Issues with 'jq not found' and genome path

[hchintalapudi]

Hi, I cloned the repository and hopefully satisfied all the software installation requirements. I ran ./install/validate.py config/bulk-config.json --ignore-input-output --software without any errors. But when I run: ./run_bulkModule.sh config/bulk-config.json GATA1_D7_30min_chr11 I get:

./run_bulkModule.sh: line 20: jq: command not found
./run_bulkModule.sh: line 21: jq: command not found
./run_bulkModule.sh: line 22: jq: command not found
organism_build should be one of hg38, hg19, mm10 or mm9

Should I download and install jq separately? Attached is my bulk-config.json file. bulk-config.txt

Some tips appreciated, thanks!

[fl-yu]

Yes that is the issue. You configuration file seems good. jq should be installed by default in linux system but you could install it by yourself.

[hchintalapudi]

Thanks for the reply, I'm working on a cluster server and do not have sudo access. However, I downloaded the appropriate jq binary executable file for linux 64 from https://stedolan.github.io/jq/download/ and I run it:

jq
jq - commandline JSON processor [version 1.6]

Usage:  /dartfs-hpc/rc/lab/L/LeachLab/HIMANSHU/jq [options] <jq filter> [file...]
    /dartfs-hpc/rc/lab/L/LeachLab/HIMANSHU/jq [options] --args <jq filter> [strings...]
    /dartfs-hpc/rc/lab/L/LeachLab/HIMANSHU/jq [options] --jsonargs <jq filter> [JSON_TEXTS...]

jq is a tool for processing JSON inputs, applying the given filter to
its JSON text inputs and producing the filter's results as JSON on
standard output.

The simplest filter is ., which copies jq's input to its output
unmodified (except for formatting, but note that IEEE754 is used
for number representation internally, with all that that implies).

For more advanced filters see the jq(1) manpage ("man jq")
and/or https://stedolan.github.io/jq

Example:

    $ echo '{"foo": 0}' | jq .
    {
        "foo": 0
    }

For a listing of options, use /dartfs-hpc/rc/lab/L/LeachLab/HIMANSHU/jq --help.

And I added the path of this jq to my ~/.bashrc file. But when I run ./run_bulkModule.sh config/bulk-config.json GATA1_D7_30min_chr11 I get the same error:

./run_bulkModule.sh: line 20: jq: command not found
./run_bulkModule.sh: line 21: jq: command not found
./run_bulkModule.sh: line 22: jq: command not found
organism_build should be one of hg38, hg19, mm10 or mm9

[fl-yu]

I wonder if you run separately on compuational node. Can you try to add jq to PATH in your submited script using something like export PATH=/path/to/jq:"$PATH"

[hchintalapudi]

I changed jq to absolute/path/jq in run_bulkModule.sh and the pipeline runs finally! I've been getting other issues, checking logs and changing things. Like with this command from the pipeline script:

$bowtie2bin/bowtie2 -p $cores --dovetail --phred33 -x $bt2idx/genome -1 $trimdir2/"$base"_1.paired.fastq.gz -2 $trimdir2/"$base"_2.paired.fastq.gz) 2> $logdir/"$base".bowtie2 | $samtoolsbin/samtools view -bS - > $aligndir/"$base".bam

I don't understand why there is $bt2idx/genome instead of $bt2idx, since $bt2idx has the path to the index. I'm checking my log and this is the error I receive:

(ERR): "/dartfs-hpc/rc/lab/L/LeachLab/HIMANSHU/genomes/hg38/hg38/genome" does not exist or is not a Bowtie 2 index
Exiting now ...

Probably removing 'genome' from all bowtie2 commands in src/bulk/bulk-pipeline.sh is the solution? Thanks for your help!

[fl-yu]

Yes that is the issue of the genome path. It should work after remove the 'genome'. If you follow my tutorial to download the reference genome, the genome file with FASTA format should have the same name (genome.fa) for different genome versions (hg19 or hg38). If users use their own data, sometimes the rule of naming is different which can cause the problem.

[hchintalapudi]

Hi, I'm having issues with the MEME analysis for de novo motif finding. Could you help me with what the issue is?

Thanks for the amazing tool! slurm-97220.out.txt