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ratschlab
IndexError when running spladder
- spladder version:3.0.1
- Python version:3.6
- Operating System:CentOS
Description
I use spladder to detect splicing events in one sample with bam file, The command is: spladder build --parallel 20 -b *bam -a gencode.v32.annotation.gtf -o .
But it shows index error below. And one of the file (merge_graphs_mult_exon_skip_C3.confirmed.txt.gz) has incomplete information. The last line is only "chr2 + mult_exon_skip.4684 3 ENSG00000064012.21" and contains no alternative splicing events.
What I Did
command(s)
1. STAR --genomeDir ./STAR_index/ --readFilesIn XX.R1.fastq XX.R2.fastq --runThreadN 20 --outFilterMultimapScoreRange 1 --outFilterMultimapNmax 20 --outFilterMismatchNmax 10 --alignIntronMax 500000 --alignMatesGapMax 1000000 --sjdbScore 2 --alignSJDBoverhangMin 1 --genomeLoad NoSharedMemory --limitBAMsortRAM 70000000000 --readFilesCommand cat --outFilterMatchNminOverLread 0.33 --outFilterScoreMinOverLread 0.33 --sjdbOverhang 100 --outSAMstrandField intronMotif --outSAMattributes NH HI NM MD AS XS --sjdbGTFfile gencode.v32.annotation.gtf --limitSjdbInsertNsj 2000000 --outSAMunmapped None --outSAMtype BAM SortedByCoordinate --outSAMheaderHD @HD VN:1.4 --twopassMode Basic --outSAMmultNmax 1 --quantMode TranscriptomeSAM --outFileNamePrefix .
2. spladder build --parallel 20 -b *bam -a gencode.v32.annotation.gtf -o .
If there was a crash, please include the traceback here.
``Reporting confirmed mult_exon_skip events:
writing mult_exon_skip events in gff3 format to .//merge_graphs_mult_exon_skip_C3.confirmed.gff3
writing mult_exon_skip events in flat txt format to .//merge_graphs_mult_exon_skip_C3.confirmed.txt.gz
Traceback (most recent call last):
File "/data/myang9/software/miniconda3/bin/spladder", line 8, in <module>
sys.exit(main())
File "/data/myang9/software/miniconda3/lib/python3.9/site-packages/spladder/spladder.py", line 229, in main
options.func(options)
File "/data/myang9/software/miniconda3/lib/python3.9/site-packages/spladder/spladder_build.py", line 163, in spladder
analyze_events(event_type, options.bam_fnames, options)
File "/data/myang9/software/miniconda3/lib/python3.9/site-packages/spladder/alt_splice/analyze.py", line 191, in analyze_events
write_events_txt(fn_out_conf_txt, options.samples[sample_idx], events_all, fn_out_count, event_idx=confirmed_idx)
File "/data/myang9/software/miniconda3/lib/python3.9/site-packages/spladder/alt_splice/write.py", line 89, in write_events_txt
counts = event_counts_chunk[:, :, i - chunk_idx_event[0]]
IndexError: index 1344 is out of bounds for axis 2 with size 1113`
I have met the same error using command: spladder build -b xxx.bam -a gencode.v39.annotation.gtf -o xxx
which says:
Reporting confirmed exon_skip events:
writing exon_skip events in gff3 format to xxx/merge_graphs_exon_skip_C3.confirmed.gff3
writing exon_skip events in flat txt format to xxx/merge_graphs_exon_skip_C3.confirmed.txt.gz
Traceback (most recent call last):
File "/usr/local/bin/spladder", line 11, in
I'm running into this as well, unfortunately. I placed a breakpoint() around the
counts = event_counts_chunk[:, :, i - chunk_idx_event[0]]
line, but can't really figure out how it works.
@akahles @warrenmcg @izcram @ratsch What would you need to reproduce this? Would the following files be sufficient:
- merge_graphs_exon_skip_C3.confirmed.pickle
- merge_graphs_exon_skip_C3.counts.hdf5
- merge_graphs_exon_skip_C3.pickle
Thanks!
I got this same problem while testing a sample of a bam, but when I tried the complete bam it worked ok. I just mention it because it may help to figure out the problem.
Has anyone resolved this? I have it both on small datasets and the whole BAM file. I discovered that the problem occurs mainly when aligning with STAR, but not when using BWA. Is there something that needs to be considered?
It occurs on exon_skip events:
Reporting confirmed exon_skip events:
writing exon_skip events in gff3 format to testspladderSTAR_exonskip/merge_graphs_exon_skip_C3.confirmed.gff3
writing exon_skip events in flat txt format to testspladderSTAR_exonskip/merge_graphs_exon_skip_C3.confirmed.txt.gz
Traceback (most recent call last):
File "/home/sej9799/mambaforge/envs/spladder/bin/spladder", line 8, in
I solved that for "my" case.
Context: I use a BAM file with a single chromosome for testing. Possible cause: The GTF annotation file refers chromosomes / contigs that are not present in the BAM file. Solution: slice the GTF to include only the chromosomes / contigs present in the BAM.
Thanks a lot for reporting this. I have difficulty reproducing the issue. Would one of you be able to provide a minimal failing example? This would greatly speed up the debugging on my end. Usually, it should not be a problem if the chromosome/contig sets in alignment and annotation files are not the same. As long as the intersection is not empty, SplAdder should generate output.
Best, Andre
So this basiclally means that no output can be generated? Is there a way to generate normal normal even when no output is going to be generated?