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Unable to run the trio_longread.php pipeline #288

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noob9721 opened this issue Aug 27, 2024 · 3 comments
Open

Unable to run the trio_longread.php pipeline #288

noob9721 opened this issue Aug 27, 2024 · 3 comments
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@noob9721
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Hello,
I was able to install the megSAP pipeline and the NGSD database according to the instructions provided on GitHub and am now trying to run the trio_longread.php pipeline on our ONT data but couldn't get it to run. This is the command that I'm using:
php trio_longread.php -f /path/to/father.bam -m /path/to/mother.bam -c /path/to/child.bam -out_folder /home/labnigro/trio001 -steps vc,cn,sv,an,db -threads 20
but I get this error:

ERROR: 'load_system: Cannot determine processing system - processed sample name 'FISCF001' is invalid!' in /home/labnigro/megSAP/src/Common/genomics.php:398.

I tried to find a solution to this and it seems this has something to do with the NGSD database but I read that the NGSD database implementation is optional but I couldn't figure out how to NOT include it while running. I am stuck here and unable to go forward.
What might be the problem?

@imgag imgag deleted a comment Aug 27, 2024
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@marc-sturm
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If the samples are not contained in the NGSD database, you have to provide the processing system definition using the -system parameter.

Here an example of system definition:

> name_short = "LR-ONT-SQK-LSK114"
> name_manufacturer = "Oxford Nanopore Tech. Ligation Sequencing Kit V14 (SQK-LSK114)"
> target_file = "[path_to_genome_bed_file]/WGS_hg38.bed"
> adapter1_p5 = ""
> adapter2_p7 = ""
> shotgun = 0
> umi_type = "n/a"
> type = "lrGS"
> build = "GRCh38"

The WGS_hg38.bed file should look like that:

> chr1    0       248956422
> chr2    0       242193529
> chr3    0       198295559
> chr4    0       190214555
> chr5    0       181538259
> chr6    0       170805979
> chr7    0       159345973
> chr8    0       145138636
> chr9    0       138394717
> chr10   0       133797422
> chr11   0       135086622
> chr12   0       133275309
> chr13   0       114364328
> chr14   0       107043718
> chr15   0       101991189
> chr16   0       90338345
> chr17   0       83257441
> chr18   0       80373285
> chr19   0       58617616
> chr20   0       64444167
> chr21   0       46709983
> chr22   0       50818468
> chrX    0       156040895
> chrY    0       57227415

I hope that helps you

@noob9721
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noob9721 commented Aug 27, 2024

Hello, this worked! Thank you!
But then it ran again for a minute and then gave a new error:

SampleSimilarity 2024_07
Command line parsing exception: Input file '/home/labnigro/Public/Nanopore_data/MNESYS_2_26042024/FIPAD001_10kb/20240426_1417_3A_PAW10574_341a28e4/FIPAD001.GSvar' given for parameter 'in' is not readable.
Call this tool with the argument '--help' for help.
ERROR: 'Call of external tool '/home/labnigro/megSAP//data/tools/ngs-bits/bin/SampleSimilarity' returned error code '1'.' in /home/labnigro/megSAP/src/Common/ToolBase.php:743.

and here is the log from it
trio_20240827114937.log

Another thing that I need clearance on is if I want to use the GRCH38_alt.fa instead of GRCH38.fa, where do I need to adjust the script?
Lend a hand, please?

@marc-sturm
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Did you analyze the samples individually with megSAP as well?
It looks like the single sample GSvar files are missing.
I would analyze the samples individually first.
Alternatively you can try and run the pipeline with -no_check to skip the correlation checks of the samples.

Currently megSAP does not support alt-chromsomes.
You should not change the genome used by megSAP.

@marc-sturm marc-sturm self-assigned this Aug 27, 2024
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