PloidyPlot: Something went wrong with command:

[Malabady]

Hi, I am getting the following error:

PloidyPlot: Something went wrong with command: Logex -T4 '.trim=A[12-]' Outdata/FastK_table

my command is: PloidyPlot -e12 -k -v -T4 -oOutdata/kmerpairs Outdata/FastK_table

Any suggestions?

Many thanks,

[KamilSJaron]

Does it also say sh: Logex: command not found? It looks like an incomplete installation (missing some parts of FastK)

[Malabady]

No, it doesn’t say that. In fact, I checked the Logex command and it is installed already.

From: Kamil S. Jaron @.> Date: Wednesday, October 23, 2024 at 3:07 PM To: KamilSJaron/smudgeplot @.> Cc: Magdy S Alabady @.>, Author @.> Subject: Re: [KamilSJaron/smudgeplot] PloidyPlot: Something went wrong with command: (Issue #166) [EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Does it also say sh: Logex: command not found? It looks like an incomplete installation (missing some parts of FastK)

— Reply to this email directly, view it on GitHubhttps://github.com/KamilSJaron/smudgeplot/issues/166#issuecomment-2433218749, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACHNEMGJIFKLEB2FN57MT4DZ47XWXAVCNFSM6AAAAABQKKG2ESVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMZTGIYTQNZUHE. You are receiving this because you authored the thread.Message ID: @.***>

[yaradua]

The problem is with the installation of the fastK. you need to direct the installation to the bin directory and all the programs will be installed

[KamilSJaron]

AH, thanks @yaradua.

@Malabady Can you double check you have the installation available in the environment? If that's not going to help, can you past the whole error?

[Malabady]

Thanks, @yaradua and @KamilSJaron

the smudgeplot tool is installed as a module on our computer cluster with the FastK tool. I load the module as follows:

ml Smudgeplot/0.3.0dev-foss-2022a-Sploidyplot-branch after loading the module, all commands are in the environment path. I checked "FastK", "PloidyPlot", and "Logex" and they all are in the path. for instance, here is the Logex command:

07:04:45    $ Logex
Usage: Logex  [-T<int(4)>] [-[hH][<int(1)>:]<int>]
                <output:name=expr> ... <source_root>[.ktab] ...
      -T: Use -T threads.
      -h: Generate histograms.
      -H: Generate histograms only, no tables.

Then, I ran the following commands:

FastK -v -t24 -k31 -M300 -T4 Indata/*.fasta.gz -NOutdata/FastK_table

PloidyPlot -e12 -k -v -T4 -oOutdata/kmerpairs Outdata/FastK_table

here is the complete stdout and stderr

Using 3 threads to read 3 fasta files some or all of which are compressed

Determining minimizer scheme & partition for FastK_table
  Estimate 339.653G 31-mers
  Dividing data into 12 blocks
  Using 5-minimizers with 1024 core prefixes

Phase 1: Partitioning K-mers into 36 Super-mer Files

  There are 1,057,160,093 reads totalling 463,388,761,914 bps

     Part:           31-mer      super-mers  ave. length
        0:   35,357,798,942   2,367,911,641         14.9
        1:   35,154,763,597   2,669,851,643         13.2
        2:   38,938,442,209   2,416,621,617         16.1
        3:   35,376,383,886   3,379,431,155         10.5
        4:   35,231,744,001   2,654,632,960         13.3
        5:   36,043,428,326   3,595,457,451         10.0
        6:   37,334,894,602   3,068,535,603         12.2
        7:   35,415,697,671   2,555,267,339         13.9
        8:   35,384,503,758   3,177,470,552         11.1
        9:   36,336,968,042   3,168,617,920         11.5
       10:   35,711,734,433   2,839,981,671         12.6
       11:   34,892,586,685   2,763,644,563         12.6
      Sum:  431,178,946,152  34,657,424,115         12.4

      Range 34,892,586,685 - 38,938,442,209 (10.96%)

  Resources for phase:  93:11.448u  2:04.378s  64:24.419w  147.9%

Phase 2: Sorting & Counting K-mers in 12 blocks

      Part:    wgt'd k-mers  savings
         0:   5,003,788,576      7.1
         1:   4,997,654,629      7.0
         2:   6,927,090,730      5.6
         3:   4,925,254,790      7.2
         4:   4,922,413,475      7.2
         5:   4,924,727,592      7.3
         6:   4,968,430,478      7.5
         7:   4,744,539,388      7.5
         8:   4,807,449,310      7.4
         9:   5,323,877,363      6.8
        10:   4,927,074,619      7.2
        11:   4,885,068,823      7.1
       All:  61,357,369,773      7.0

  Resources for phase:  116:13.454u  2:05.208s  37:55.233w  312.0%

Phase 3 (-t option): Merging K-mer Table Parts

  There are 1,986,881,634 31-mers that occur 24-or-more times

  The table occupies 14.04 GB

  Resources for phase:  1:43.007u  14.257s  41.225w  284.4%

Total Resources:  211:07.910u  4:23.845s  103:00.878w  209.2%  109MB

  The input table is untrimmed and not symmetric

  Trimming k-mers in table with count < 12
PloidyPlot: Something went wrong with command:
    Logex -T4 '.trim=A[12-]' Outdata/FastK_table

[Malabady]

Hi All,

I want to report that our team were able to find the problem. the values for the parameters "T" and "t" in the FastK command were flipped:

FastK -v -t24 -k31 -M300 -T4 Indata/*.fasta.gz -NOutdata/FastK_table

once fixed as follows, everything worked just fine:

FastK -v -t4 -k31 -M300 -T24 Indata/*.fasta.gz -NOutdata/FastK_table thank you for your time,

[KamilSJaron]

AAAaaaaaaaaaaa, that's something I should have spotted!

Thank you @Malabady for reporting this back, it will be very useful to know when others will run into the same issue. (The -T and -t parameters of FastK have very unfortunate names!!!)