Yumy526
commented
6 months ago It has been running smoothly, thanks for the help
Closed Yumy526 closed 6 months ago
Yumy526
commented
6 months ago It has been running smoothly, thanks for the help
My files are all complete，but error happened my code: python /public/home/ymwang/tools/rMATS-long-main/scripts/rmats_long.py --abundance /public/home/ymwang/PacBio/7_isoform/resultpart/samples_N2_R0_abundance.esp --updated-gtf /public/home/ymwang/PacBio/7_isoform/resultpart/samples_N2_R0_updated.gtf --gencode-gtf /public/home/ymwang/PacBio/6_bambu/mm10.ncbiRefSeq.gtf --group-1 /public/home/ymwang/PacBio/8_rMats/group_1.txt --group-2 /public/home/ymwang/PacBio/8_rMats/group_2.txt --group-1-name 2cellA --group-2-name 2cellB --out-dir /public/home/ymwang/PacBio/7_isoform/resultpart/rMats/ --plot-file-type .png
my group_1.txt: 2cell_10A,2cell_11A,2cell_13A my group_2.txt: 2cell_10B,2cell_11B,2cell_13B
my samples.tsv.updated: /public/home/ymwang/PacBio/6_bambu/bam/twocellsingle/diymatrix/sam/2cell_13B.sam 2cell_13 5 /public/home/ymwang/PacBio/6_bambu/bam/twocellsingle/diymatrix/sam/2cell_11A.sam 2cell_11 2 /public/home/ymwang/PacBio/6_bambu/bam/twocellsingle/diymatrix/sam/2cell_13A.sam 2cell_13 4 /public/home/ymwang/PacBio/6_bambu/bam/twocellsingle/diymatrix/sam/2cell_10A.sam 2cell_10 0 /public/home/ymwang/PacBio/6_bambu/bam/twocellsingle/diymatrix/sam/2cell_10B.sam 2cell_10 1 /public/home/ymwang/PacBio/6_bambu/bam/twocellsingle/diymatrix/sam/2cell_11B.sam 2cell_11 3
error： running: ['/public/home/ymwang/miniconda3/envs/gra/bin/python', '/public/home/ymwang/tools/rMATS-long-main/scripts/detect_differential_isoforms.py', '--abundance', '/public/home/ymwang/PacBio/7_isoform/resultpart/samples_N2_R0_abundance.esp', '--out-dir', '/public/home/ymwang/PacBio/7_isoform/resultpart/rMats/', '--group-1', '/public/home/ymwang/PacBio/8_rMats/group_1.txt', '--group-2', '/public/home/ymwang/PacBio/8_rMats/group_2.txt', '--adj-pvalue', '0.05', '--delta-proportion', '0.1', '--num-threads', '1'] running: ['Rscript', '/public/home/ymwang/tools/rMATS-long-main/scripts/detect_differential_isoforms.R', '/public/home/ymwang/PacBio/7_isoform/resultpart/samples_N2_R0_abundance.esp', '/public/home/ymwang/PacBio/7_isoform/resultpart/rMats/', '1', '/public/home/ymwang/PacBio/8_rMats/group_1.txt', '/public/home/ymwang/PacBio/8_rMats/group_2.txt']
Attaching package: ‘DRIMSeq’
The following object is masked from ‘package:base’:
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 1 did not have 4 elements Calls: main ... read_tsv_with_rows_as_first_column -> -> scan
Execution halted
Traceback (most recent call last):
File "/public/home/ymwang/tools/rMATS-long-main/scripts/detect_differential_isoforms.py", line 150, in
main()
File "/public/home/ymwang/tools/rMATS-long-main/scripts/detect_differential_isoforms.py", line 146, in main
detect_differential_isoforms(args)
File "/public/home/ymwang/tools/rMATS-long-main/scripts/detect_differential_isoforms.py", line 134, in detect_differential_isoforms
detect_isoforms(script_dir, args.abundance, args.out_dir, args.num_threads,
File "/public/home/ymwang/tools/rMATS-long-main/scripts/detect_differential_isoforms.py", line 85, in detect_isoforms
rmats_long_utils.run_command(command)
File "/public/home/ymwang/tools/rMATS-long-main/scripts/rmats_long_utils.py", line 283, in run_command
subprocess.run(command, check=True)
File "/public/home/ymwang/miniconda3/envs/gra/lib/python3.12/subprocess.py", line 571, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['Rscript', '/public/home/ymwang/tools/rMATS-long-main/scripts/detect_differential_isoforms.R', '/public/home/ymwang/PacBio/7_isoform/resultpart/samples_N2_R0_abundance.esp', '/public/home/ymwang/PacBio/7_isoform/resultpart/rMats/', '1', '/public/home/ymwang/PacBio/8_rMats/group_1.txt', '/public/home/ymwang/PacBio/8_rMats/group_2.txt']' returned non-zero exit status 1.
Traceback (most recent call last):
File "/public/home/ymwang/tools/rMATS-long-main/scripts/rmats_long.py", line 653, in
main()
File "/public/home/ymwang/tools/rMATS-long-main/scripts/rmats_long.py", line 646, in main
summary = rmats_long(args)
^^^^^^^^^^^^^^^^
File "/public/home/ymwang/tools/rMATS-long-main/scripts/rmats_long.py", line 608, in rmats_long
detect_differential_isoforms(args.abundance, args.out_dir,
File "/public/home/ymwang/tools/rMATS-long-main/scripts/rmats_long.py", line 293, in detect_differential_isoforms
rmats_long_utils.run_command(command)
File "/public/home/ymwang/tools/rMATS-long-main/scripts/rmats_long_utils.py", line 283, in run_command
subprocess.run(command, check=True)
File "/public/home/ymwang/miniconda3/envs/gra/lib/python3.12/subprocess.py", line 571, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['/public/home/ymwang/miniconda3/envs/gra/bin/python', '/public/home/ymwang/tools/rMATS-long-main/scripts/detect_differential_isoforms.py', '--abundance', '/public/home/ymwang/PacBio/7_isoform/resultpart/samples_N2_R0_abundance.esp', '--out-dir', '/public/home/ymwang/PacBio/7_isoform/resultpart/rMats/', '--group-1', '/public/home/ymwang/PacBio/8_rMats/group_1.txt', '--group-2', '/public/home/ymwang/PacBio/8_rMats/group_2.txt', '--adj-pvalue', '0.05', '--delta-proportion', '0.1', '--num-threads', '1']' returned non-zero exit status 1.
This is very important to me and would love to hear from you