LANL-Bioinformatics/PanGIA

PanGIA-Docker error

Closed this issue · 8 comments

jagos01 commented

Hello,
I installed the docker version of PanGIA. I ran some nanopore data using all 3 processes (pre-processing, PanGIA and supplementary classification). All finished running except PanGIA which had the following error in pangia.log:

[00:00:11] Running read-mapping...
[00:00:11] Mapping to /home/edge/edge_dev/scripts/microbial_profiling/../../database/PanGIA/NCBI_genomes_refseq89_BAV.fa...
[00:00:11] [ERROR] error occurred while running read mapping (code: 1, message: + minimap2 -aL -t 12 -x map-ont /home/edge/edge_dev/scripts/microbial_profiling/../../database/PanGIA/NCBI_genomes_refseq89_BAV.fa /home/edge/edge_dev/edge_ui/EDGE_output//9da940633105a9e2be60b7f0bf03add4/ReadsBasedAnalysis/Taxonomy/allReads.fastq

This is from process-current.log:
Tool (pangia) - PID: 17739, starting...
[RUN_TOOL] [pangia] COMMAND: uge-pangia.sh -i '/home/edge/edge_dev/edge_ui/EDGE_output//9da940633105a9e2be60b7f0bf03add4/ReadsBasedAnalysis/Taxonomy/allReads.fastq' -p allReads -o /home/edge/edge_dev/edge_ui/EDGE_output//9da940633105a9e2be60b7f0bf03add4/ReadsBasedAnalysis/Taxonomy/1_allReads/pangia -t 12 -d 'NCBI_genomes_refseq89_BAV.fa NCBI_genomes_refseq89_adds.fa' -x /home/edge/edge_dev/scripts/microbial_profiling/../../database/PanGIA -s n -b '' -r DEPTH_COV -T standalone -A 60 -W 24 -S 0 -R 10 -B 3 -L 200 -D 0.01 -G 0.005 -C 0.001 -a ' -se --nanopore'
[RUN_TOOL] [pangia] Logfile: /home/edge/edge_dev/edge_ui/EDGE_output//9da940633105a9e2be60b7f0bf03add4/ReadsBasedAnalysis/Taxonomy/log/allReads-pangia.log
[RUN_TOOL] [pangia] Error occured.
[RUN_TOOL] [pangia] Running time: 00:00:13

This is from error.log:
convert: unable to open image /home/edge/edge_dev/edge_ui/EDGE_output//9da940633105a9e2be60b7f0bf03add4/QcReads/Log_LengthvsQualityScatterPlot_kde.pdf': No such file or directory @ error/blob.c/OpenBlob/2643. convert: no images defined /home/edge/edge_dev/edge_ui/EDGE_output//9da940633105a9e2be60b7f0bf03add4/HTML_Report/images/QC_length_quality.png' @ error/convert.c/ConvertImageCommand/3046.
Use of uninitialized value in division (/) at /home/edge/edge_dev/scripts/pangia_report/create_pangia_report_w_temp.pl line 24.

Do you have any suggestions on how to resolve this issue with PanGIA?
Thanks,
Scott

poeli commented

Do you have minimap2's index (.mmi) files in the database directory?

jagos01 commented

Today I installed PanGIA as outlined on the GitHub page. I ran PanGAI with the following command:

./pangia.py -i /home/dnd/data/MinION/HybridAssembly/Ft_Lux_clones/Guppy_hac_calls/Demux/1st_Run/barcode05.fastq -db ./PanGIA/NCBI_genomes_refseq89_BAV.fa ./PanGIA/NCBI_genomes_refseq89_adds.fa -t 24 --keepTemp -np -o /home/dnd/data/MinION/HybridAssembly/Ft_Lux_clones/Analysis/ -p FtLux_BC05.

This is nanopore sequence data and the error (as seen in the attached screenshot) seems to be from minimap2. I do not get this error when using short read data. Any suggestions to resolve the minimap2/nanopore issue would be appreciated.
Thanks,
Scott

PanGIA Error_Screenshot

poeli commented

Hi Scott,

I presumed it's due to the absence of minimap2 index file. I will upload these files to our downloading site today. Sorry for the inconvenience!

Thanks,
Paul

jagos01 commented

I do not have the index files in the database directory. How do I generate the index files for the databases I downloaded? For example NCBI_genome_refseq89_BAV and NCBI_genome_refseq89_adds.

jagos01 commented

Thank you.

poeli commented

If you prefer to create the index yourself, the original FASTA files can be downloaded from here:
https://edge-dl.lanl.gov/PanGIA/database/FASTA/

You can download these *.fa files, create minimap2 index and dump them to *.fa.mmi.

jagos01 commented
poeli commented

You're welcome. Glad to hear that Scott! I'm still uploading...