Nanopore assembly and PanGIA

[Scott]

Hello,

I am analyzing nanopore sequence data using the latest docker image (bioedge/edge_dev-Docker). I tried taxonomy classification using GOTTCHA and PanGIA. GOTTCHA worked fined but PanGIA failed.  The contents of allReads-pangia.log are below:

/home/edge/edge_dev/scripts/microbial_profiling/script/uge-pangia.sh: illegal option -- s
/home/edge/edge_dev/scripts/microbial_profiling/script/uge-pangia.sh: illegal option -- e
/home/edge/edge_dev/scripts/microbial_profiling/script/uge-pangia.sh: illegal option -- -
/home/edge/edge_dev/scripts/microbial_profiling/script/uge-pangia.sh: illegal option -- n
+ [[ -s '' ]]
+ [[ -z /home/edge/edge_dev ]]
+ pangia.py --debug -r DEPTH_COV -i /home/edge/edge_dev/edge_ui/EDGE_output//1b4a616b0c317d221adbf13a4a13f1b2/ReadsBasedAnalysis/Taxonomy/allReads.fastq -t 7 -o /home/edge/edge_dev/edge_ui/EDGE_output//1b4a616b0c317d221adbf13a4a13f1b2/ReadsBasedAnalysis/Taxonomy/1_allReads/pangia -p allReads -d /home/edge/edge_dev/scripts/microbial_profiling/../../database/PanGIA/NCBI_genomes_refseq86_BAV.fa /home/edge/edge_dev/scripts/microbial_profiling/../../database/PanGIA/NCBI_genomes_refseq86_Human.fa /home/edge/edge_dev/scripts/microbial_profiling/../../database/PanGIA/NCBI_genomes_refseq86_Plasmodium.fa -ms 0 -mr 3 -mb 1 -ml 50 nopore
usage: pangia.py [-h] (-i [FASTQ] [[FASTQ] ...] | -s [SAMFILE])
                 [-d [[BWA_INDEX] [[BWA_INDEX] ...]]] [-dp [PATH]]
                 [-asl <INT>] [-ams <INT>] [-ao <STR>] [-mm2] [-se]
                 [-st {bg,standalone,both}]
                 [-m {report,class,extract,lineage}]
                 [-rf {basic,r,rnb,rnr,rni,patho,score,ref,full,all} [{basic,r,rnb,rnr,rni,patho,score,ref,full,all} ...]]
                 [-da] [-par <INT>] [-xnm <INT>] [-x [TAXID]] [-r [FIELD]]
                 [-t <INT>] [-o [DIR]] [-td [DIR]] [-kt] [-p <STR>] [-ps]
                 [-sb] [-lb <FILE>] [-rc {R_MAT,R_IDT,R_SCR}] [-ms <FLOAT>]
                 [-mr <INT>] [-mb <INT>] [-ml <INT>] [-mc <FLOAT>]
                 [-md <FLOAT>] [-mrd <FLOAT>] [-np] [-pd] [-if <STR>] [-nc]
                 [-c] [--silent] [--debug]
pangia.py: error: unrecognized arguments: nopore

Is Pangia compatible with long reads (eg. nano-edge option)? 

Thanks,

Scott

[Lo, Chien-Chi]

Hi Scott,

 

Sorry for the error. It is a bug introduced by a recent commit to “Auto Adjust bwa alignment score by reads length for PanGIA pipeline.” (#5425692). Here is the fix. (#9c64c702)

 

You can fix the bug by the command below in the running EDGE container. (if the container name is edge).

$ docker exec edge  sed -ie "s/\\\'-sb -se --nanopore\\\'/-sb -se --nanopore/g" /home/edge/edge/scripts/microbial_profiling/microbial_profiling_configure.pl

 

I will push the bug fix to docker image.

 

Thanks,

Chienchi

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[Scott]

Thanks for the quick reply.  PanGIA pipeline is working with nanopore reads.

Scott