WARNING:iss.generator:--coverage_file disables --n_reads

[sahilrishav2]

Hello,

I am trying to simulate the reads using iss generate --draft *.fna --model novaseq --output synthetic_reads_10X --cpus 20 --coverage_file coverage_ten_strains.txt --n_reads 4M but it gave this error:

INFO:iss.app:Starting iss generate
INFO:iss.generator:Using kde ErrorModel
INFO:iss.util:Stitching input files together
WARNING:iss.generator:--coverage_file is an experimental feature
WARNING:iss.generator:--coverage_file disables --n_reads
INFO:iss.generator:Using coverage file:coverage_ten_strains.txt
INFO:iss.app:Using 20 cpus for read generation
INFO:iss.app:Generating 4000000 reads
INFO:iss.util:Stitching input files together
Traceback (most recent call last):
  File "/home/rishav//.local/bin/iss", line 8, in <module>
    sys.exit(main())
  File "/home/rishav/.local/lib/python3.10/site-packages/iss/app.py", line 454, in main
    args.func(args)
  File "/home/rishav/.local/lib/python3.10/site-packages/iss/app.py", line 126, in generate_reads
    util.concatenate(temp_R1, args.output + "_R1.fastq")
  File "/home/rishav/.local/lib/python3.10/site-packages/iss/util.py", line 233, in concatenate
    with open(file_name, "rb") as f:
FileNotFoundError: [Errno 2] No such file or directory: 'synthetic_reads_10X.iss.tmp.18_R1.fastq'

but when i ran this command iss generate --draft *.fna --model novaseq --output synthetic_reads_10X --cpus 20 --coverage_file coverage_ten_strains.txt it ran successfully. So, i think the problem is with the --n_reads parameter, i am unable to set it with coverage_file parameter options.

Could you please help me with this concern

[HadrienG]

Hi!

Thanks for reporting this. Insilicoseq is not supposed to crash in this way, as you should not be able to specify --n_reads and --coverage_file simultaneously. The number of reads will be calculated from the required coverage.

[sahilrishav2]

Than you for your response. I want to know if number of reads could be calculated by sequencing coverage then how can we calculate sequencing depth.

On Thu, Jun 13, 2024, 19:03 Hadrien Gourlé @.***> wrote:

Hi!

Thanks for reporting this. Insilicoseq is not supposed to crash in this way, as you should not be able to specify --n_reads and --coverage_file simultaneously. The number of reads will be calculated from the required coverage.

— Reply to this email directly, view it on GitHub https://github.com/HadrienG/InSilicoSeq/issues/263#issuecomment-2165690104, or unsubscribe https://github.com/notifications/unsubscribe-auth/BEQ2WNJQCRA2J46MEBNX2WDZHGNRBAVCNFSM6AAAAABIMEDGAGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNRVGY4TAMJQGQ . You are receiving this because you authored the thread.Message ID: @.***>

[HadrienG]

Could you clarify what you mean by coverage versus depth? Those terms are often used ambiguously/interchangeably 😊

[sahilrishav2]

Kindly go through this link:

https://bioinfo.cd-genomics.com/sequencing-depth-coverage-read-types.html

On Thu, Jun 13, 2024, 19:16 Hadrien Gourlé @.***> wrote:

Could you clarify what you mean by coverage versus depth? Those terms are often used ambiguously/interchangeably 😊

— Reply to this email directly, view it on GitHub https://github.com/HadrienG/InSilicoSeq/issues/263#issuecomment-2165726386, or unsubscribe https://github.com/notifications/unsubscribe-auth/BEQ2WNMUTU5ISEWH6UWZ7RDZHGPE5AVCNFSM6AAAAABIMEDGAGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNRVG4ZDMMZYGY . You are receiving this because you authored the thread.Message ID: @.***>

[sahilrishav2]

@HadrienG , thank you for your time and response. Now, I get it.