/fastq-trim/Shv196_R1_val_1.fq.gz /mnt/singlecellproject/our_data/syncrip/fastq-trim/Shv196_R2_val_2.fq.gz
readFilesCommand "gunzip -c"
outReadsUnmapped None
outSAMstrandField intronMotif
twopassMode Basic
Final effective command line:
STAR --runThreadN 12 --genomeDir /mnt/cancerproject/tools/STAR-Fusion.v0.13.0/GRCh38_gencode_v44_CTAT_lib_Oct292023.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx --readFilesIn /mnt/singlecellproject/our_data/syncrip/fastq-trim/Shv196_R1_val_1.fq.gz /mnt/singlecellproject/our_data/syncrip/fastq-trim/Shv196_R2_val_2.fq.gz --readFilesCommand "gunzip -c" --outReadsUnmapped None --outSAMstrandField intronMotif --twopassMode Basic
Number of fastq files for each mate = 1
Input read files for mate 1 :
-rw-r--r-- 1 mirable cancerproject 1856178975 Apr 2 15:01 /mnt/singlecellproject/our_data/syncrip/fastq-trim/Shv196_R1_val_1.fq.gz
readsCommandsFile:
exec > "./_STARtmp/tmp.fifo.read1"
echo FILE 0
gunzip -c "/mnt/singlecellproject/our_data/syncrip/fastq-trim/Shv196_R1_val_1.fq.gz"
Input read files for mate 2 :
-rw-r--r-- 1 mirable cancerproject 1886728438 Apr 2 15:01 /mnt/singlecellproject/our_data/syncrip/fastq-trim/Shv196_R2_val_2.fq.gz
readsCommandsFile:
exec > "./_STARtmp/tmp.fifo.read2"
echo FILE 0
gunzip -c "/mnt/singlecellproject/our_data/syncrip/fastq-trim/Shv196_R2_val_2.fq.gz"
WARNING --outSAMstrandField=intronMotif, therefore STAR will output XS attribute
ParametersSolo: --soloCellFilterType CellRanger2.2 filtering parameters: 3000 0.99 10
Finished loading and checking parameters
Reading genome generation parameters:
STAR --runMode genomeGenerate --runThreadN 10 --genomeDir /seq/RNASEQ/__ctat_genome_lib_building/Oct2023_GRCh38_gencodeV44/ctat_genome_lib_build_dir/ref_genome.fa.star.idx --genomeFastaFiles /seq/RNASEQ/__ctat_genome_lib_building/Oct2023_GRCh38_gencodeV44/GRCh38.primary_assembly.genome.fa.pseudo_masked.fa --limitGenomeGenerateRAM 40419136213 --limitSjdbInsertNsj 10000000 --sjdbGTFfile /seq/RNASEQ/__ctat_genome_lib_building/Oct2023_GRCh38_gencodeV44/gencode.v44.annotation.gtf.revised.custom.gtf --sjdbOverhang 150
GstrandBit=33
versionGenome 2.7.4a ~RE-DEFINED
genomeType Full ~RE-DEFINED
genomeFastaFiles /seq/RNASEQ/__ctat_genome_lib_building/Oct2023_GRCh38_gencodeV44/GRCh38.primary_assembly.genome.fa.pseudo_masked.fa ~RE-DEFINED
genomeSAindexNbases 14 ~RE-DEFINED
genomeChrBinNbits 18 ~RE-DEFINED
genomeSAsparseD 1 ~RE-DEFINED
genomeTransformType None ~RE-DEFINED
genomeTransformVCF - ~RE-DEFINED
sjdbOverhang 150 ~RE-DEFINED
sjdbFileChrStartEnd - ~RE-DEFINED
sjdbGTFfile /seq/RNASEQ/__ctat_genome_lib_building/Oct2023_GRCh38_gencodeV44/gencode.v44.annotation.gtf.revised.custom.gtf ~RE-DEFINED
sjdbGTFchrPrefix - ~RE-DEFINED
sjdbGTFfeatureExon exon ~RE-DEFINED
sjdbGTFtagExonParentTranscripttranscript_id ~RE-DEFINED
sjdbGTFtagExonParentGene gene_id ~RE-DEFINED
sjdbInsertSave Basic ~RE-DEFINED
genomeFileSizes 3258551081 26056003771 ~RE-DEFINED
Genome version is compatible with current STAR
Started loading the genome: Fri Apr 5 14:40:23 2024
Genome: size given as a parameter = 3258551081
SA: size given as a parameter = 26056003771
SAindex: size given as a parameter = 1
Read from SAindex: pGe.gSAindexNbases=14 nSAi=357913940
nGenome=3258551081; nSAbyte=26056003771
GstrandBit=33 SA number of indices=6130824416
Shared memory is not used for genomes. Allocated a private copy of the genome.
Genome file size: 3258551081 bytes; state: good=1 eof=0 fail=0 bad=0
Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 3258551081 bytes
SA file size: 26056003771 bytes; state: good=1 eof=0 fail=0 bad=0
Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 26056003771 bytes
Loading SAindex ... done: 1610612861 bytes
Finished loading the genome: Fri Apr 5 14:41:28 2024
Processing splice junctions database sjdbN=399213, pGe.sjdbOverhang=150
alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824
Created thread # 1
Created thread # 2
Starting to map file # 0
mate 1: /mnt/singlecellproject/our_data/syncrip/fastq-trim/Shv196_R1_val_1.fq.gz
mate 2: /mnt/singlecellproject/our_data/syncrip/fastq-trim/Shv196_R2_val_2.fq.gz
Created thread # 3
Created thread # 4
Created thread # 5
Created thread # 6
Created thread # 7
Created thread # 8
Created thread # 9
Created thread # 10
Created thread # 11
Thread #0 end of input stream, nextChar=-1
Completed: thread #6
Completed: thread #9
Completed: thread #1
Completed: thread #2
Completed: thread #3
Completed: thread #10
Completed: thread #8
Completed: thread #4
Completed: thread #0
Joined thread # 1
Joined thread # 2
Joined thread # 3
Joined thread # 4
Completed: thread #5
Joined thread # 5
Joined thread # 6
Completed: thread #11
Completed: thread #7
Joined thread # 7
Joined thread # 8
Joined thread # 9
Joined thread # 10
Joined thread # 11
Apr 05 14:45:31 Loaded database junctions from the generated genome /mnt/cancerproject/tools/STAR-Fusion.v0.13.0/GRCh38_gencode_v44_CTAT_lib_Oct292023.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx//sjdbList.out.tab: 399213 total junctions
Apr 05 14:45:32 Loaded database junctions from the 1st pass file: ./_STARpass1//SJ.out.tab: 646773 total junctions
Apr 05 14:45:32 Finished preparing junctions
Apr 05 14:45:32 ..... inserting junctions into the genome indices
Apr 05 14:45:50 Finished SA search: number of new junctions=65909, old junctions=399213
Apr 05 14:46:01 Finished sorting SA indicesL nInd=39545180
Genome size with junctions=3278389690 3138387968 140001722
GstrandBit1=32 GstrandBit=33
Apr 05 14:47:13 Finished inserting junction indices
Apr 05 14:47:25 Finished SAi
Apr 05 14:47:25 ..... finished inserting junctions into genome
Input read files for mate 1 :
-rw-r--r-- 1 mirable cancerproject 1856178975 Apr 2 15:01 /mnt/singlecellproject/our_data/syncrip/fastq-trim/Shv196_R1_val_1.fq.gz
readsCommandsFile:
exec > "./_STARtmp/tmp.fifo.read1"
echo FILE 0
gunzip -c "/mnt/singlecellproject/our_data/syncrip/fastq-trim/Shv196_R1_val_1.fq.gz"
Input read files for mate 2 :
-rw-r--r-- 1 mirable cancerproject 1886728438 Apr 2 15:01 /mnt/singlecellproject/our_data/syncrip/fastq-trim/Shv196_R2_val_2.fq.gz
readsCommandsFile:
exec > "./_STARtmp/tmp.fifo.read2"
echo FILE 0
gunzip -c "/mnt/singlecellproject/our_data/syncrip/fastq-trim/Shv196_R2_val_2.fq.gz"
Created thread # 1
Created thread # 2
Starting to map file # 0
mate 1: /mnt/singlecellproject/our_data/syncrip/fastq-trim/Shv196_R1_val_1.fq.gz
mate 2: /mnt/singlecellproject/our_data/syncrip/fastq-trim/Shv196_R2_val_2.fq.gz
Created thread # 3
Created thread # 4
Created thread # 5
Created thread # 6
Created thread # 7
Created thread # 8
Created thread # 9
Created thread # 10
Created thread # 11
Thread #3 end of input stream, nextChar=-1
Completed: thread #5
Completed: thread #8
Completed: thread #1
Completed: thread #0
Joined thread # 1
Completed: thread #6
Completed: thread #10
Completed: thread #7
Completed: thread #3
Completed: thread #11
Completed: thread #4
Completed: thread #2
Joined thread # 2
Joined thread # 3
Joined thread # 4
Joined thread # 5
Joined thread # 6
Joined thread # 7
Joined thread # 8
Completed: thread #9
Joined thread # 9
Joined thread # 10
Joined thread # 11
ALL DONE!
If you looks at the command line in Log.out, it's cut after --outSAMstrandField intronMotif, which means that there was problem with formatting - likely a space after backslash \ .