Finder failed to analy

[jb018]

Hi Sagnik

I'm trying to run finder on the provided example data. However, it's just failing and trowing the following error.

Any help is appreciated.

finder -no_cleanup -mf test_metadata.csv -n 30 -gdir_star $PWD/star_index_without_transcriptome -out_dir $PWD/FINDER_test_ARATH -g $PWD/Arabidopsis_thaliana.TAIR10.dna_sm.toplevel.fa -p $PWD/uniprot_ARATH.fasta -gdir_olego olego_index -preserve [E::hts_open_format] Failed to open file /data/apps/finder/example/FINDER_test_ARATH/alignments/dummy_data2_olego_round5.sorted.bam samtools merge: fail to open "/data/apps/finder/example/FINDER_test_ARATH/alignments/dummy_data2_olego_round5.sorted.bam": No such file or directory [E::hts_open_format] Failed to open file /data/apps/finder/example/FINDER_test_ARATH/alignments/dummy_data1_olego_round5.sorted.bam samtools merge: fail to open "/data/apps/finder/example/FINDER_test_ARATH/alignments/dummy_data1_olego_round5.sorted.bam": No such file or directory [E::hts_open_format] Failed to open file /data/apps/finder/example/FINDER_test_ARATH/alignments/dummy_data1_final.sortedByCoord.out.bam samtools index: failed to open "/data/apps/finder/example/FINDER_test_ARATH/alignments/dummy_data1_final.sortedByCoord.out.bam": No such file or directory [E::hts_open_format] Failed to open file /data/apps/finder/example/FINDER_test_ARATH/alignments/dummy_data1_final.sortedByCoord.out.bam samtools index: failed to open "/data/apps/finder/example/FINDER_test_ARATH/alignments/dummy_data1_final.sortedByCoord.out.bam": No such file or directory [E::hts_open_format] Failed to open file /data/apps/finder/example/FINDER_test_ARATH/alignments/dummy_data2_final.sortedByCoord.out.bam samtools index: failed to open "/data/apps/finder/example/FINDER_test_ARATH/alignments/dummy_data2_final.sortedByCoord.out.bam": No such file or directory [E::hts_open_format] Failed to open file /data/apps/finder/example/FINDER_test_ARATH/alignments/dummy_data2_final.sortedByCoord.out.bam samtools index: failed to open "/data/apps/finder/example/FINDER_test_ARATH/alignments/dummy_data2_final.sortedByCoord.out.bam": No such file or directory open: No such file or directory open: No such file or directory open: No such file or directory open: No such file or directory sh: line 1: 148093 Segmentation fault (core dumped) /data/apps/finder/dep/psiclass_terminal_exon_length_modified//subexon-info /data/apps/finder/example/FINDER_test_ARATH/alignments/dummy_data1_final.sortedByCoord.out.bam /data/apps/finder/example/FINDER_test_ARATH/alignments/dummy_data1_introns --noStats > /data/apps/finder/example/FINDER_test_ARATH/alignments/dummy_data1_exons sh: line 1: 148092 Segmentation fault (core dumped) /data/apps/finder/dep/psiclass_terminal_exon_length_modified//subexon-info /data/apps/finder/example/FINDER_test_ARATH/alignments/dummy_data2_final.sortedByCoord.out.bam /data/apps/finder/example/FINDER_test_ARATH/alignments/dummy_data2_introns --noStats > /data/apps/finder/example/FINDER_test_ARATH/alignments/dummy_data2_exons [E::hts_open_format] Failed to open file /data/apps/finder/example/FINDER_test_ARATH/alignments/dummy_data2_final.sortedByCoord.out.bam samtools view: failed to open "/data/apps/finder/example/FINDER_test_ARATH/alignments/dummy_data2_final.sortedByCoord.out.bam" for reading: No such file or directory [E::hts_open_format] Failed to open file /data/apps/finder/example/FINDER_test_ARATH/alignments/dummy_data1_final.sortedByCoord.out.bam samtools view: failed to open "/data/apps/finder/example/FINDER_test_ARATH/alignments/dummy_data1_final.sortedByCoord.out.bam" for reading: No such file or directory mv: cannot stat ‘/data/apps/finder/example/FINDER_test_ARATH/assemblies_psiclass_modified/combined/psiclass_output_sample_0.gtf’: No such file or directory mv: cannot stat ‘/data/apps/finder/example/FINDER_test_ARATH/assemblies_psiclass_modified/combined/psiclass_output_sample_1.gtf’: No such file or directory mv: cannot stat ‘/data/apps/finder/example/FINDER_test_ARATH/assemblies_psiclass_modified/combined/psiclass_output_vote.gtf’: No such file or directory Traceback (most recent call last): File "/data/apps/finder/finder", line 675, in main() File "/data/apps/finder/finder", line 636, in main orchestrateGeneModelPrediction(options,logger_proxy,logging_mutex) File "/data/apps/finder/finder", line 449, in orchestrateGeneModelPrediction findTranscriptsInEachSampleNotReportedInCombinedAnnotations(options,logger_proxy,logging_mutex) File "/data/apps/finder/scripts/findTranscriptsInEachSampleNotReportedInCombinedAnnotations.py", line 17, in findTranscriptsInEachSampleNotReportedInCombinedAnnotations combined_transcript_info=readAllTranscriptsFromGTFFileInParallel([combined_gtf_filename,"combined","combined"])[0] File "/data/apps/finder/scripts/fileReadWriteOperations.py", line 279, in readAllTranscriptsFromGTFFileInParallel fhr=open(gtf_filename,"r") FileNotFoundError: [Errno 2] No such file or directory: '/data/apps/finder/example/FINDER_test_ARATH/assemblies_psiclass_modified/combined/combined.gtf'

Kind regards