search

cbcrg / piper-nf

RNA mapping pipeline
GNU General Public License v3.0
18 stars 5 forks source link

BLAST Database error: No alias or index file found for nucleotide database [ncbi-blast-db/db] in search path #2

Open stevekm opened 6 years ago

stevekm commented 6 years ago

I was trying to run this pipeline as described, using the Docker container, but get this error:

$ ./nextflow run cbcrg/piper-nf -with-docker
N E X T F L O W  ~  version 0.26.4
Launching `cbcrg/piper-nf` [evil_minsky] - revision: 4be8aafcf0 [master]
Using genomes-db path: /Users/steve/projects/piper-nf/db
P I P E R - RNA mapping pipeline - ver 1.4.2
============================================
query               : /Users/steve/.nextflow/assets/cbcrg/piper-nf/tutorial/5_RNA_queries.fa
genomes-db          : /Users/steve/projects/piper-nf/db
query-chunk-size    : 1000
genomes-file        : -
genomes-list        : -
genomes-folder      : /Users/steve/.nextflow/assets/cbcrg/piper-nf/tutorial/genomes/
result-dir          : result
blast-strategy      : ncbi-blast
align-strategy      : slow_pair
exonerate-success:  : 1
exonerate-mode:     : 1000
exonerate-chunk-size: 2500
repeat-cov          : 20

Validating genome: briggsae -- file: /Users/steve/.nextflow/assets/cbcrg/piper-nf/tutorial/genomes/briggsae/c_briggsae.WS227.genomic_softmasked.fa
Validating genome: elegans -- file: /Users/steve/.nextflow/assets/cbcrg/piper-nf/tutorial/genomes/elegans/c_elegans.WS227.genomic_softmasked.fa
Splitting query file: /Users/steve/.nextflow/assets/cbcrg/piper-nf/tutorial/5_RNA_queries.fa ..
Created 1 input chunks to path: /Users/steve/projects/piper-nf/work/9a/d3f9e7eeaa0f13b191a2748dad34cf
[warm up] executor > local
[skipping] Stored process > formatBlast (1)
[skipping] Stored process > formatBlast (2)
[3e/b0d2d0] Submitted process > formatChr (2)
[0d/15ff8e] Submitted process > blast (1)
[b5/83029f] Submitted process > blast (2)
[e5/99690a] Submitted process > formatChr (1)
ERROR ~ Error executing process > 'blast (2)'

Caused by:
  Process `blast (2)` terminated with an error exit status (2)

Command executed:

  fmt='6 qseqid sseqid evalue score qgi bitscore length nident positive mismatch pident ppos qacc gaps gaopen qaccver qlen qframe qstart qend sframe sstart send'
  blastn -db ncbi-blast-db/db -query blastQuery -outfmt "$fmt" -num_threads 1 > elegans.mf2

Command exit status:
  2

Command output:
  (empty)

Command error:
  a3ed95caeb02: Waiting
  81af76ff1eef: Waiting
  0e9211f73d40: Waiting
  b3cc1d3383ee: Waiting
  c21247be3b57: Waiting
  9c240be878fb: Waiting
  5e61605063f5: Verifying Checksum
  5e61605063f5: Download complete
  4422a4c28c57: Verifying Checksum
  4422a4c28c57: Download complete
  a3ed95caeb02: Verifying Checksum
  a3ed95caeb02: Download complete
  0e9211f73d40: Verifying Checksum
  0e9211f73d40: Download complete
  81af76ff1eef: Verifying Checksum
  81af76ff1eef: Download complete
  c21247be3b57: Verifying Checksum
  c21247be3b57: Download complete
  f9d590e330de: Download complete
  3addeeabbda6: Verifying Checksum
  3addeeabbda6: Download complete
  39a402810303: Verifying Checksum
  39a402810303: Download complete
  9c240be878fb: Verifying Checksum
  9c240be878fb: Download complete
  cb3849ddee7b: Verifying Checksum
  cb3849ddee7b: Download complete
  cc15a4015f34: Verifying Checksum
  cc15a4015f34: Download complete
  5539a8911461: Verifying Checksum
  5539a8911461: Download complete
  f9d590e330de: Pull complete
  5e61605063f5: Pull complete
  4422a4c28c57: Pull complete
  a3ed95caeb02: Pull complete
  0e9211f73d40: Pull complete
  b3cc1d3383ee: Verifying Checksum
  b3cc1d3383ee: Download complete
  b3cc1d3383ee: Pull complete
  81af76ff1eef: Pull complete
  c21247be3b57: Pull complete
  9c240be878fb: Pull complete
  3addeeabbda6: Pull complete
  39a402810303: Pull complete
  cb3849ddee7b: Pull complete
  cc15a4015f34: Pull complete
  5539a8911461: Pull complete
  Digest: sha256:2764ad180360e5a772fef7218842a2c3bb833568770c9d0f01ea1bf1fcc02f5b
  Status: Image is up to date for cbcrg/piper-nf:latest
  BLAST Database error: No alias or index file found for nucleotide database [ncbi-blast-db/db] in search path [/Users/steve/projects/piper-nf/work/b5/83029f6d17fd3bdbe1023bd073d990::]

Work dir:
  /Users/steve/projects/piper-nf/work/b5/83029f6d17fd3bdbe1023bd073d990

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '.nextflow.log' file for details
WARN: Killing pending tasks (3)

Any ideas? Is there something missing from the Docker container?

pditommaso commented 6 years ago

mm, likely something is messed up in the blast db folder folder created in the previous step. Delete the folder /Users/steve/projects/piper-nf/db and launch it again. If the error persists include the complete log again.