mckellardw/ref_snake

Snakemake workflow to automatically build and organize reference genomes for common alignment tasks

ref_snake's Issues

Error in 1_kallisto.smk

I'm pretty sure all the executable paths are updated now for my configuration. Everything runs fine until I get to line 35 in 1_kallisto.smk (rule kb_velocity). I am getting the error below and am finding the error about a corrupted file a little cryptic. Any suggestions?

Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 16 Rules claiming more threads will be scaled down. Select jobs to execute... Waiting at most 5 seconds for missing files. MissingOutputException in rule kb_velocity in file /gpfs/commons/groups/vickovic_lab/cslater/code/ref_snake/rules/1_kallisto.smk, line 35: Job 0 completed successfully, but some output files are missing. Missing files after 5 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait: out/homo_sapiens/genome/kb_velo/transcriptome.idx Removing output files of failed job kb_velocity since they might be corrupted: out/homo_sapiens/genome/kb_velo, out/homo_sapiens/genome/kb_velo/t2g.txt, out/homo_sapiens/genome/kb_velo/cdna.fa, out/homo_sapiens/genome/kb_velo/intron.fa, out/homo_sapiens/genome/kb_velo/cdna.t2c, out/homo_sapiens/genome/kb_velo/intron.t2c Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Removing output files of failed job kb_velocity since they might be corrupted: out/homo_sapiens/genome/kb_velo Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2024-02-15T202658.101792.snakemake.log

2024-02-15T202658.101792.snakemake.log

custom references

• For multi-species references (barnyard expts), custom references, or non-ensembl annotations (gencode!), we need a way to specify inputs
• Use a sample sheet style, where either a list of species or a list of files are passed to populate the inputs for the references

bowtie2 compatibility

Add biotype-specific references

Subset out the gtf(s) by biotype so that biotype-specific references can be built. Useful for computational rRNA depletion