test.sh blast_align.sh - misses KPN.fna file

[smoe]

Hello,

When executing the test script as in

$ PATH=$PATH:/home/moeller/git/med-team/mmmulti/plasmidid/bin TEST_DATA/test.sh || true
Executing:../plasmidID -1 KPN_TEST_R1.fastq.gz -2 KPN_TEST_R2.fastq.gz -d plasmids_TEST_database.fasta -c contigs_KPN_TEST.fasta -s KPN --no-trim
Forward reads: KPN_TEST_R1.fastq.gz
Reverse reads: KPN_TEST_R2.fastq.gz
PlasmidDatabase: plasmids_TEST_database.fasta
Contigs: contigs_KPN_TEST.fasta
Options: --no-trim


------------------
Starting plasmidID version:1.6.3
------------------


CHECKING DEPENDENCIES AND MANDATORY FILES

DEPENDENCY                    STATUS
----------                    ------
blastn                       INSTALLED 
bowtie2-build                INSTALLED 
bowtie2                      INSTALLED 
bedtools                     INSTALLED 
prokka                       INSTALLED 
samtools                     INSTALLED 
mash                         INSTALLED 
circos                       INSTALLED 

Default output directory is: /home/moeller/git/med-team/mmmulti/plasmidid

Log will be saved in: /home/moeller/git/med-team/mmmulti/plasmidid/NO_GROUP/KPN/logs/plasmidID.log


No trim selected, skipping trimming step

Contigs supplied, ommiting assembly step


------------------
#Pipeline summary#
------------------
Reads R1                               KPN_TEST_R1.fastq.gz
Reads R2                               KPN_TEST_R2.fastq.gz
Will be mapped with ddbb               plasmids_TEST_database.fasta
Entries covered more than              80 %
Will be clustered by                   0.5 % identity
And used to reconstruct contigs in     contigs_KPN_TEST.fasta

 STARTING KMER FILTERING, CLUSTERING and MAPPING 


SCREENING READS WITH KMERS (Fri Jun 26 18:49:54 CEST 2020)
 Reads will be screened against database supplied for further filtering and mapping,
 this will reduce the input sequences to map against KPN

CLUSTERING SEQUENCES BY KMER DISTANCE (Fri Jun 26 18:49:59 CEST 2020)
 Sequences obtained after screen will be clustered to reduce redundancy,
 one representative, the largest, will be considered for further analysis KPN

MAPPING READS (Fri Jun 26 18:49:59 CEST 2020)
 Reads will be mapped against database supplied for further coverage calculation,
 this will determine the most likely plasmids in the sample KPN

FILTERING DATABASE BY COVERAGE (Fri Jun 26 18:51:03 CEST 2020)
 Coverage will be calculated and the entries covered more than 80%
 will pass to further analysis

 STARTING CONTIG ALIGNMENT and ANNOTATON


OBTAINING KARYOTYPE TRACKS (Fri Jun 26 18:51:05 CEST 2020)
 A file with the informatin of putative plasmid and its length will be generated.


OBTAINING COVERAGE TRACK (Fri Jun 26 18:51:05 CEST 2020)
 A bedgraph file containing mapping information for filtered plasmids will be generated.



-------------------------
#Pipeline reconstruction#
-------------------------
Contigs                                contigs_KPN_TEST.fasta
Will be aligned to                     KPN.coverage_adapted_filtered_80_term.fasta
That contains                          7 plasmids
And each contig aligned more than      20 %
and have at least                      90 % identity
Will be represented and annotated       

ANNOTATING CONTIGS (Fri Jun 26 18:51:07 CEST 2020)
 A file including all automatic annotations on contigs will be generated.


ALIGNING CONTIGS TO FILTERED PLASMIDS (Fri Jun 26 18:51:07 CEST 2020)
 Contigs are aligned to filtered plasmids and those are selected by alignment identity and alignment percentage in order to create links, full length and annotation tracks


---------------------------------------

ERROR in Script plasmidID on or near line 836; exiting with status 1
MESSAGE:

See /home/moeller/git/med-team/mmmulti/plasmidid/logs/plasmidID.log for more information.
command:
blast_align.sh -i  /home/moeller/git/med-team/mmmulti/plasmidid/NO_GROUP/KPN/data/KPN".fna" -d /home/moeller/git/med-team/mmmulti/plasmidid/NO_GROUP/KPN/mapping/KPN.coverage_adapted_filtered_80_term.fasta -o  /home/moeller/git/med-team/mmmulti/plasmidid/NO_GROUP/KPN/data -p plasmids

and there is no log file from what I saw. Executing the blast_align directly, I get

$ PATH=$PATH:$(pwd)/bin blast_align.sh -i  /home/moeller/git/med-team/mmmulti/plasmidid/NO_GROUP/KPN/data/KPN".fna" -d /home/moeller/git/med-team/mmmulti/plasmidid/NO_GROUP/KPN/mapping/KPN.coverage_adapted_filtered_80_term.fasta -o  /home/moeller/git/med-team/mmmulti/plasmidid/NO_GROUP/KPN/data -p plasmids

#Executing /home/moeller/git/med-team/mmmulti/plasmidid/bin/blast_align.sh 

KPN.fna not supplied, please, introduce a valid file
ERROR: 1 missing files, aborting execution

And a log file says that it is all prokka's fault:

#Executing /home/moeller/git/med-team/mmmulti/plasmidid/bin/prokka_annotation.sh 


DEPENDENCY                    STATUS
----------                    ------
prokka                       INSTALLED 
PREFIX KPN
Output directory is /home/moeller/git/med-team/mmmulti/plasmidid/NO_GROUP/KPN/data
Fri Jun 26 18:51:07 CEST 2020
Annotating /home/moeller/git/med-team/mmmulti/plasmidid/TEST_DATA/contigs_KPN_TEST.fasta with prokka
[18:51:07] This is prokka 1.14.6
[18:51:07] Written by Torsten Seemann <torsten.seemann@gmail.com>
[18:51:07] Homepage is https://github.com/tseemann/prokka
[18:51:07] Local time is Fri Jun 26 18:51:07 2020
[18:51:07] You are moeller
[18:51:07] Operating system is linux
[18:51:07] You have BioPerl 1.7.7
Argument "1.7.7" isn't numeric in numeric lt (<) at /usr/bin/prokka line 259.
[18:51:07] System has 2 cores.
[18:51:07] Will use maximum of 1 cores.
[18:51:07] Annotating as >>> Bacteria <<<
[18:51:07] The sequence databases have not been indexed. Please run 'prokka --setupdb' first.
Fri Jun 26 18:51:07 CEST 2020
done annotating /home/moeller/git/med-team/mmmulti/plasmidid/TEST_DATA/contigs_KPN_TEST.fasta with prokka
Removing unwanted files
ls: cannot access '/home/moeller/git/med-team/mmmulti/plasmidid/NO_GROUP/KPN/data/KPN.???': No such file or directory



#Executing /home/moeller/git/med-team/mmmulti/plasmidid/bin/blast_align.sh 

KPN.fna not supplied, please, introduce a valid file

I have then run the "prokka --setupdb" but this has not changed anything. Is there something you suggest for me do/check/..?

Many thanks!

Steffen

[saramonzon]

Tests are being updated in 1.6.4, if error persists please reopen!

[mdb571]

I'm still getting this error while running the tests. Any workaround for this ?

[saramonzon]

Hi @mdb571, thanks for getting in contact, I'll check this as soon as possible!

[mdb571]

Any update ?