brianjohnhaas
commented
2 years ago Hi Junfeng,
This looks like it might be using an old version of the python pandas library. Can you try installing a newer pandas and see if that helps? It should just resume after the pandas upgrade.
best,
~brian
On Mon, Dec 6, 2021 at 5:04 AM asaki1986 @.***> wrote:
Hi,
Many thanks for developing such a great tool as implementation of STAR-Fusion, especially for discover the intron-splicing variants using RNASeq data.
Error was found using STAR_to_cancer_introns command as follows,
@.*** HE211203-2-TNA-GW21T430A06_S39]$python3 ~jjiang/work/fusion/CTAT-SPLICING/STAR_to_cancer_introns.py --SJ_tab_file ./SJ.out.tab --chimJ_file ./Chimeric.out.junction --vis --bam_file ./Aligned.out.sorted.bam --output_prefix GW21T430A06 --sample_name GW21T430A06 --ctat_genome_lib ~jjiang/work/fusion/STAR-Fusion/ctat-genome-lib-builder/GRCh37_gencode_v19_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ 17:56:39 : INFO : CMD: /home/jjiang/work/fusion/CTAT-SPLICING/util/ annotate_cancer_introns.pl --introns_file GW21T430A06.introns --ctat_genome_lib /home/jjiang/work/fusion/STAR-Fusion/ctat-genome-lib-builder/GRCh37_gencode_v19_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ --intron_col 0 > GW21T430A06.cancer.introns.prelim already processed. Skipping. 17:56:39 : INFO : CMD: /home/jjiang/work/fusion/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates GW21T430A06.cancer.introns.prelim --min_total_reads 5 > GW21T430A06.cancer.introns already processed. Skipping. 17:56:39 : INFO : Running: /home/jjiang/work/fusion/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns GW21T430A06.introns --cancer_introns GW21T430A06.cancer.introns --genome_lib_dir /home/jjiang/work/fusion/STAR-Fusion/ctat-genome-lib-builder/GRCh37_gencode_v19_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ --output_bed GW21T430A06.introns.for_IGV.bed 17:56:39 : INFO : Creating the BED File. Traceback (most recent call last): File "/home/jjiang/work/fusion/CTAT-SPLICING/util/make_igv_splice_bed.py", line 252, in
main() File "/home/jjiang/work/fusion/CTAT-SPLICING/util/make_igv_splice_bed.py", line 246, in main bed_file = bed_file.createBedFile() File "/home/jjiang/work/fusion/CTAT-SPLICING/util/make_igv_splice_bed.py", line 62, in createBedFile bed_file = split_intron(dt) File "/home/jjiang/work/fusion/CTAT-SPLICING/util/make_igv_splice_bed.py", line 21, in split_intron split1.drop(columns =[1], inplace = True) TypeError: drop() got an unexpected keyword argument 'columns' 17:56:40 : ERROR : Error: Command '/home/jjiang/work/fusion/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns GW21T430A06.introns --cancer_introns GW21T430A06.cancer.introns --genome_lib_dir /home/jjiang/work/fusion/STAR-Fusion/ctat-genome-lib-builder/GRCh37_gencode_v19_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ --output_bed GW21T430A06.introns.for_IGV.bed ' returned non-zero exit status 1., exit val: 1 17:56:40 : ERROR : Error, command: [ /home/jjiang/work/fusion/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns GW21T430A06.introns --cancer_introns GW21T430A06.cancer.introns --genome_lib_dir /home/jjiang/work/fusion/STAR-Fusion/ctat-genome-lib-builder/GRCh37_gencode_v19_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ --output_bed GW21T430A06.introns.for_IGV.bed ] failed, stack trace: [ st: file:/home/jjiang/work/fusion/CTAT-SPLICING/PyLib/Pipeliner.py, lineno:86 st: file:/home/jjiang/work/fusion/CTAT-SPLICING/STAR_to_cancer_introns.py, lineno:224 st: file:/home/jjiang/work/fusion/CTAT-SPLICING/STAR_to_cancer_introns.py, lineno:400 ] Traceback (most recent call last): File "/home/jjiang/work/fusion/CTAT-SPLICING/STAR_to_cancer_introns.py", line 400, in main() File "/home/jjiang/work/fusion/CTAT-SPLICING/STAR_to_cancer_introns.py", line 225, in main pipeliner.run() File "/home/jjiang/work/fusion/CTAT-SPLICING/PyLib/Pipeliner.py", line 71, in run cmd.run(checkpoint_dir) File "/home/jjiang/work/fusion/CTAT-SPLICING/PyLib/Pipeliner.py", line 132, in run raise RuntimeError(errmsg) RuntimeError: Error, command: [ /home/jjiang/work/fusion/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns GW21T430A06.introns --cancer_introns GW21T430A06.cancer.introns --genome_lib_dir /home/jjiang/work/fusion/STAR-Fusion/ctat-genome-lib-builder/GRCh37_gencode_v19_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ --output_bed GW21T430A06.introns.for_IGV.bed ] failed, stack trace: [ st: file:/home/jjiang/work/fusion/CTAT-SPLICING/PyLib/Pipeliner.py, lineno:86 st: file:/home/jjiang/work/fusion/CTAT-SPLICING/STAR_to_cancer_introns.py, lineno:224 st: file:/home/jjiang/work/fusion/CTAT-SPLICING/STAR_to_cancer_introns.py, lineno:400 ] Any suggestion will be appreciated.
Thanks, Junfeng
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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
asaki1986
Hi,
Many thanks for developing such a great tool as implementation of STAR-Fusion, especially for discover the intron-splicing variants using RNASeq data.
Error was found using STAR_to_cancer_introns command as follows,
[jjiang@gojira HE211203-2-TNA-GW21T430A06_S39]$python3 ~jjiang/work/fusion/CTAT-SPLICING/STAR_to_cancer_introns.py --SJ_tab_file ./SJ.out.tab --chimJ_file ./Chimeric.out.junction --vis --bam_file ./Aligned.out.sorted.bam --output_prefix GW21T430A06 --sample_name GW21T430A06 --ctat_genome_lib ~jjiang/work/fusion/STAR-Fusion/ctat-genome-lib-builder/GRCh37_gencode_v19_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ 17:56:39 : INFO : CMD: /home/jjiang/work/fusion/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file GW21T430A06.introns --ctat_genome_lib /home/jjiang/work/fusion/STAR-Fusion/ctat-genome-lib-builder/GRCh37_gencode_v19_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ --intron_col 0 > GW21T430A06.cancer.introns.prelim already processed. Skipping. 17:56:39 : INFO : CMD: /home/jjiang/work/fusion/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates GW21T430A06.cancer.introns.prelim --min_total_reads 5 > GW21T430A06.cancer.introns already processed. Skipping. 17:56:39 : INFO : Running: /home/jjiang/work/fusion/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns GW21T430A06.introns --cancer_introns GW21T430A06.cancer.introns --genome_lib_dir /home/jjiang/work/fusion/STAR-Fusion/ctat-genome-lib-builder/GRCh37_gencode_v19_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ --output_bed GW21T430A06.introns.for_IGV.bed 17:56:39 : INFO : Creating the BED File. Traceback (most recent call last): File "/home/jjiang/work/fusion/CTAT-SPLICING/util/make_igv_splice_bed.py", line 252, in <module> main() File "/home/jjiang/work/fusion/CTAT-SPLICING/util/make_igv_splice_bed.py", line 246, in main bed_file = bed_file.createBedFile() File "/home/jjiang/work/fusion/CTAT-SPLICING/util/make_igv_splice_bed.py", line 62, in createBedFile bed_file = split_intron(dt) File "/home/jjiang/work/fusion/CTAT-SPLICING/util/make_igv_splice_bed.py", line 21, in split_intron split1.drop(columns =[1], inplace = True) TypeError: drop() got an unexpected keyword argument 'columns' 17:56:40 : ERROR : Error: Command '/home/jjiang/work/fusion/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns GW21T430A06.introns --cancer_introns GW21T430A06.cancer.introns --genome_lib_dir /home/jjiang/work/fusion/STAR-Fusion/ctat-genome-lib-builder/GRCh37_gencode_v19_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ --output_bed GW21T430A06.introns.for_IGV.bed ' returned non-zero exit status 1., exit val: 1 17:56:40 : ERROR : Error, command: [ /home/jjiang/work/fusion/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns GW21T430A06.introns --cancer_introns GW21T430A06.cancer.introns --genome_lib_dir /home/jjiang/work/fusion/STAR-Fusion/ctat-genome-lib-builder/GRCh37_gencode_v19_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ --output_bed GW21T430A06.introns.for_IGV.bed ] failed, stack trace: [ st: file:/home/jjiang/work/fusion/CTAT-SPLICING/PyLib/Pipeliner.py, lineno:86 st: file:/home/jjiang/work/fusion/CTAT-SPLICING/STAR_to_cancer_introns.py, lineno:224 st: file:/home/jjiang/work/fusion/CTAT-SPLICING/STAR_to_cancer_introns.py, lineno:400 ] Traceback (most recent call last): File "/home/jjiang/work/fusion/CTAT-SPLICING/STAR_to_cancer_introns.py", line 400, in <module> main() File "/home/jjiang/work/fusion/CTAT-SPLICING/STAR_to_cancer_introns.py", line 225, in main pipeliner.run() File "/home/jjiang/work/fusion/CTAT-SPLICING/PyLib/Pipeliner.py", line 71, in run cmd.run(checkpoint_dir) File "/home/jjiang/work/fusion/CTAT-SPLICING/PyLib/Pipeliner.py", line 132, in run raise RuntimeError(errmsg) RuntimeError: Error, command: [ /home/jjiang/work/fusion/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns GW21T430A06.introns --cancer_introns GW21T430A06.cancer.introns --genome_lib_dir /home/jjiang/work/fusion/STAR-Fusion/ctat-genome-lib-builder/GRCh37_gencode_v19_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ --output_bed GW21T430A06.introns.for_IGV.bed ] failed, stack trace: [ st: file:/home/jjiang/work/fusion/CTAT-SPLICING/PyLib/Pipeliner.py, lineno:86 st: file:/home/jjiang/work/fusion/CTAT-SPLICING/STAR_to_cancer_introns.py, lineno:224 st: file:/home/jjiang/work/fusion/CTAT-SPLICING/STAR_to_cancer_introns.py, lineno:400 ]Any suggestion will be appreciated.
Thanks, Junfeng