error while running the command

[Ram-Nagar]

Hi there, I tried to run TC hunter but it is throwing the following error

"Expected a command, got TC_hunter_BWA.nf -- Check the available commands and options and syntax with 'help'"

Could you please help me understand with this error is about?

[Ram-Nagar]

I tried without 'nextflow' at the start of the command then got the following error

N E X T F L O W ~ version 19.01.0
Launching /home/pjain/tools/TC_hunter/TC_hunter_BWA.nf [special_albattani] - revision: 98a1ef61a1
WARN: Access to undefined parameter workingDir -- Initialise it to a default value eg. params.workingDir = some_value
WARN: Access to undefined parameter construct_file -- Initialise it to a default value eg. params.construct_file = some_value
ERROR ~ Argument of file function cannot be null

[vborjesson]

Hi, I’ll try to help you. Can you please send me some more information about how your running the tool: - how does the config file look? - and how do you run the tool? Best Vanja tis 31 maj 2022 kl. 08:04 skrev Ramawatar Nagar ***@***.***>:

…

Hi there, I tried to run TC hunter but it is throwing the following error "Expected a command, got TC_hunter_BWA.nf -- Check the available commands and options and syntax with 'help'" Could you please help me understand with this error is about? — Reply to this email directly, view it on GitHub <#3>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFO7V6VA3IL5PG2R4JTG6ITVMWTXLANCNFSM5XMLQBMA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[Ram-Nagar]

As instructed in the installation, I made a conda environment using the TC_hunter.yml file. then prepared a config file using the example config file.

here is the config file

params {

    // ----------------- General --------------------------------

    workingDir = '/mnt/e/DATA_ANALYSIS/new_rice_data_analysis/vector_backbone/full_vector' // Working directory path
    tc_hunter_path = 'TC_hunter.nf' // TC_hunter path
    construct_file = '' // file

    construct_length = // number
    construct_name = '' // Name most match reference sequence identfier
    mapq = 30 // mapping quality threshold for soft clipped links
    supporting_reads = 1 // number of reads that neads to support an insertion site to be called, default is 1



    // ----------------- TC_hunter.nf ------------------------

    // Add path to joint reference file plus bam file
    bam = '' // path to bam folder with an asterix e.g. bamfiles/*bam
    reference = '' // concatenated fasta file with host and construct sequence




    // ----------------- TC_hunter_BWA.nf --------------------------------

    bwa_threads = 8

    // Add path to fastq-files. If you're running several samples at the same time, add path to directory with folders of specific samples. If you're running one samples at a time; add the path to folder containing fastq-files.


    host_reference = '' // fasta file
    construct_ref = '' // fasta file

    folder = '' // folder with samples
    sample = '' // folder with R1.fa + R2.fa

    help = false

}

then tried running the command

$nextflow TC_hunter_BWA.nf -c tchunter_BWA_example.config -with-report tchunter_out

and without adding nextflow

$TC_hunter_BWA.nf -c tchunter_BWA_example.config -with-report tchunter_out

Thanks
Ram

[vborjesson]

Hi again, I think that you missed to add some info to your config file. Try to add all info about the construct and also the fasta or bam directory. Let me know if you still have any problem after doing this. Best, Vanja fre 3 juni 2022 kl. 05:56 skrev Ramawatar Nagar ***@***.***>:

…

As instructed in the installation, I made a conda environment using the TC_hunter.yml file. then prepared a config file using the example config file. here is the config file params { // ----------------- General -------------------------------- workingDir = '/mnt/e/DATA_ANALYSIS/new_rice_data_analysis/vector_backbone/full_vector' // Working directory path tc_hunter_path = 'TC_hunter.nf' // TC_hunter path construct_file = '' // file construct_length = // number construct_name = '' // Name most match reference sequence identfier mapq = 30 // mapping quality threshold for soft clipped links supporting_reads = 1 // number of reads that neads to support an insertion site to be called, default is 1 // ----------------- TC_hunter.nf ------------------------ // Add path to joint reference file plus bam file bam = '' // path to bam folder with an asterix e.g. bamfiles/*bam reference = '' // concatenated fasta file with host and construct sequence // ----------------- TC_hunter_BWA.nf -------------------------------- bwa_threads = 8 // Add path to fastq-files. If you're running several samples at the same time, add path to directory with folders of specific samples. If you're running one samples at a time; add the path to folder containing fastq-files. host_reference = '' // fasta file construct_ref = '' // fasta file folder = '' // folder with samples sample = '' // folder with R1.fa + R2.fa help = false } then tried running the command $nextflow TC_hunter_BWA.nf -c tchunter_BWA_example.config -with-report tchunter_out and without adding nextflow $TC_hunter_BWA.nf -c tchunter_BWA_example.config -with-report tchunter_out Thanks Ram — Reply to this email directly, view it on GitHub <#3 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFO7V6SE7HPGA7YENFXCK2TVNF65RANCNFSM5XMLQBMA> . You are receiving this because you commented.Message ID: ***@***.***>

[swttalyan]

I am also facing problems with running the TC_hunter on the test dataset.
I have created the conda environment using the step 2 as I couldn;t manage to create using yml file and encountering following error. N E X T F L O W ~ version 19.01.0 Launching TC_hunter.nf[intergalactic_ptolemy] - revision: 3e241744da [warm up] executor > local [56/e2897e] Submitted process > samtools_index (1) [56/e2897e] NOTE: Processsamtools_index (1) terminated with an error exit status (1) -- Error is ignored

I would really appreicate if someone can help me running this pipeline, then I would like to run it on my own dataset.

best
Sweta

[xiekunwhy]

same error samtools_index (1) terminated with an error exit status (1) -- Error is ignored