Test file error

[yxu405]

Hi guys, I am not sure if I am installing incorrectly. But I followed the installation instructions and didn't quite see any errors installing the dependencies. I am not sure if I am running this correctly.

After the last step of the installation, I ran the following commands:

1. conda activate IGv2
2. IG phase subset_bam/reads.bam test

And here is the error message it popped up. I am not sure if I was supposed to run it in the base environment. I did install whatshap like stated in the instructions. For some reason it is not detecting it. I also tried running IG in my base environment. It didn't quite detect other dependencies.

---

Checking test/tmp/ccs.fasta
Running command...
bam2fasta -o test/tmp/ccs.fasta subset_bam/reads.bam
zcat test/tmp/ccs.fasta.fasta.gz | sed 's/ccs/0_8/g' | sed 's//fwd//g' | sed 's//rev//g' > test/tmp/ccs.fasta

terminate called after throwing an instance of 'std::out_of_range'
what(): map::at
Aborted (core dumped)

gzip: test/tmp/ccs.fasta.fasta.gz: unexpected end of file

Mapping CCS reads...

Checking test/tmp/snvs_candidates.vcf
Running command...
CONDA_BASE=$(conda info --base)
source ${CONDA_BASE}/etc/profile.d/conda.sh
conda activate whatshap-latest
whatshap find_snv_candidates --sample sample /private/home/yxu267/anaconda3/envs/IGv2/lib/python2.7/site-packages/IGenotyper-1.1-py2.7.egg/IGenotyper/data/reference.fasta test/preprocessed/ccs_to_ref.sorted.bam --pacbio -o test/tmp/snvs_candidates.vcf #> /dev/null 2>&1 conda deactivate
sh: 2: source: not found

CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run

$ conda init <SHELL_NAME>

Currently supported shells are:

• bash
• fish
• tcsh
• xonsh
• zsh
• powershell

See 'conda init --help' for more information and options.

IMPORTANT: You may need to close and restart your shell after running 'conda init'.

sh: 4: whatshap: not found

---

Checking test/variants/snvs_from_ccs.vcf
Running command...
CONDA_BASE=$(conda info --base)
source ${CONDA_BASE}/etc/profile.d/conda.sh
conda activate whatshap-latest
whatshap genotype --sample sample --ignore-read-groups --reference /private/home/yxu267/anaconda3/envs/IGv2/lib/python2.7/site-packages/IGenotyper-1.1-py2.7.egg/IGenotyper/data/reference.fasta -o test/variants/snvs_from_ccs.vcf test/tmp/snvs_candidates.vcf test/preprocessed/ccs_to_ref.sorted.bam #> /dev/null 2>&1 conda deactivate
sh: 2: source: not found

CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run

$ conda init <SHELL_NAME>

Currently supported shells are:

• bash
• fish
• tcsh
• xonsh
• zsh
• powershell

See 'conda init --help' for more information and options.

IMPORTANT: You may need to close and restart your shell after running 'conda init'.

sh: 4: whatshap: not found

---

Checking test/variants/snvs_phased_from_ccs.vcf
Running command...
CONDA_BASE=$(conda info --base)
source ${CONDA_BASE}/etc/profile.d/conda.sh
conda activate whatshap-latest
whatshap phase --sample sample --reference /private/home/yxu267/anaconda3/envs/IGv2/lib/python2.7/site-packages/IGenotyper-1.1-py2.7.egg/IGenotyper/data/reference.fasta --ignore-read-groups --distrust-genotypes -o test/variants/snvs_phased_from_ccs.vcf test/variants/snvs_from_ccs.vcf test/preprocessed/ccs_to_ref.sorted.bam #> /dev/null 2>&1
conda deactivate
sh: 2: source: not found

CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run

$ conda init <SHELL_NAME>

Currently supported shells are:

• bash
• fish
• tcsh
• xonsh
• zsh
• powershell

See 'conda init --help' for more information and options.

IMPORTANT: You may need to close and restart your shell after running 'conda init'.

sh: 4: whatshap: not found

CommandNotFoundError: Your shell has not been properly configured to use 'conda deactivate'.
To initialize your shell, run

$ conda init <SHELL_NAME>

Currently supported shells are:

• bash
• fish
• tcsh
• xonsh
• zsh
• powershell

See 'conda init --help' for more information and options.

IMPORTANT: You may need to close and restart your shell after running 'conda init'.

---

Traceback (most recent call last):
File "/private/home/yxu267/anaconda3/envs/IGv2/bin/IG", line 11, in
load_entry_point('IGenotyper==1.1', 'console_scripts', 'IG')()
File "/private/home/yxu267/anaconda3/envs/IGv2/lib/python2.7/site-packages/IGenotyper-1.1-py2.7.egg/IGenotyper/main.py", line 35, in main
command.main(args)
File "/private/home/yxu267/anaconda3/envs/IGv2/lib/python2.7/site-packages/IGenotyper-1.1-py2.7.egg/IGenotyper/commands/phase.py", line 114, in main
run_phasing(**vars(args))
File "/private/home/yxu267/anaconda3/envs/IGv2/lib/python2.7/site-packages/IGenotyper-1.1-py2.7.egg/IGenotyper/commands/phase.py", line 90, in run_phasing
phase_ccs(files,sample)
File "/private/home/yxu267/anaconda3/envs/IGv2/lib/python2.7/site-packages/IGenotyper-1.1-py2.7.egg/IGenotyper/phasing/reads.py", line 89, in phase_ccs
phase_alignments(files.phased_snps_vcf,files.ccs_to_ref,sample,files.ccs_to_ref_phased)
File "/private/home/yxu267/anaconda3/envs/IGv2/lib/python2.7/site-packages/IGenotyper-1.1-py2.7.egg/IGenotyper/phasing/reads.py", line 67, in phase_alignments
vcf = read_in_phased_vcf(vcffn,sample)
File "/private/home/yxu267/anaconda3/envs/IGv2/lib/python2.7/site-packages/IGenotyper-1.1-py2.7.egg/IGenotyper/common/vcffn.py", line 49, in read_in_phased_vcf
vcf_reader = vcf.Reader(open(vcffn, 'r'))
IOError: [Errno 2] No such file or directory: 'test/variants/snvs_phased_from_ccs.vcf'