Mapping rate in round 2 0.0

[kmkocot]

I'm having an issue with the pipeline that I can't quite narrow down. Here's what's printed to the screen: wirenia@wirenia:~/Desktop/2021-04-21_Hanleya_finder$ ./run_finder.sh cat: output/alignments/Hanleya_hanleyi_mantle_round1_SJ.out.tab: No such file or directory cat: output/alignments/Hanleya_hanleyi_mantle_round2_SJ.out.tab: No such file or directory mv: cannot stat 'output/alignments/Hanleya_hanleyi_mantle_final_Log.final.out': No such file or directory cat: output/alignments/Hanleya_hanleyi_mantle_round3_SJ.out.tab: No such file or directory cat: output/alignments/Hanleya_hanleyi_mantle_round4_SJ.out.tab: No such file or directory samtools index: "output/alignments/Hanleya_hanleyi_mantle_final.sortedByCoord.out.bam" is in a format that cannot be usefully indexed samtools index: "output/alignments/Hanleya_hanleyi_mantle_final.sortedByCoord.out.bam" is in a format that cannot be usefully indexed [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). Can not open output/alignments/Hanleya_hanleyi_mantle_final.sortedByCoord.out.bam. mv: cannot stat 'output/assemblies_psiclass_modified/combined/psiclass_output_sample_0.gtf': No such file or directory mv: cannot stat 'output/assemblies_psiclass_modified/combined/psiclass_output_vote.gtf': No such file or directory Traceback (most recent call last): File "/home/wirenia/finder/finder", line 641, in <module> main() File "/home/wirenia/finder/finder", line 602, in main orchestrateGeneModelPrediction(options,logger_proxy,logging_mutex) File "/home/wirenia/finder/finder", line 415, in orchestrateGeneModelPrediction findTranscriptsInEachSampleNotReportedInCombinedAnnotations(options,logger_proxy,logging_mutex) File "/home/wirenia/finder/scripts/findTranscriptsInEachSampleNotReportedInCombinedAnnotations.py", line 17, in findTranscriptsInEachSampleNotReportedInCombinedAnnotations combined_transcript_info=readAllTranscriptsFromGTFFileInParallel([combined_gtf_filename,"combined","combined"])[0] File "/home/wirenia/finder/scripts/fileReadWriteOperations.py", line 232, in readAllTranscriptsFromGTFFileInParallel fhr=open(gtf_filename,"r") FileNotFoundError: [Errno 2] No such file or directory: 'output/assemblies_psiclass_modified/combined/combined.gtf'

progress.log says: 2021-04-23 00:46:46,664 - finder - INFO - Software paths have been set 2021-04-23 00:47:07,129 - finder - INFO - Generating STAR index 2021-04-23 01:09:17,755 - finder - INFO - STAR index generation complete 2021-04-23 01:09:17,786 - finder - INFO - Generating OLego index 2021-04-23 02:16:37,614 - finder - INFO - OLego index built 2021-04-23 02:16:37,648 - finder - INFO - validateCommandLineArguments execution successful 2021-04-23 02:16:37,676 - finder - INFO - Metadata information created 2021-04-23 02:16:37,676 - finder - INFO - readMetaDataFile execution successful 2021-04-23 02:16:37,689 - finder - INFO - expandGzippedFiles execution successful 2021-04-23 02:16:37,717 - finder - INFO - Starting FINDER from None checkpoint 2021-04-23 02:16:37,718 - finder - INFO - Program params - Namespace(addUTR=True, checkpoint=None, compressed_data_files=None, cpu='35', error_corrected_raw_data='output/raw_data_error_corrected', exonerate_gff3='protein_evidence.gff3', files_for_ncrna={'mature_ATGC': '/home/wirenia/finder/dep/mature_ATGC.fa'}, final_GTF_files='output/final_GTF_files', genome='final.purged.fa.PolcaCorrected.fa.masked', genome_dir_olego='output/indices/olego_index', genome_dir_star='output/indices/star_index_without_transcriptome', indices='output/indices', md=None, metadatafile='metadata.csv', mrna_md={'mantle': {'Hanleya_hanleyi_mantle': {'bioproject': 'DUMMY', 'condition': 'mantle', 'Date': '1/12/17', 'Ended': 'PE', 'desc': 'cDNA;Illumina HiSeq 2500', 'read_length': '101', 'error_corrected': 0, 'location_directory': '/home/wirenia/Desktop/2021-04-21_Hanleya_finder', 'downloaded_from_NCBI': 0}}}, no_cleanup=False, output_assemblies_psiclass_terminal_exon_length_modified='output/assemblies_psiclass_modified', output_braker='output/braker', output_directory='output', output_fasta_N_removed='output/raw_fasta_N_removed', output_rcorrector=None, output_sample_fastq=None, output_star='output/alignments', paired_end_adapterfile=None, perform_post_completion_data_cleanup=False, preserve_raw_input_data=False, protein='protein_evidence.fas', raw_data_downloaded_from_NCBI='output/raw_data_downloaded_from_NCBI', record_time={}, run_tests=False, single_end_adapterfile=None, skip_cpd=False, smrna_md={}, softwares={'psiclass': '/home/wirenia/finder/dep/psiclass_terminal_exon_length_modified/psiclass', 'junc': '/home/wirenia/finder/dep/psiclass_terminal_exon_length_modified//junc', 'subexon-info': '/home/wirenia/finder/dep/psiclass_terminal_exon_length_modified//subexon-info', 'addXS': '/home/wirenia/finder/dep/psiclass_terminal_exon_length_modified//addXS', 'fastq-sample': '/home/wirenia/finder/dep/fastq-tools-0.8/scripts/fastq-sample', 'download_and_dump_fastq_from_SRA': '/home/wirenia/finder/dep/../utils/downloadAndDumpFastqFromSRA.py', 'transferGenomicNucleotideCountsToTranscriptome': '/home/wirenia/finder/dep/../scripts/transferGenomicNucleotideCountsToTranscriptome.py', 'find_exonic_troughs': '/home/wirenia/finder/dep/../scripts/find_exonic_troughs.R', 'olego': '/home/wirenia/finder/dep/olego/olego', 'olegoindex': '/home/wirenia/finder/dep/olego/olegoindex', 'mergePEsam.pl': '/home/wirenia/finder/dep/olego/mergePEsam.pl', 'xa2multi': '/home/wirenia/finder/dep/olego/xa2multi.pl', 'gmst': '/home/wirenia/finder/dep/gmst.pl', 'prodigal': '/home/wirenia/finder/dep/Prodigal/prodigal', 'canon-gff3': '/home/wirenia/finder/dep/canon-gff3', 'convert_exonerate_gff_to_gtf': '/home/wirenia/finder/dep/../utils/convert_exonerate_gff_to_gtf.py', 'augustus_main_dir': '/home/wirenia/finder/dep/Augustus', 'braker': '/home/wirenia/finder/dep/BRAKER/scripts/braker.pl', 'GENEMARK_PATH': '/home/wirenia/finder/dep/gmes_linux_64', 'AUGUSTUS_CONFIG_PATH': 'output/braker/Augustus/config', 'AUGUSTUS_BIN_PATH': 'output/braker/Augustus/bin', 'AUGUSTUS_SCRIPTS_PATH': 'output/braker/Augustus/scripts', 'GUSHR_PATH': '/home/wirenia/finder/dep/GUSHR'}, space_saved=None, temp_dir='output/temp', total_space=None, verbose=3) 2021-04-23 02:16:37,719 - finder - INFO - Started processing data for mantle 2021-04-23 02:16:37,731 - finder - INFO - Downloading missing data from NCBI started 2021-04-23 02:16:37,731 - finder - INFO - Downloading missing data from NCBI finished for mantle 2021-04-23 02:16:38,384 - finder - INFO - STAR Round1 run for Hanleya_hanleyi_mantle completed 2021-04-23 02:16:38,385 - finder - INFO - Mapping of reads for round1 completed for mantle 2021-04-23 02:16:38,629 - finder - INFO - Selecting high confidence junctions after round1 mapping completed for mantle 2021-04-23 02:16:38,665 - finder - INFO - Raw read download from NCBI cleanup completed for mantle 2021-04-23 02:16:38,686 - finder - INFO - STAR Round2 run for Hanleya_hanleyi_mantle completed 2021-04-23 02:16:38,687 - finder - INFO - Mapping of reads for round2 completed for mantle 2021-04-23 02:16:38,888 - finder - INFO - Selecting high confidence junctions after round2 mapping completed for mantle 2021-04-23 02:16:38,889 - finder - INFO - Mapping rate in round2 mantle Hanleya_hanleyi_mantle 0.0 2021-04-23 02:16:38,890 - finder - INFO - Resorting to alignment with relaxed parameters for these runs due to poor mapping Hanleya_hanleyi_mantle 2021-04-23 02:16:38,975 - finder - INFO - STAR relaxed alignment run for Hanleya_hanleyi_mantle completed 2021-04-23 02:16:38,976 - finder - INFO - Mapping of reads for round3 completed for mantle 2021-04-23 02:16:39,005 - finder - INFO - Selecting high confidence junctions after round3 mapping completed for mantle 2021-04-23 02:16:39,006 - finder - INFO - Mapping of reads for round4 completed for mantle 2021-04-23 02:16:39,033 - finder - INFO - Selecting high confidence junctions after round4 mapping completed for mantle 2021-04-23 02:16:39,034 - finder - INFO - Mapping with OLego for micro-exon detection completed for mantle 2021-04-23 02:16:39,453 - finder - INFO - Merging of alignments from all rounds of mapping completed for mantle 2021-04-23 02:16:39,518 - finder - INFO - Removing intermediate alignment files completed for mantle 2021-04-23 02:16:39,528 - finder - INFO - Mapping of all runs completed for mantle 2021-04-23 02:16:40,360 - finder - INFO - Information collection about alignments completed 2021-04-23 02:16:43,663 - finder - INFO - Generation of assemblies with PsiCLASS completed

The onlly files in /output/temp/ are download_these_runs and finding_finder

The *relaxed.error file says: `EXITING because of FATAL ERROR: could not open genome file output/indices/star_index_without_transcriptome//genomeParameters.txt SOLUTION: check that the path to genome files, specified in --genomeDir is correct and the files are present, and have user read permsissions

Apr 23 02:16:38 ...... FATAL ERROR, exiting`

My genome file name is correctly specified in the input script.

Any ideas?

Thanks! Kevin