Tag: config.txt

I cannot find the file in configuration file

Pindel Error: I cannot find the file in configuration file 1 Hi, I come across this error while running pindel v0.3 in docker my bam file is named as “main.clean.bam” and my config file has : main.clean.bam 270 main The error is: I cannot find the file ‘main.clean.bam’. referred to…

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Homer not finding hg38 genome – Support scientifique et technique

Hi everyone,I am trying to annotate a .bed file using homer annotatePeaks.pl module load homer/ annotatePeaks.pl ConsensusPeaks.bed hg38 -gtf gencode.v43.annotation.gtf.gz > ConsensusPeaks.annotatedPeaks I obtain the following error message !!!!Genome /shared/ifbstor1/software/miniconda/envs/homer-4.11/share/homer/hg38 not found in /shared/ifbstor1/software/miniconda/envs/homer-4.11/share/homer/.//config.txt To check if is available, run “perl /shared/ifbstor1/software/miniconda/envs/homer-4.11/share/homer/.//configureHomer.pl -list” If so, add it by typing “perl…

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Java -xmx option does not limit memory usage in the ImputePipelinePlugin?

Java -xmx option does not limit memory usage in the ImputePipelinePlugin? 0 Hello! I am currently trying to run the pathfinding step in the PHG pipeline (v1.2) by using the -ImputePipelinePlugin -imputeTarget pathToVCF options, but might be running into memory issues. I used the command in this way: singularity exec…

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Nextflow memory issues custom config -c

Nextflow memory issues custom config -c 1 Hi all, I am trying to run nextflow on my laptop nextflow run nf-core/rnaseq \ –input samplesheet.csv \ –genome mm10 \ -profile docker I am having issues with memory: Error executing process > ‘NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (KO_3)’ Caused by: Process requirement exceed available memory –…

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HTSeqGenie run error

Hi, I am running the HTSeqGenie on both MacOS and Linux with the test TP53 samples. They both gave me error in reading the fastq files. It seems having problems reading the fastq.gz files in each parallel process. Could anyone help me with this please? Error are at below: checkConfig.R/checkConfig.template:…

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Genome hg19**not found in homer config

I want to use the Homer to do annotation. After I input “annotatePeaks.pl 31512_TH0_D0.bed hg19 > 31512_TH0_D0.ann.txt” , it shows “!!!!Genome hg19 not found in /home/jenny/NGStools/homer/.//config.txt” I used the command “perl /home/jenny/NGStools/homer/configureHomer.pl -install hg19” to install it, and I am sure I installed the hg19 for the homer Then input…

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Error with file guillaumeKUnitigsAtLeast32bases_all.fasta, kUnitigLengths.txt is of size 0, must be at least of size 1.

Hello, I am trying running an assembly with MaSuRCa but am getting an error at the step: “Computing super reads from PE”. here’s the output with the error: [xxxx@vic Bovidae]$ cd Assembly_test/ [xxxx@vic Assembly_test]$ ls assemble.sh guillaumeKUnitigsAtLeast32bases_all.fasta.tmp masurca_assembly.o4302352 meanAndStdevByPrefix.pe.txt pe_data.tmp quorum_mer_db.jf work1 environment.sh guillaumeKUnitigsAtLeast32bases_all.jump.fasta masurca_config.txt pe.cor.fa pe.renamed.fastq super1.err ESTIMATED_GENOME_SIZE.txt masurca_assembly.e4302352…

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Jetson nano (B01) configures pytorch and torchvision environment + tensorrtx model transformation + deepstream deployment yolov5 (pro test available)

jetson nano To configure pytorch and torchvision Environmental Science +tensorrt Model transformation +Deepstream Deploy yolov5( Close test available ) Because a game came into contact with jetson nano, Need to use pycharm Train your own model plus yolov5 Target detection , And deployed to jetson nano On , It didn’t…

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HOMER hg19 not found in config.txt

Hi! I am trying to run findMotif.pl from HOMER, in order to detect some regulatory motifs in a set of fasta sequences. When I type: findMotifs.pl sequences.fasta hg19 . I get the following error: !!! hg19 not found in /mnt/lustre/scratch/home/programs/HOMER/.//config.txt Try typing “perl /mnt/lustre/scratch/home/programs/HOMER//.//configureHomer.pl -list” to see available promoter sets…

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