Closed kubu4 closed 9 months ago
Here's my command:
ShortStack \ --genomefile "${genome_fasta}" \ --readfile ${trimmed_fastqs_list} \ --known_miRNAs ${deep_dive_data_dir}/${mirbase_mature_fasta_version} \ --dn_mirna \ --threads ${threads} \ --outdir ${output_dir_top}/ShortStack
Error message:
ShortStack version 4.0.2 Beginning run Options: { 'adapter': None, 'align_only': False, 'autotrim': False, 'autotrim_key': 'TCGGACCAGGCTTCATTCCCC', 'bamfile': None, 'dicermax': 24, 'dicermin': 21, 'dn_mirna': True, 'genomefile': '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fa', 'known_miRNAs': '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/data/mirbase-mature-v22.1.fa', 'locifile': None, 'locus': None, 'mincov': 1, 'mmap': 'u', 'nohp': False, 'outdir': '/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/13-Apul-sRNAseq-ShortStack/ShortStack', 'pad': 200, 'readfile': [], 'show_secondaries': False, 'strand_cutoff': 0.8, 'threads': 40} Required executable RNAfold : /home/sam/programs/mambaforge/envs/ShortStack4_env/bin/RNAfold Required executable strucVis : /home/sam/programs/mambaforge/envs/ShortStack4_env/bin/strucVis Required executable bowtie : /home/sam/programs/mambaforge/envs/ShortStack4_env/bin/bowtie Required executable bowtie-build : /home/sam/programs/mambaforge/envs/ShortStack4_env/bin/bowtie-build Required executable ShortTracks : /home/sam/programs/mambaforge/envs/ShortStack4_env/bin/ShortTracks Required executable wigToBigWig : /home/sam/programs/mambaforge/envs/ShortStack4_env/bin/wigToBigWig Required executable samtools : /home/sam/programs/mambaforge/envs/ShortStack4_env/bin/samtools Beginning alignment phase Creating browser tracks by readlength and strand using ShortTracks Traceback (most recent call last): File "/home/sam/programs/mambaforge/envs/ShortStack4_env/bin/ShortStack", line 3582, in <module> merged_bam, read_count = align(args, fai, trimmed_files) File "/home/sam/programs/mambaforge/envs/ShortStack4_env/bin/ShortStack", line 792, in align callShortTracks(final_bams[0], 'readlength', True) IndexError: list index out of range
Do you happen to have any suggestions on how to troubleshoot this? Thanks in advance for any ideas you might have!
Gah! I'm now seeing (of course, as soon I created the issue) that the readfile list is empty! Sorry for the trouble!
Here's my command:
Error message:
Do you happen to have any suggestions on how to troubleshoot this? Thanks in advance for any ideas you might have!