project_all_alignment.fna file not found

[molbio7]

Hi,

I'm getting this error and seems like an project_all_alignment.fna file is not generated.

error logs below:
[22:46:43] Checking version: samtools --version is >= 1.3 - ok, have 1.14
[22:46:43] Checking version: bcftools --version is >= 1.3 - ok, have 1.14
[22:46:43] Checking version: nucmer --version is >= 3.1 - ok, have 3.1
[22:46:44] Checking version: bowtie2 --version is >= 2.3 - ok, have 2.4
[22:46:44] Checking version: bwa is >= 0.7 - ok, have 0.7
[22:46:44] Checking version: FastTree -expert is >= 2.1 - ok, have 2.1
[22:46:50] Checking version: bbmap.sh -v is >= 38.06 - ok, have 38.95
[22:46:50] Checking version: raxmlHPC-PTHREADS -version is >= 8.2 - ok, have 8.2
Uncaught exception from user code:
Error running iqtree -m TEST -b 100 -s /snp_bacteria/workdir/results/test_all_alignment.fna -nt 48 2>>/snp_bacteria/workdir/results/test.error >>/snp_bacteria/workdir/results/test.log

.
PhaME::buildTree("/snp_bacteria/PhaME/src", "/snp_bacteria/workdir/results", 48, 3, "test", 1, 100, "/snp_bacteria/workdir/results/tes"..., ...) called at /snp_bacteria/PhaME/src/phame line 817

Smartmatch is experimental at /bin/../lib/misc_funcs.pm line 26.
ERROR: File not found /snp_bacteria/workdir/results/test_all_alignment.fna

IQ-TREE multicore version 2.2.0-beta COVID-edition for Linux 64-bit built Dec 21 2021 built Dec 21 2021
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.

Host: (AVX512, FMA3, 3022 GB RAM)
Command: iqtree -m TEST -b 100 -s /snp_bacteria/workdir/results/test_all_alignment.fna -nt 48
Seed: 593485 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Tue Mar 8 08:35:35 2022
Kernel: AVX+FMA - 48 threads (96 CPU cores detected)

Reading alignment file /snp_bacteria/workdir/results/test_all_alignment.fna ... ERROR: File not found /snp_bacteria/workdir/results/test_all_alignment.fna

I'm using a complete reference genome and working directory contains other assembled genomes (incomplete) in fasta format.

   refdir = /snp_bacteria/ref # directory where reference files are located
  workdir = /workdir where contigs/reads files are located and output is stored

reference = 1  # 0:pick a random reference; 1:use given reference; 2: use ANI based reference
  reffile = GCA_000196095.1.fasta  # reference filename 

  project = test  # main alignment file name

  cdsSNPS = 0  # 0:no cds SNPS; 1:cds SNPs

  buildSNPdb = 0 # 0: only align to reference 1: build SNP database of all complete genome

FirstTime = 1  # 1:yes; 2:update existing SNP alignment

     data = 3  # *See below 0:only complete(F); 1:only contig(C); 2:only reads(R); 
               # 3:combination F+C; 4:combination F+R; 5:combination C+R; 
               # 6:combination F+C+R; 7:realignment  *See below 
    reads = 2  # 1: single reads; 2: paired reads; 3: both types present;

     tree = 3  # 0:no tree; 1:use FastTree; 2:use RAxML; 3:use both;
bootstrap = 1  # 0:no; 1:yes;  # Run bootstrapping  *See below
        N = 100  # Number of bootstraps to run *See below    

PosSelect = 0  # 0:No; 1:use PAML; 2:use HyPhy; 3:use both

     code = 0  # 0:Bacteria; 1:Virus; 2: Eukarya

    clean = 0  # 0:no clean; 1:clean

  threads = 48  # Number of threads to use

   cutoff = 0.1  # Linear alignment (LA) coverage against reference - ignores SNPs/alignments from organism that have lower cutoff.

• When using data option 1,2,5 need a complete reference to align/map to.
• Use data option 7 when need to extract SNPs using a sublist of already aligned genomes.

Could you please advise?

thanks

[eamiddlebrook]

Hi MolBio7,
It looks like the path is looking for something in root ("/workingdir") instead of perhaps something in your home dir ("/home/user/WorkingDir").
refdir should also be changed

Let me know if that works.

Best,
Earl