STAR fusion error

Question

[dimitrischat]

Hi. I am trying to install and run STAR-fusion in Ubuntu. I got STAR version 2.7.0d installed but when i try to run STAR-fusion(version 1.5.0) it returns this problem :

ERROR Sorry, version [2.7.0d] is not supported. Please use at least STAR version 2.6.1

I also installed STAR version 2.6.1d just to see if it would make a difference but it didn't. Same error. I installed all other dependencies that STAR-fusion requires.

Any suggestions? Thanks in advance.

[ATpoint]

 conda install -c bioconda star-fusion

[michael.ante]

According to this Tweet rather use conda create -n star-fusion -c bioconda star-fusion and activate the environment each time you want to run star-fusion.

[dimitrischat]

thanks a lot. I installed it like you said. But when i type :

conda activate star-fusion

nothing happens. I also tried after activating enviroment :

star-fusion

but still nothing

Answer 1

[michael.ante]

You're right. With the standard conda install, you'll get STAR 2.7 installed. If your remove the environment (conda remove -n star-fusion --all) and re-install it with conda create -n star-fusion -c bioconda star-fusion star=2.6.1, you'll be able to run star fusion:

conda activate star-fusion
STAR-Fusion

Quick guide to running:

STAR-Fusion --left_fq reads_1.fq --right_fq reads_2.fq --genome_lib_dir /path/to/ctat_genome_lib_build_dir

[dimitrischat]

i force installed the 2.6.1d so now it works. Also i downloaded the plug and play genome resource library so i guess thats ok. My command is :

STAR-Fusion --left_fq GlentisS1_S17_R1_001.fastq.gz --right_fq GlentisS1_S17_R2_001.fastq.gz --genome_lib_dir '/..../GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir' --CPU 10 --output_dir STAR-Fusion_outdir/

But the outcome is :

CMD: mkdir -p /home/app/Desktop/Untitled Folder/GlentisRNASeq/top_dir/STAR-Fusion_outdir//_starF_checkpoints
CMD: mkdir -p /home/app/Desktop/Untitled Folder/GlentisRNASeq/top_dir/STAR-Fusion_outdir//star-fusion.preliminary
* Running CMD: /home/app/anaconda3/bin/STAR --genomeDir /media/app/New_Volume/jim/reference/Star-Fusion_genome_resource_lib/hg38/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa.star.idx  --outReadsUnmapped None  --chimSegmentMin 12  --chimJunctionOverhangMin 12  --chimOutJunctionFormat 1  --alignSJDBoverhangMin 10  --alignMatesGapMax 100000  --alignIntronMax 100000  --alignSJstitchMismatchNmax 5 -1 5 5  --runThreadN 10 --outSAMstrandField intronMotif  --outSAMunmapped Within  --outSAMtype BAM Unsorted  --readFilesIn /home/app/Desktop/Untitled Folder/GlentisRNASeq/top_dir/GlentisS1_S17_R1_001.fastq.gz /home/app/Desktop/Untitled Folder/GlentisRNASeq/top_dir/GlentisS1_S17_R2_001.fastq.gz  --outSAMattrRGline ID:GRPundef  --chimMultimapScoreRange 10 --chimMultimapNmax 10 --chimNonchimScoreDropMin 10  --peOverlapNbasesMin 12 --peOverlapMMp 0.1  --genomeLoad NoSharedMemory  --twopassMode Basic  --readFilesCommand 'gunzip -c' 
gzip: /home/app/Desktop/Untitled is a directory -- ignored
gzip: Folder/GlentisRNASeq/top_dir/GlentisS1_S17_R1_001.fastq.gz: No such file or directory
gzip: /home/app/Desktop/Untitled is a directory -- ignored
Segmentation fault (core dumped)
Error, cmd: /home/app/anaconda3/bin/STAR --genomeDir /media/app/New_Volume/jim/reference/Star-Fusion_genome_resource_lib/hg38/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa.star.idx  --outReadsUnmapped None  --chimSegmentMin 12  --chimJunctionOverhangMin 12  --chimOutJunctionFormat 1  --alignSJDBoverhangMin 10  --alignMatesGapMax 100000  --alignIntronMax 100000  --alignSJstitchMismatchNmax 5 -1 5 5  --runThreadN 10 --outSAMstrandField intronMotif  --outSAMunmapped Within  --outSAMtype BAM Unsorted  --readFilesIn /home/app/Desktop/Untitled Folder/GlentisRNASeq/top_dir/GlentisS1_S17_R1_001.fastq.gz /home/app/Desktop/Untitled Folder/GlentisRNASeq/top_dir/GlentisS1_S17_R2_001.fastq.gz  --outSAMattrRGline ID:GRPundef  --chimMultimapScoreRange 10 --chimMultimapNmax 10 --chimNonchimScoreDropMin 10  --peOverlapNbasesMin 12 --peOverlapMMp 0.1  --genomeLoad NoSharedMemory  --twopassMode Basic  --readFilesCommand 'gunzip -c'  died with ret 35584 No such file or directory at /home/app/anaconda3/lib/STAR-Fusion/PerlLib/Pipeliner.pm line 181.
    Pipeliner::run(Pipeliner=HASH(0x55ed47235e50)) called at /home/app/anaconda3/lib/STAR-Fusion/STAR-Fusion line 862
    main::run_STAR(Pipeliner=HASH(0x55ed47235e50), "/home/app/Desktop/Untitled Folder/GlentisRNASeq/top_dir/Glent"..., "/home/app/Desktop/Untitled Folder/GlentisRNASeq/top_dir/Glent"..., "") called at /home/app/anaconda3/lib/STAR-Fusion/STAR-Fusion line 509

When i try with .fastq rather than .fastq.gz i get fatal error

ERROR EXITING because of fatal input ERROR: could not open readFilesIn=Folder/GlentisRNASeq/top_dir/GlentisS1_S17_R1_001.fastq

[michael.ante]

Try to avoid spaces in file/folder names or use the appropriated comment function (like /home/app/Desktop/Untitled\ Folder/)

[dimitrischat]

it made a difference..it worked for a long time till reported other error. I searched inside the genome resource library foder and i cant find that file(that reports the error) : "ref_annot.gtf" , but there are : "ref_annot.gtf.gene_spans" , "ref_annot.gtf.mini.sortu" . By the way this is the plug n play resource lib from https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/

ERROR Error, cannot locate reference annotation file: /media/app/New_Volume/jim/reference/Star-Fusion_genome_resource_lib/hg38/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_annot.gtf at /home/app/anaconda3/lib/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes line 67. Error, cmd: /home/app/anaconda3/lib/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /media/app/New_Volume/jim/reference/Star-Fusion_genome_resource_lib/hg38/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir -J Chimeric.out.junction > /home/app/Desktop/GlentisRNASeq/top_dir/STAR-Fusion_outdir//star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt died with ret 512 No such file or directory at /home/app/anaconda3/lib/STAR-Fusion/PerlLib/Pipeliner.pm line 181. Pipeliner::run(Pipeliner=HASH(0x55ac64617e40)) called at /home/app/anaconda3/lib/STAR-Fusion/STAR-Fusion line 676

EDIT :

I think the hg38 version plug n play is corrupt(or maybe my downloaded file was corrupt). With hg19 plug n play STAR-Fusion worked. Also at the end it reports : * STAR-Fusion complete. See output: star-fusion.fusion_candidates.tsv (or .abridged.tsv version) , i am guessing thats the : star-fusion.fusion_predictions.tsv ? Because there is no "star-fusion.fusion_candidates.tsv" . There are only "star-fusion.fusion_candidates.preliminary" and variations of that file in star-fusion.preliminary folder. Thanks