Uncaught exception from user code: Error running buildSNPDB.pl

[dineshkumarsrk]

I have successfully installed Phame on my Desktop computer through conda (Ubuntu 16.04 64 bit OS; 8 GB RAM, Core i7 processor). I had ran the test files successfully, however while I run my genomes of interest I end up with a error as follows,

(base) ga214@ga:~/Downloads/PhaME/src$ ./phame ecoli.ctl 
[12:48:23] Checking version: samtools --version is >= 1.3 - ok, have 1.13
[12:48:23] Checking version: bcftools --version is >= 1.3 - ok, have 1.13
[12:48:23] Checking version: nucmer --version is >= 3.1 - ok, have 3.1
[12:48:23] Checking version: bowtie2 --version is >= 2.3 - ok, have 2.4
[12:48:23] Checking version: bwa is >= 0.7 - ok, have 0.7
[12:48:23] Checking version: FastTree -expert is >= 2.1 - ok, have 2.1
[12:48:25] Checking version: bbmap.sh -v is >= 38.06 - ok, have 38.91
[12:48:25] Checking version: raxmlHPC-PTHREADS -version is >= 8.2 - ok, have 8.2
[00:00:03]  Dependencies look good!
PhaME v1.0.5 

[00:00:03]  Loading information
	refdir = /home/ga214/Downloads/PhaME/test/data/citri
	workdir = /home/ga214/Downloads/PhaME/test/workdirs
	outdir = /home/ga214/Downloads/PhaME/test/workdirs/results
	project = Testecoli
	cdsSNPS = 0
	buildSNPdb:	0
	data:	3
	No Trees to be made.
	Reference:	/home/ga214/Downloads/PhaME/test/data/citri/X_citri_str_UnB-Xtec2D_REFERENCE.fasta
	SNPs filter:	0
	Code:	bacteria
	Log file:	/home/ga214/Downloads/PhaME/test/workdirs/results/Testecoli.log
	Error file:	/home/ga214/Downloads/PhaME/test/workdirs/results/Testecoli.error
[00:00:03]  Checking directories and files... 
[00:00:03]  Running PhaME for Complete and genomes with contigs
[00:00:03]  Complete. 
[00:00:03]  Preparing files... 
[00:00:50]  Complete. 
[00:00:50]  Running NUCmer on complete genomes
[00:01:25]  NUCmer on genomes complete
[00:01:25]  Running NUCmer on contigs
[04:36:46]  Beginning SNP detection pipeline
[04:36:46]  Starting with gaps
[04:37:09]  Gap identification complete
[04:37:09]  Preparing to identify SNPs
Uncaught exception from user code:
	Error running buildSNPDB.pl -i /home/ga214/Downloads/PhaME/test/workdirs/results -r /home/ga214/Downloads/PhaME/test/workdirs/files/X_citri_str_UnB_Xtec2D_REFERENCE.fna -l /home/ga214/Downloads/PhaME/test/workdirs/working_list.txt -p Testecoli -c 0 -g 0.1 2>>/home/ga214/Downloads/PhaME/test/workdirs/results/Testecoli.error >> /home/ga214/Downloads/PhaME/test/workdirs/results/Testecoli.log
	
	.
	PhaME::buildSNPDB("/home/ga214/Downloads/PhaME/test/workdirs/results", "/home/ga214/Downloads/PhaME/src", "/home/ga214/Downloads/PhaME/test/workdirs/files/X_citri_str_U"..., "/home/ga214/Downloads/PhaME/test/workdirs/working_list.txt", "Testecoli", 0, "/home/ga214/Downloads/PhaME/test/workdirs/results/Testecoli.e"..., "/home/ga214/Downloads/PhaME/test/workdirs/results/Testecoli.log", ...) called at ./phame line 794

Please help me to fix this issue.

Thanks in advance.

[tsierocinski]

got similar errors on test files:

docker run --mount type=bind,source=$(pwd),destination="/data" quay.io/biocontainers/phame:1.0.3--0 phame /data/t1_ebola_preads.ctl
[00:00:00] Checking version: samtools --version is >= 1.3 - ok, have 1.9
[00:00:00] Checking version: bcftools --version is >= 1.3 - ok, have 1.9
[00:00:00] Checking version: nucmer --version is >= 3.1 - ok, have 3.1
[00:00:00] Checking version: bowtie2 --version is >= 2.3 - ok, have 2.3
[00:00:00] Checking version: bwa is >= 0.7 - ok, have 0.7
[00:00:00] Checking version: FastTree -expert is >= 2.1 - ok, have 2.1
[00:00:00] Checking version: bbmap.sh -v is >= 38.06 - ok, have 38.22
[00:00:00] Checking version: raxmlHPC-PTHREADS -version is >= 8.2 - ok, have 8.2
[00:00:00] Dependencies look good!

[00:00:00] Loading information
Refd: /data/ebola_ref
Workd: /data/workdirs/t1_ebola_preads
Outd: /data/workdirs/t1_ebola_preads/results
Reference: /data/ebola_ref/KJ660347.ref_genome.fasta
Code: virus
Log file: /data/workdirs/t1_ebola_preads/results/t1.log
Error file: /data/workdirs/t1_ebola_preads/results/t1.error
[00:00:00] Checking directories and files...
[00:00:00] Complete.
[00:00:00] Preparing files...
[00:00:00] Complete.
[00:00:00] Running NUCmer on complete genomes
[00:00:10] NUCmer on genomes complete
[00:00:10] Preparing to map reads
[00:00:10] Mapping reads to reference
[00:00:17] Read Mapping complete
[00:00:17] Beginning SNP detection pipeline
[00:00:17] Starting with gaps
[00:00:17] Gap identification complete
[00:00:17] Preparing to identify SNPs
[00:00:18] SNP database complete
[00:00:18] Reconstructing all SNPs phylogeny
Uncaught exception from user code:
Error running iqtree -m TEST -s /data/workdirs/t1_ebola_preads/results/t1_all_snp_alignment.fna -nt 2 -bc 0 2>>/data/workdirs/t1_ebola_preads/results/t1.error >> /data/workdirs/t1_ebola_preads/results/t1.log

.
PhaME::buildTree("/usr/local/bin", "/data/workdirs/t1_ebola_preads/results", 2, 4, "t1_all", 0, "/data/workdirs/t1_ebola_preads/results/t1.error", "/data/workdirs/t1_ebola_preads/results/t1.log") called at /usr/local/bin/phame line 766