Testing Flair: missing file

[RDorney]

Copy and paste the exact command you tried to run ~/flair/test$ make test

How did you install Flair?

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

2. git cloned the current repository to obtain the test directory

What happened? flair align -r test_input/reads.fa --genome test_input/genome.fa -t 4 -o test_output/test.align [M::mm_idx_gen::7.1431.44] collected minimizers [M::mm_idx_gen::9.2452.02] sorted minimizers [M::main::9.2452.02] loaded/built the index for 3 target sequence(s) [M::mm_mapopt_update::10.0451.94] mid_occ = 262 [M::mm_idx_stat] kmer size: 15; skip: 5; is_hpc: 0; #seq: 3 [M::mm_idx_stat::10.5291.89] distinct minimizers: 49293178 (70.30% are singletons); average occurrences: 1.945; average spacing: 2.930; total length: 280976917 [M::worker_pipeline::12.6062.23] mapped 1883 sequences [M::main] Version: 2.24-r1122 [M::main] CMD: minimap2 -ax splice --secondary=no -t 4 test_input/genome.fa test_input/reads.fa [M::main] Real time: 12.683 sec; CPU: 28.199 sec; Peak RSS: 2.720 GB diff <(sort test_expected/test.align.bed) <(sort test_output/test.align.bed) > test_diffs/test.align.diff flair correct -q test_input/test.align.bed -j test_input/shortread_junctions.tab -f test_input/annotation.incomplete.gtf -g test_input/genome.fa -o test_output/test.correct Step 1/5: Splitting junctions from GTF by chromosome: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 55/55 [00:00<00:00, 192720.74it/s] Step 2/5: Processing additional junction file test_input/shortread_junctions.tab ...index file test_input/genome.fa.fai not found, generating... | 0/55 [00:00<?, ?it/s] Step 3/5: Preparing annotated junctions to use for correction: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 3/3 [00:00<00:00, 7584.64it/s] Step 4/5: Preparing reads for correction: 1883it [00:00, 527615.37it/s] | 0/3 [00:00<?, ?it/s] Step 5/5: Correcting Splice Sites: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 3/3 [00:01<00:00, 2.21it/s] Step 5/5: Correcting Splice Sites: 33%|█████████████████████████████████████████████████████████ | 1/3 [00:01<00:02, 1.35s/it]

diff <(sort test_expected/test.correct_all_inconsistent.bed) <(sort test_output/test.correct_all_inconsistent.bed) > test_diffs/test.correct.inconsistent.diff diff <(sort test_expected/test.correct_all_corrected.bed) <(sort test_output/test.correct_all_corrected.bed) > test_diffs/test.correct.corrected.diff flair collapse -r test_input/reads.fa -q test_input/test.corrected.bed -g test_input/genome.fa -t 4 --generate_map --temp_dir test_output/temp_collapse --keep_intermediate -f test_input/annotation.gtf -o test_output/test.collapse -p test_input/promoter_regions.bed Filtering out reads without promoter-supported TSS Annotated ends extracted from GTF Read data extracted Single-exon genes grouped, collapsing Renaming isoforms using gtf Aligning reads to first-pass isoform reference [M::mm_idx_gen::0.0011.76] collected minimizers [M::mm_idx_gen::0.0022.54] sorted minimizers [M::main::0.0022.53] loaded/built the index for 12 target sequence(s) [M::mm_mapopt_update::0.0032.45] mid_occ = 10 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 12 [M::mm_idx_stat::0.0032.38] distinct minimizers: 1443 (31.74% are singletons); average occurrences: 2.435; average spacing: 5.400; total length: 18969 [M::worker_pipeline::0.4303.78] mapped 1883 sequences [M::main] Version: 2.24-r1122 [M::main] CMD: minimap2 -a -t 4 -N 4 test_output/test.collapse.firstpass.fa test_input/reads.fa [M::main] Real time: 0.430 sec; CPU: 1.626 sec; Peak RSS: 0.018 GB Filtering isoforms by read coverage diff <(sort test_expected/test.collapse.isoforms.gtf) <(sort test_output/test.collapse.isoforms.gtf) > test_diffs/test.collapse.isoforms.gtf.diff flair quantify -r test_input/reads_manifest.txt -i test_input/test.collapse.isoforms.fa --isoform_bed test_input/test.collapse.isoforms.bed --generate_map --temp_dir test_output/test.collapse.temp --tpm --sample_id_only --check_splice --stringent -o test_output/test.quantify Writing temporary files with prefixes similar to test_output/test.collapse.temp/tmpw_n4ecmp Step 3/3. Writing counts to test_output/test.quantify.counts.tsv diff <(sort test_expected/test.quantify.tpm.tsv) <(sort test_output/test.quantify.tpm.tsv) > test_diffs/test.quantify.diff flair diffExp -q test_input/counts_matrix_diffexp.tsv -o test_output/test.diffexp -e 1 -of stat_bin() using bins = 30. Pick better value with binwidth. stat_bin() using bins = 30. Pick better value with binwidth. diff <(sort test_expected/test.diffexp.genes_deseq2_MCF7_v_A549.tsv) <(sort test_output/test.diffexp/genes_deseq2_MCF7_v_A549.tsv) > test_diffs/test.diffexp.dge.diff diff <(sort test_expected/test.diffexp.isoforms_deseq2_MCF7_v_A549.tsv) <(sort test_output/test.diffexp/isoforms_deseq2_MCF7_v_A549.tsv) > test_diffs/test.diffexp.die.diff diff <(sort test_expected/test.diffexp.isoforms_drimseq_MCF7_v_A549.tsv) <(sort test_output/test.diffexp/isoforms_drimseq_MCF7_v_A549.tsv) > test_diffs/test.diffexp.drimseq.diff flair diffSplice -i test_input/test.collapse.isoforms.bed -q test_input/counts_matrix_diffsplice.tsv --test -o test_output/test.diffsplice -of DRIMSeq testing for each AS event type diff <(sort test_output/test.diffsplice/drimseq_alt3_A_v_B.tsv) <(sort test_expected/test.diffsplice.drimseq_alt3_A_v_B.tsv) > test_diffs/test.diffsplice.alt3.diff diff <(sort test_output/test.diffsplice/diffsplice.alt3.events.quant.tsv) <(sort test_expected/test.diffsplice.alt3.events.quant.tsv) > test_diffs/test.diffsplice.alt3.quant.diff predictProductivity -i test_input/test.collapse.isoforms.bed -g test_input/annotation.gtf -f test_input/genome.fa > test_output/test.predict_productivity.bed --longestORF diff <(sort test_expected/test.predict_productivity.bedi) <(sort test_output/test.predict_productivity.bed) > test_diffs/test.predict_productivity.diff sort: cannot read: test_expected/test.predict_productivity.bedi: No such file or directory make: *** [makefile:72: test-predict-productivity] Error 1

What else do we need to know? i checked the folder and noticed I do have test.predict_productivity.bed but not as .bedi. I don't know where to find or how to make a .bedi format (flair) ryleyd@minion:~/flair/test$ ls makefile README.md test_diffs test_expected test_input test_output (flair) ryleyd@minion:~/flair/test$ ls test_expected/ test.align.bed test.correct_all_corrected.bed test.diffexp.genes_deseq2_MCF7_v_A549.tsv test.diffexp.isoforms_drimseq_MCF7_v_A549.tsv test.diffsplice.alt3.events.quant.tsv test.predict_productivity.bed test.collapse.isoforms.gtf test.correct_all_inconsistent.bed test.diffexp.isoforms_deseq2_MCF7_v_A549.tsv test.diff_iso_usage.tsv test.diffsplice.drimseq_alt3_A_v_B.tsv test.quantify.tpm.tsv

[RDorney]

there was a typo in the makefile to cause the '.bedi' instead of just '.bed'

[Jeltje]

Thanks for spotting this! I have corrected the typo; it should be available in the next release.