Fastmer.py error

[Ashma45]

Hi, I am using assembly_accuracy first time. I am getting the following error. Can you help me fix the issue?

Thank you

(base) [achakraw@vacc-user1 assembly_accuracy]$ ~/WGS/test/raw_reads/prokka_reads/assembly_accuracy/fastmer.py --reference GCF_000013425.1_ASM1342v1_genomic.fna --assembly 105_r2_prokka/*fsa --min-mapping-quality 10

Traceback (most recent call last): File "/users/a/c/achakraw/WGS/test/raw_reads/prokka_reads/assembly_accuracy/fastmer.py", line 304, in subprocess.check_call(mm2_cmd, stdout=devnull, stderr=devnull, shell=True) File "/users/a/c/achakraw/miniconda3/lib/python3.6/subprocess.py", line 311, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command 'minimap2 -Y -a -x asm5 GCF_000013425.1_ASM1342v1_genomic.fna 105_r2_prokka/fsa | samtools sort -T 105_r2_prokka/fsa.assembly_analysis.sorted.bam.tmp -o 105_r2_prokka/*fsa.assembly_analysis.sorted.bam -' returned non-zero exit status 127.

[jts]

Hi,

This repository is largely unmaintained so I apologize for the poor documentation and lack of error handling.

This error is likely because minimap2 is not found on your PATH.

Jared

On Sep 2, 2020, at 8:28 PM, Ashma Chakrawarti notifications@github.com wrote:

 Hi, I am using assembly_accuracy first time. I am getting the following error. Can you help me fix the issue?

Thank you

(base) [achakraw@vacc-user1 assembly_accuracy]$ ~/WGS/test/raw_reads/prokka_reads/assembly_accuracy/fastmer.py --reference GCF_000013425.1_ASM1342v1_genomic.fna --assembly 105_r2_prokka/fsa --min-mapping-quality 10 Traceback (most recent call last): File "/users/a/c/achakraw/WGS/test/raw_reads/prokka_reads/assembly_accuracy/fastmer.py", line 304, in subprocess.check_call(mm2_cmd, stdout=devnull, stderr=devnull, shell=True) File "/users/a/c/achakraw/miniconda3/lib/python3.6/subprocess.py", line 311, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command 'minimap2 -Y -a -x asm5 GCF_000013425.1_ASM1342v1_genomic.fna 105_r2_prokka/fsa | samtools sort -T 105_r2_prokka/fsa.assembly_analysis.sorted.bam.tmp -o 105_r2_prokka/fsa.assembly_analysis.sorted.bam -' returned non-zero exit status 127.

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[Ashma45]

Thank you, Jared!

I too doubted that minimap2 was not present on my PATH. But it is present when I check using minimap -h I see the documentation mentions pyvcf and pysam. I installed both using conda but when I call pyvcf -h it returns as command not found.

[jts]

Is samtools available on your PATH as well?

[Ashma45]

Yes, the samtools is available on PATH. This time the error is as following

Traceback (most recent call last): File "./fastmer.py", line 6, in import vcf ModuleNotFoundError: No module named 'vcf'

From: Jared Simpson notifications@github.com Sent: Saturday, September 5, 2020 10:30 AM To: jts/assembly_accuracy assembly_accuracy@noreply.github.com Cc: Ashma Chakrawarti Ashma.Chakrawarti@uvm.edu; Author author@noreply.github.com Subject: Re: [jts/assembly_accuracy] Fastmer.py error (#1)

Is samtools available on your PATH as well?

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[jts]

Both of those are python packages - can you try to install them using pip?

Jared

On Thu, Sep 10, 2020 at 1:20 PM Ashma Chakrawarti notifications@github.com wrote:

Thank you, Jared!

I too doubted that minimap2 was not present on my PATH. But it is present when I check using minimap -h I see the documentation mentions pyvcf and pysam. I installed both using conda but when I call pyvcf -h it returns as command not found.

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