flair collapse failing but error message isn't informative

[markram4]

Copy and paste the exact command you tried to run flair collapse -g /cluster/pixstor/slotkinr-lab/mkramer/annotations/arabidopsis/At_v2/At_array.v2.RUBY.fa -q ruby_round1_merge.non_pA_all_corrected.bed -r /cluster/pixstor/slotkinr-lab/mkramer/projects/target_capture/ruby_round1/data/4_cutadapt_trim_5p_3p_adapters/5p/ruby_round1_merged.trimmed.3p.trimmed.5p.fastq --gtf /cluster/pixstor/slotkinr-lab/mkramer/annotations/arabidopsis/At_v2/At_array.v2.Arabidopsis_thaliana.TAIR10.56.targetChr.all.flair.gtf --output /cluster/pixstor/slotkinr-lab/mkramer/projects/target_capture/ruby_round1/data/6_minimap/2_map_to_capture/output/mapped_to_targets/flair/02_collapse/ruby_round1_merge.non_pA_all_corrected --generate_map --trust_ends --no_gtf_end_adjustment --max_ends 10000 --threads 8 --temp_dir /cluster/pixstor/slotkinr-lab/mkramer/projects/target_capture/tmp --keep_intermediate &

How did you install Flair? (We'd prefer it if you used one of the top two because they are the least likely to have package compatibility problems.)

1. bioconda (e.g. conda create -n flair -c conda-forge -c bioconda flair)

What happened?

Read data extracted
Single-exon genes grouped, collapsing
Renaming isoforms using gtf
Aligning reads to first-pass isoform reference
[M::mm_idx_gen::0.023*1.07] collected minimizers
[M::mm_idx_gen::0.027*1.72] sorted minimizers
[M::main::0.027*1.72] loaded/built the index for 819 target sequence(s)
[M::mm_mapopt_update::0.028*1.70] mid_occ = 72
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 819
[M::mm_idx_stat::0.028*1.68] distinct minimizers: 24665 (27.88% are singletons); average occurrences: 7.179; average spacing: 5.401; total length: 956397
[M::worker_pipeline::55.314*7.42] mapped 749805 sequences
[M::worker_pipeline::95.711*7.57] mapped 749823 sequences
[M::worker_pipeline::137.787*7.64] mapped 730521 sequences
[M::worker_pipeline::181.483*7.68] mapped 882797 sequences
[M::worker_pipeline::217.464*7.69] mapped 1244651 sequences
[M::worker_pipeline::268.611*7.71] mapped 1112451 sequences
[M::worker_pipeline::312.232*7.72] mapped 1038374 sequences
[M::worker_pipeline::356.258*7.73] mapped 1002897 sequences
[M::worker_pipeline::409.759*7.73] mapped 1084268 sequences
[M::worker_pipeline::464.462*7.64] mapped 1132555 sequences
[M::worker_pipeline::514.777*7.65] mapped 1181024 sequences
[M::worker_pipeline::770.447*5.86] mapped 1307645 sequences
[M::worker_pipeline::849.144*5.81] mapped 929774 sequences
Failed at counting step for isoform read support```
We know it's ugly but we promise it helps us solve problems faster.

**What else do we need to know?**
Go ahead, every bit helps.