Errors in phylotyping step

[samfux84]

Hi,

I installed phyla_AMPHORA and its dependencies as described in the documentation. Then I tried to run the example from the testData (ecoli.fasta).

I was running the following 3 commands as described in the documentation:

MarkerScanner.pl -Phylum 3 -DNA ecoli.fasta
MarkerAlignTrim.pl -WithReference -OutputFormat phylip
Phylotyping.pl -CPUs 24 > phylotype.result

The first command worked as described and produced the .pep files.

[samapps@e1001 test2]$ export OMP_NUM_THREADS=24
[samapps@e1001 test2]$ MarkerScanner.pl -Phylum 3 -DNA ecoli.fasta  
Find and extract open reading frames (ORFs)
[samapps@e1001 test2]$

[samapps@euler04 test2]$ ls
ecoli.fasta      Gamma.139.pep  Gamma.175.pep  Gamma.215.pep  Gamma.24.pep   Gamma.285.pep  Gamma.327.pep  Gamma.36.pep  Gamma.68.pep
ecoli.fasta.orf  Gamma.140.pep  Gamma.176.pep  Gamma.217.pep  Gamma.250.pep  Gamma.286.pep  Gamma.328.pep  Gamma.37.pep  Gamma.69.pep
Gamma.100.pep    Gamma.141.pep  Gamma.177.pep  Gamma.218.pep  Gamma.252.pep  Gamma.287.pep  Gamma.32.pep   Gamma.38.pep  Gamma.70.pep
Gamma.101.pep    Gamma.142.pep  Gamma.178.pep  Gamma.219.pep  Gamma.253.pep  Gamma.288.pep  Gamma.332.pep  Gamma.3.pep   Gamma.71.pep
Gamma.103.pep    Gamma.143.pep  Gamma.179.pep  Gamma.220.pep  Gamma.254.pep  Gamma.289.pep  Gamma.333.pep  Gamma.40.pep  Gamma.72.pep
Gamma.104.pep    Gamma.144.pep  Gamma.17.pep   Gamma.221.pep  Gamma.255.pep  Gamma.28.pep   Gamma.334.pep  Gamma.41.pep  Gamma.73.pep
Gamma.105.pep    Gamma.145.pep  Gamma.180.pep  Gamma.223.pep  Gamma.256.pep  Gamma.291.pep  Gamma.335.pep  Gamma.42.pep  Gamma.74.pep
Gamma.106.pep    Gamma.146.pep  Gamma.182.pep  Gamma.224.pep  Gamma.257.pep  Gamma.294.pep  Gamma.336.pep  Gamma.43.pep  Gamma.75.pep
Gamma.107.pep    Gamma.147.pep  Gamma.183.pep  Gamma.225.pep  Gamma.258.pep  Gamma.295.pep  Gamma.337.pep  Gamma.44.pep  Gamma.76.pep
Gamma.108.pep    Gamma.148.pep  Gamma.184.pep  Gamma.226.pep  Gamma.259.pep  Gamma.296.pep  Gamma.339.pep  Gamma.45.pep  Gamma.77.pep
Gamma.109.pep    Gamma.149.pep  Gamma.185.pep  Gamma.227.pep  Gamma.25.pep   Gamma.297.pep  Gamma.33.pep   Gamma.46.pep  Gamma.78.pep
Gamma.10.pep     Gamma.14.pep   Gamma.186.pep  Gamma.228.pep  Gamma.260.pep  Gamma.298.pep  Gamma.340.pep  Gamma.47.pep  Gamma.79.pep
Gamma.111.pep    Gamma.150.pep  Gamma.187.pep  Gamma.229.pep  Gamma.261.pep  Gamma.299.pep  Gamma.343.pep  Gamma.48.pep  Gamma.7.pep
Gamma.112.pep    Gamma.151.pep  Gamma.188.pep  Gamma.22.pep   Gamma.263.pep  Gamma.300.pep  Gamma.344.pep  Gamma.49.pep  Gamma.80.pep
Gamma.115.pep    Gamma.153.pep  Gamma.189.pep  Gamma.230.pep  Gamma.264.pep  Gamma.302.pep  Gamma.347.pep  Gamma.4.pep   Gamma.81.pep
Gamma.116.pep    Gamma.154.pep  Gamma.18.pep   Gamma.231.pep  Gamma.265.pep  Gamma.304.pep  Gamma.348.pep  Gamma.50.pep  Gamma.82.pep
Gamma.117.pep    Gamma.156.pep  Gamma.190.pep  Gamma.232.pep  Gamma.266.pep  Gamma.305.pep  Gamma.349.pep  Gamma.52.pep  Gamma.84.pep
Gamma.118.pep    Gamma.157.pep  Gamma.192.pep  Gamma.233.pep  Gamma.268.pep  Gamma.306.pep  Gamma.350.pep  Gamma.53.pep  Gamma.86.pep
Gamma.119.pep    Gamma.158.pep  Gamma.195.pep  Gamma.234.pep  Gamma.26.pep   Gamma.307.pep  Gamma.352.pep  Gamma.54.pep  Gamma.87.pep
Gamma.11.pep     Gamma.159.pep  Gamma.196.pep  Gamma.235.pep  Gamma.270.pep  Gamma.308.pep  Gamma.353.pep  Gamma.55.pep  Gamma.88.pep
Gamma.122.pep    Gamma.15.pep   Gamma.197.pep  Gamma.236.pep  Gamma.271.pep  Gamma.310.pep  Gamma.354.pep  Gamma.56.pep  Gamma.89.pep
Gamma.123.pep    Gamma.160.pep  Gamma.198.pep  Gamma.237.pep  Gamma.272.pep  Gamma.311.pep  Gamma.355.pep  Gamma.57.pep  Gamma.8.pep
Gamma.124.pep    Gamma.161.pep  Gamma.199.pep  Gamma.238.pep  Gamma.274.pep  Gamma.312.pep  Gamma.356.pep  Gamma.58.pep  Gamma.90.pep
Gamma.125.pep    Gamma.162.pep  Gamma.1.pep    Gamma.239.pep  Gamma.275.pep  Gamma.314.pep  Gamma.357.pep  Gamma.59.pep  Gamma.91.pep
Gamma.126.pep    Gamma.163.pep  Gamma.200.pep  Gamma.23.pep   Gamma.277.pep  Gamma.316.pep  Gamma.358.pep  Gamma.5.pep   Gamma.92.pep
Gamma.128.pep    Gamma.164.pep  Gamma.201.pep  Gamma.241.pep  Gamma.278.pep  Gamma.317.pep  Gamma.359.pep  Gamma.60.pep  Gamma.93.pep
Gamma.130.pep    Gamma.166.pep  Gamma.202.pep  Gamma.242.pep  Gamma.279.pep  Gamma.318.pep  Gamma.35.pep   Gamma.61.pep  Gamma.95.pep
Gamma.131.pep    Gamma.167.pep  Gamma.204.pep  Gamma.243.pep  Gamma.27.pep   Gamma.319.pep  Gamma.360.pep  Gamma.62.pep  Gamma.96.pep
Gamma.132.pep    Gamma.168.pep  Gamma.20.pep   Gamma.244.pep  Gamma.280.pep  Gamma.320.pep  Gamma.361.pep  Gamma.63.pep  Gamma.97.pep
Gamma.133.pep    Gamma.169.pep  Gamma.210.pep  Gamma.245.pep  Gamma.281.pep  Gamma.322.pep  Gamma.362.pep  Gamma.64.pep  Gamma.98.pep
Gamma.134.pep    Gamma.170.pep  Gamma.212.pep  Gamma.246.pep  Gamma.282.pep  Gamma.323.pep  Gamma.363.pep  Gamma.65.pep  Gamma.99.pep
Gamma.137.pep    Gamma.172.pep  Gamma.213.pep  Gamma.248.pep  Gamma.283.pep  Gamma.324.pep  Gamma.365.pep  Gamma.66.pep  Gamma.9.pep
Gamma.138.pep    Gamma.174.pep  Gamma.214.pep  Gamma.249.pep  Gamma.284.pep  Gamma.325.pep  Gamma.366.pep  Gamma.67.pep
[samapps@euler04 test2]$

The second command was also running fine and I got the .aln and .mask files:

[samapps@e1001 test2]$ MarkerAlignTrim.pl -WithReference -OutputFormat phylip                       
Aligning Gamma.280 ...

Aligning Gamma.89 ...

Aligning Gamma.142 ...

Aligning Gamma.164 ...

Aligning Gamma.163 ...

Aligning Gamma.355 ...

Aligning Gamma.22 ...

Aligning Gamma.217 ...

Aligning Gamma.82 ...

Aligning Gamma.286 ...

Aligning Gamma.202 ...

Aligning Gamma.88 ...

[samapps@euler04 test2]$ ls
ecoli.fasta      Gamma.144.mask  Gamma.184.mask  Gamma.22.mask   Gamma.268.mask  Gamma.311.mask  Gamma.359.mask  Gamma.64.mask
ecoli.fasta.orf  Gamma.144.pep   Gamma.184.pep   Gamma.22.pep    Gamma.268.pep   Gamma.311.pep   Gamma.359.pep   Gamma.64.pep
Gamma.100.aln    Gamma.145.aln   Gamma.185.aln   Gamma.230.aln   Gamma.26.aln    Gamma.312.aln   Gamma.35.aln    Gamma.65.aln
Gamma.100.mask   Gamma.145.mask  Gamma.185.mask  Gamma.230.mask  Gamma.26.mask   Gamma.312.mask  Gamma.35.mask   Gamma.65.mask
Gamma.100.pep    Gamma.145.pep   Gamma.185.pep   Gamma.230.pep   Gamma.26.pep    Gamma.312.pep   Gamma.35.pep    Gamma.65.pep
Gamma.101.aln    Gamma.146.aln   Gamma.186.aln   Gamma.231.aln   Gamma.270.aln   Gamma.314.aln   Gamma.360.aln   Gamma.66.aln
Gamma.101.mask   Gamma.146.mask  Gamma.186.mask  Gamma.231.mask  Gamma.270.mask  Gamma.314.mask  Gamma.360.mask  Gamma.66.mask
Gamma.101.pep    Gamma.146.pep   Gamma.186.pep   Gamma.231.pep   Gamma.270.pep   Gamma.314.pep   Gamma.360.pep   Gamma.66.pep
Gamma.103.aln    Gamma.147.aln   Gamma.187.aln   Gamma.232.aln   Gamma.271.aln   Gamma.316.aln   Gamma.361.aln   Gamma.67.aln

(truncated output)

But when running the third command, I only receive error messages:

[samapps@e1001 test2]$ Phylotyping.pl -CPUs 24 > phylotype.result 
Error occured when assigning phylotype for Gamma.7
Error occured when assigning phylotype for Gamma.294
Error occured when assigning phylotype for Gamma.103
Error occured when assigning phylotype for Gamma.68
Error occured when assigning phylotype for Gamma.133
Error occured when assigning phylotype for Gamma.124

(truncated output)

and at the end

cat: *.phylotype: No such file or directory

Do you have any idea what could be the reason for the errors during the Phylotyping.pl run ?

[anausc]

Hi samfux84,
I have the same error as you. Did you fix it finally?

[samfux84]

@anausc Unfortunately we could not fix the problem.