Trouble with configuration for Reaper / Sequence Imp / Kraken

Question

[benoahb]

Hi all,

I am trying to set up a pipeline to analyse my small RNA seq and I'm having trouble with the trimming part using Kraken. I understand that it has to be something with the geometry/configuration files but I can't seem to fix it. Do you have any suggestions?

Using Sequence Imp pipeline

~/bin/seqimp-17-087/bin/imp_commandline.pl --step=organise --description=<Description file> \
 --user-configuration=<Configuration_SeqImp_default.txt> --dataDir=data

I get this...

Pipeline version:   17-087

This is the configuration file selected: /Users/Benoah/WDirectory/20190506_Kraken/seqimp/Configuration_SeqImp_default.txt

Parsing the analysis configuration file
Parsing the config file
geoConfig not specified, using default: /Users/Benoah/bin/seqimp-17-087/config/seqimp_config/geometry_config.txt
reap2imp not specified, using default: /Users/Benoah/bin/seqimp-17-087/config/seqimp_config/reap2imp_mappings.txt
Config file parsing complete

Preparing to read the geometry configuration file
Reading table
Argument "5p_ad" isn't numeric in postincrement (++) at /Users/Benoah/bin/seqimp-17-087/bin/imp_commandline.pl line 1025, <TABLE> line 1.
Argument "3p_ad" isn't numeric in postincrement (++) at /Users/Benoah/bin/seqimp-17-087/bin/imp_commandline.pl line 1025, <TABLE> line 1.
Argument "5p_seq_insert" isn't numeric in postincrement (++) at /Users/Benoah/bin/seqimp-17-087/bin/imp_commandline.pl line 1025, <TABLE> line 1.
Argument "3p_seq_insert" isn't numeric in postincrement (++) at /Users/Benoah/bin/seqimp-17-087/bin/imp_commandline.pl line 1025, <TABLE> line 1.
Reading of table complete

Preparing to load description file
Can not access the description file

With the configuration file as follow

Name    File     Geometry   Barcodes     3p_ad  3p_seq_insert
KRV_WT  RDVJ272.fastq.gz    3p_seq_insert   CATTTT  ATCTCGTATGCCGTCTTCTGCTTG    AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
KRV_ctrl    RDVJ273.fastq.gz    3p_seq_insert   CCAACA  ATCTCGTATGCCGTCTTCTGCTTG    AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC

And if I just use reaper,

reaper -i RDVJ272.fastq.gz -basename ../reaper/RDVJ272.out.fastq.gz -meta ../reaper/barcodes -geom 3p-bc

I get this

need column 3p-si
failed to parse barcode spec file

With the barcode file as follow

tabu    3p_ad   barcode 3p-si
GTTCAGAGTTCTACAGTCCGACGATC  ATCTCGTATGCCGTCTTCTGCTTG    CATTTT  AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
GTTCAGAGTTCTACAGTCCGACGATC  ATCTCGTATGCCGTCTTCTGCTTG    CCAACA  AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC