powerpak/pathospot-compare

NoMethodError: undefined method `map' for nil:NilClass

Opened this issue · 1 comments

rainwala commented

Just after the cluster calcualtion stage, the rake all command fails, with:

Sketching out.repeat_mask/SAMPLE606-636_93_barcode23_consensus_short-name.repeat_mask.fasta...
Writing to out.repeat_mask.msh...
Calculating Mash distance matrix: 100%|████████████████████████████████████████████████████████████████████| 374/374 [00:13<00:00, 26.75it/s]
Constructing clusters: 100%|██████████████████████████████████████████████████████████████████████| 139502/139502 [00:08<00:00, 15582.42it/s]
rake aborted!
NoMethodError: undefined method `map' for nil:NilClass
Did you mean?  tap
/vagrant/Rakefile:282:in `parsnp_ggr_to_parsnp_inputs'
/vagrant/Rakefile:287:in `block in <top (required)>'
/var/lib/gems/2.3.0/gems/rake-13.0.1/exe/rake:27:in `<top (required)>'
Tasks: TOP => all => parsnp => out.2020-05-31.parsnp.vcfs.npz
(See full trace by running task with --trace)
rainwala commented

Weirdly, when I ran it again with trace as suggested (rake all --trace), it seemed to complete just fine!

`mkdir -p out.3.parsnp
WARN: Deleting extraneous files/symlinks in out.3.clust before running parsnp
rm out.3.clust/sample_31-55_barcode19_consensus_short-name.repeat_mask.fasta out.3.clust/SAMPLE142-174_88_barcode12_consensus_short-name.repeat_mask.fasta out.3.clust/SAMPLE466-506-90_barcode03_consensus_short-name.repeat_mask.fasta out.3.clust/sample_31-55_barcode18_consensus_short-name.repeat_mask.fasta out.3.clust/sample_31-55_barcode16_consensus_short-name.repeat_mask.fasta out.3.clust/Sample4_30_721_barcode22_consensus_short-name.repeat_mask.fasta out.3.clust/SAMPLE511-545_91_barcode09_consensus_short-name.repeat_mask.fasta out.3.clust/Sample4_30_721_barcode01_consensus_short-name.repeat_mask.fasta out.3.clust/Sample547_576_234_720_barcode15_consensus_short-name.repeat_mask.fasta out.3.clust/SAMPLE19-551_700-704_730-738_309_347_76_barcode12_consensus_short-name.repeat_mask.fasta
|--Parsnp v1.2--|
For detailed documentation please see --> http://harvest.readthedocs.org/en/latest

SETTINGS:
|-refgenome: out.3.clust/SAMPLE142-174_88_barcode02_consensus_short-name.repeat_mask.fasta
|-aligner: libMUSCLE
|-seqdir: out.3.clust
|-outdir: out.3.parsnp
|-OS: Linux
|-threads: 32
*****************************`

`<>

-->Reading Genome (asm, fasta) files from out.3.clust..
|->[OK]
-->Reading Genbank file(s) for reference (.gbk) ..
|->[WARNING]: no genbank file provided for reference annotations, skipping..
-->Running Parsnp multi-MUM search and libMUSCLE aligner..
|->[OK]
-->Running PhiPack on LCBs to detect recombination..
|->[SKIP]
-->Reconstructing core genome phylogeny..
|->[OK]
-->Creating Gingr input file..
|->[OK]
-->Calculating wall clock time..
|->Aligned 74 genomes in 2.04 seconds

<<Parsnp finished! All output available in out.3.parsnp>>

Validating output directory contents...
1)parsnp.tree: newick format tree [OK]
2)parsnp.ggr: harvest input file for gingr (GUI) [OK]
3)parsnp.xmfa: XMFA formatted multi-alignment [OK]`

** Execute out.3.parsnp/parsnp.vcf Loading out.3.parsnp/parsnp.ggr... Writing parsnp.complete.vcf... ** Execute out.2020-05-31.parsnp.vcfs.npz INFO: 4 VCF files will be processed. Reading VCF file: 100%|█████████████████████████████████████████████████████████████████████████████████| 111/111 [00:00<00:00, 27483.34it/s] WARN: Couldn't find .fasta + .bed annotations for SAMPLE142-174_88_barcode04_consensus_short-name Reading VCF file: 100%|█████████████████████████████████████████████████████████████████████████████████| 103/103 [00:00<00:00, 28072.86it/s] WARN: Couldn't find .fasta + .bed annotations for SAMPLE142-174_88_barcode09_consensus_short-name Reading VCF file: 100%|█████████████████████████████████████████████████████████████████████████████████| 140/140 [00:00<00:00, 26768.90it/s] WARN: Couldn't find .fasta + .bed annotations for SAMPLE19-551_700-704_730-738_309_347_76_barcode02_consensus_short-name Reading VCF file: 100%|█████████████████████████████████████████████████████████████████████████████████| 890/890 [00:00<00:00, 37176.51it/s] WARN: Couldn't find .fasta + .bed annotations for SAMPLE142-174_88_barcode02_consensus_short-name

** Invoke out.2020-05-31.parsnp.heatmap.json (first_time) ** Invoke out.repeat_mask.msh.clusters.tsv (not_needed) ** Invoke out.0.parsnp/parsnp.tsv (first_time) ** Invoke out.0.parsnp/parsnp.vcf (not_needed) ** Invoke out.0.parsnp/parsnp.clean.nwk (first_time) ** Invoke out.0.parsnp/parsnp.ggr (not_needed) ** Execute out.0.parsnp/parsnp.clean.nwk ** Execute out.0.parsnp/parsnp.tsv Reading VCF file: 100%|█████████████████████████████████████████████████████████████████████████████████| 111/111 [00:00<00:00, 26328.55it/s] Calculating SNV distances: 100%|█████████████████████████████████████████████████████████████████████████| 100/100 [00:00<00:00, 6021.19it/s] ** Invoke out.0.parsnp/parsnp.clean.nwk (not_needed) ** Invoke out.1.parsnp/parsnp.tsv (first_time) ** Invoke out.1.parsnp/parsnp.vcf (not_needed) ** Invoke out.1.parsnp/parsnp.clean.nwk (first_time) ** Invoke out.1.parsnp/parsnp.ggr (not_needed) ** Execute out.1.parsnp/parsnp.clean.nwk ** Execute out.1.parsnp/parsnp.tsv Reading VCF file: 100%|█████████████████████████████████████████████████████████████████████████████████| 103/103 [00:00<00:00, 27099.07it/s] Calculating SNV distances: 100%|█████████████████████████████████████████████████████████████████████████| 100/100 [00:00<00:00, 6145.95it/s] ** Invoke out.1.parsnp/parsnp.clean.nwk (not_needed) ** Invoke out.2.parsnp/parsnp.tsv (first_time) ** Invoke out.2.parsnp/parsnp.vcf (not_needed) ** Invoke out.2.parsnp/parsnp.clean.nwk (first_time) ** Invoke out.2.parsnp/parsnp.ggr (not_needed) ** Execute out.2.parsnp/parsnp.clean.nwk ** Execute out.2.parsnp/parsnp.tsv Reading VCF file: 100%|█████████████████████████████████████████████████████████████████████████████████| 140/140 [00:00<00:00, 29251.90it/s] Calculating SNV distances: 100%|█████████████████████████████████████████████████████████████████████████| 100/100 [00:00<00:00, 6050.38it/s] ** Invoke out.2.parsnp/parsnp.clean.nwk (not_needed) ** Invoke out.3.parsnp/parsnp.tsv (first_time) ** Invoke out.3.parsnp/parsnp.vcf (not_needed) ** Invoke out.3.parsnp/parsnp.clean.nwk (first_time) ** Invoke out.3.parsnp/parsnp.ggr (not_needed) ** Execute out.3.parsnp/parsnp.clean.nwk ** Execute out.3.parsnp/parsnp.tsv Reading VCF file: 100%|█████████████████████████████████████████████████████████████████████████████████| 890/890 [00:00<00:00, 33508.95it/s] Calculating SNV distances: 100%|███████████████████████████████████████████████████████████████████████████| 74/74 [00:00<00:00, 3888.43it/s] ** Invoke out.3.parsnp/parsnp.clean.nwk (not_needed) ** Execute out.2020-05-31.parsnp.heatmap.json ** Execute parsnp ** Invoke epi (first_time) ** Invoke check ** Invoke out.2020-05-31.epi.heatmap.json (first_time) ** Execute out.2020-05-31.epi.heatmap.json ** Execute epi ** Invoke encounters (first_time) ** Invoke check ** Invoke out.2020-05-31.encounters.tsv (first_time) ** Execute out.2020-05-31.encounters.tsv ** Execute encounters ** Execute all