Problems running circlator

[jhernandez1409]

Hi, I installed circlator from here (github) and after installing all the dependencies listed here I ran 'circlator progcheck' but this is the error I keep getting and I have tried a lot of things including reinstalling all the dependencies and nothing seems to work. Help please!

Circlator version: 1.5.1

External dependencies: WARNING: Didn't find bwa in path. Looked for:bwa WARNING: Didn't find canu in path. Looked for:canu nucmer 3.1 /usr/bin/nucmer WARNING: Didn't find prodigal in path. Looked for:prodigal samtools 0.1.19 /usr/bin/samtools WARNING: Didn't find spades in path. Looked for:spades.py

Python version: 3.5.2 (default, Nov 17 2016, 17:05:23) [GCC 5.4.0 20160609]

Python dependencies: openpyxl 2.4.8 /home/jojo/.local/lib/python3.5/site-packages/openpyxl/init.py pyfastaq 3.15.0 /usr/local/lib/python3.5/dist-packages/pyfastaq-3.15.0-py3.5.egg/pyfastaq/init.py pymummer 0.10.2 /usr/local/lib/python3.5/dist-packages/pymummer-0.10.2-py3.5.egg/pymummer/init.py pysam 0.11.2.2 /home/jojo/.local/lib/python3.5/site-packages/pysam/init.py

Thanks in advance,

JoJo

[yjx1217]

Hi JoJo,

It seems that the problem lies in Circlator cannot detect those tools in your $PATH environment viriable. If you correctly add the full path to those tools to your $PATH, the problem should be solved.

You can check this link for the details on setting $PATH.

Best, Jia-Xing

[jhernandez1409]

Hi Jia-Xing

Thank you for replying. I did the following to set up the tools to my $PATH, and I did it for all the dependencies and tried multiple times but it didn't work:

export PATH=$PATH:/home/jojo/Desktop/Software_Bioinformatics/canu-1.5

Do you know another way I should do it?

Thanks,

JoJo

[yjx1217]

Hi JoJo,

You need to add the full path to the binary files, for example, for canu it will be: export PATH=$PATH:/home/jojo/Desktop/Software_Bioinformatics/canu-1.5/Linux-amd64/bin

Best, Jia-Xing

[martinghunt]

Thanks @yjx1217 for the helpful comments!

@jhernandez1409 just to expand a bit: you can test if the depenencies are installed by just trying to run them. e.g. just running:

bwa

should work and print the help, and not give an error like bwa: command not found.

[jhernandez1409]

Thank you Jia-Xing and Martin! However, I dont understand why I still have problems. Below is the output when I tried to run circlator, just in case you guys can help me with this. Thanks for all your help.

JoJo

Checking external programs __ Circlator version: 1.5.1

External dependencies: bwa 0.7.12 /usr/bin/bwa canu 1.5 /home/jojo/Desktop/Software_Bioinformatics/canu-1.5/Linux-amd64/bin/canu nucmer 3.1 /usr/bin/nucmer prodigal 2.50 /home/jojo/Desktop/Software_Bioinformatics/prodigal.v2_50/prodigal samtools 0.1.19 /usr/bin/samtools spades 3.7.1 /home/jojo/Desktop/Software_Bioinformatics/SPAdes-3.7.1/spades.py

Python version: 3.5.2 (default, Nov 17 2016, 17:05:23) [GCC 5.4.0 20160609]

Python dependencies: openpyxl 2.4.8 /home/jojo/.local/lib/python3.5/site-packages/openpyxl/init.py pyfastaq 3.15.0 /usr/local/lib/python3.5/dist-packages/pyfastaq-3.15.0-py3.5.egg/pyfastaq/init.py pymummer 0.10.2 /usr/local/lib/python3.5/dist-packages/pymummer-0.10.2-py3.5.egg/pymummer/init.py pysam 0.11.2.2 /home/jojo/.local/lib/python3.5/site-packages/pysam/init.py __ Running mapreads _ samtools 0.1.19 /usr/bin/samtools bwa 0.7.12 /usr/bin/bwa syscall: bwa index -p 01.mapreads.bam.tmp.bwa_index 00.input_assembly.fasta syscall: bwa mem -x pacbio -t 8 01.mapreads.bam.tmp.bwa_index /home/jojo/Desktop/Lab/Guatemala/Pacbio_Data/Canu_output_JoJo5_all_sensitive/JoJo5_all_canu_output_sensitive.correctedReads.fasta.gz | samtools view -F 0x0800 -T 00.input_assembly.fasta -b -o 01.mapreads.bam.tmp.unsorted.bam - syscall: samtools sort -@ 4 -m 125M 01.mapreads.bam.tmp.unsorted.bam 01.mapreads syscall: samtools index 01.mapreads.bam Running bam2reads __ Getting reads from BAM file /home/jojo/Desktop/Lab/Guatemala/Pacbio_Data/circlator_output/circlatorJoJo5all_sensitive/01.mapreads.bam Getting all reads that map to ends of contig tig00000004. Coords: 1-50000;113973-163972 Getting all reads that map to contig tig00000009 Getting all reads that map to ends of contig tig00000015. Coords: 1-50000;869169-919168 Getting all reads that map to contig tig00000016 Getting all reads that map to ends of contig tig00000017. Coords: 1-50000;3884692-3934691 Getting all unmapped reads Finished getting reads. Log file: /home/jojo/Desktop/Lab/Guatemala/Pacbio_Data/circlator_output/circlatorJoJo5all_sensitive/02.bam2reads.log Reads file: /home/jojo/Desktop/Lab/Guatemala/Pacbio_Data/circlator_output/circlatorJoJo5allsensitive/02.bam2reads.fasta __ Running assemble __ samtools 0.1.19 /usr/bin/samtools spades 3.7.1 /home/jojo/Desktop/Software_Bioinformatics/SPAdes-3.7.1/spades.py syscall: spades.py -s /home/jojo/Desktop/Lab/Guatemala/Pacbio_Data/circlator_output/circlatorJoJo5all_sensitive/02.bam2reads.fasta -o /home/jojo/Desktop/Lab/Guatemala/Pacbio_Data/circlator_output/circlatorJoJo5all_sensitive/03.assemble.tmp.spades.127.zeb7_gd1 -t 8 -k 127 --careful --only-assembler syscall: spades.py -s /home/jojo/Desktop/Lab/Guatemala/Pacbio_Data/circlator_output/circlatorJoJo5all_sensitive/02.bam2reads.fasta -o /home/jojo/Desktop/Lab/Guatemala/Pacbio_Data/circlator_output/circlatorJoJo5all_sensitive/03.assemble.tmp.spades.117.ddvu2q7j -t 8 -k 117 --careful --only-assembler syscall: spades.py -s /home/jojo/Desktop/Lab/Guatemala/Pacbio_Data/circlator_output/circlatorJoJo5all_sensitive/02.bam2reads.fasta -o /home/jojo/Desktop/Lab/Guatemala/Pacbio_Data/circlator_output/circlatorJoJo5all_sensitive/03.assemble.tmp.spades.107.hr_inz0d -t 8 -k 107 --careful --only-assembler syscall: spades.py -s /home/jojo/Desktop/Lab/Guatemala/Pacbio_Data/circlator_output/circlatorJoJo5all_sensitive/02.bam2reads.fasta -o /home/jojo/Desktop/Lab/Guatemala/Pacbio_Data/circlator_output/circlatorJoJo5all_sensitive/03.assemble.tmp.spades.97.t5_78vps -t 8 -k 97 --careful --only-assembler syscall: spades.py -s /home/jojo/Desktop/Lab/Guatemala/Pacbio_Data/circlator_output/circlatorJoJo5all_sensitive/02.bam2reads.fasta -o /home/jojo/Desktop/Lab/Guatemala/Pacbio_Data/circlator_output/circlatorJoJo5all_sensitive/03.assemble.tmp.spades.87.q72zgun8 -t 8 -k 87 --careful --only-assembler syscall: spades.py -s /home/jojo/Desktop/Lab/Guatemala/Pacbio_Data/circlator_output/circlatorJoJo5all_sensitive/02.bam2reads.fasta -o /home/jojo/Desktop/Lab/Guatemala/Pacbio_Data/circlator_output/circlatorJoJo5all_sensitive/03.assemble.tmp.spades.77.apbx71 -t 8 -k 77 --careful --only-assembler Traceback (most recent call last): File "/home/jojo/Desktop/Software_Bioinformatics/circlator-1.5.1/scripts/circlator", line 58, in exec('circlator.tasks.' + task + '.run()') File "", line 1, in File "/usr/local/lib/python3.5/dist-packages/circlator-1.5.1-py3.5.egg/circlator/tasks/all.py", line 169, in run a.run() File "/usr/local/lib/python3.5/dist-packages/circlator-1.5.1-py3.5.egg/circlator/assemble.py", line 176, in run self.run_spades(stop_at_first_success=self.spades_use_first_success) File "/usr/local/lib/python3.5/dist-packages/circlator-1.5.1-py3.5.egg/circlator/assemble.py", line 145, in run_spades raise Error('Error running SPAdes. Output directories are:\n ' + '\n '.join(kmer_to_dir.values()) + '\nThe reason why should be in the spades.log file in each directory.') circlator.assemble.Error: Error running SPAdes. Output directories are: /home/jojo/Desktop/Lab/Guatemala/Pacbio_Data/circlator_output/circlatorJoJo5all_sensitive/03.assemble.tmp.spades.97.t5_78vps /home/jojo/Desktop/Lab/Guatemala/Pacbio_Data/circlator_output/circlatorJoJo5all_sensitive/03.assemble.tmp.spades.117.ddvu2q7j /home/jojo/Desktop/Lab/Guatemala/Pacbio_Data/circlator_output/circlatorJoJo5all_sensitive/03.assemble.tmp.spades.87.q72zgun8 /home/jojo/Desktop/Lab/Guatemala/Pacbio_Data/circlator_output/circlatorJoJo5all_sensitive/03.assemble.tmp.spades.107.hr_inz0d /home/jojo/Desktop/Lab/Guatemala/Pacbio_Data/circlator_output/circlatorJoJo5all_sensitive/03.assemble.tmp.spades.77.apbx71 /home/jojo/Desktop/Lab/Guatemala/Pacbio_Data/circlator_output/circlatorJoJo5all_sensitive/03.assemble.tmp.spades.127.zeb7_gd1 The reason why should be in the spades.log file in each directory.