Installation issues

[nixon444]

Hello again,

I have installed refineM as per instructions, including seperate dependencies, but when I type 'refinem -h' I get the following:

Traceback (most recent call last): File "/usr/local/bin/refinem", line 33, in from refinem.main import OptionsParser File "/usr/local/lib/python2.7/dist-packages/refinem/main.py", line 23, in from refinem.scaffold_stats import ScaffoldStats File "/usr/local/lib/python2.7/dist-packages/refinem/scaffold_stats.py", line 29, in from refinem.coverage import Coverage File "/usr/local/lib/python2.7/dist-packages/refinem/coverage.py", line 30, in import pysam ImportError: No module named pysam

I then installed pysam on the off-chance this was a missing program but it didn't help.

Any ideas?

[raw937]

I have the same problem and issue. Traceback (most recent call last): File "/usr/local/bin/refinem", line 33, in from refinem.main import OptionsParser File "/usr/local/lib/python2.7/dist-packages/refinem/main.py", line 23, in from refinem.scaffold_stats import ScaffoldStats File "/usr/local/lib/python2.7/dist-packages/refinem/scaffold_stats.py", line 29, in from refinem.coverage import Coverage File "/usr/local/lib/python2.7/dist-packages/refinem/coverage.py", line 30, in import pysam ImportError: No module named pysam

[donovan-h-parks]

Best guess is that pysam is not installed for the correct version of Python. CheckM uses Python 2 so pysam must be installed for this version of Python.

[raw937]

? How to fix? I went pip install refinem.

[donovan-h-parks]

pip install pysam

[raw937]

installed same error refinem scaffold_stats -c 8 refine_tmac/Paenibacillus_tmac-D7_raw-assem.fa refine_tmac/ refine_tmac/refinem_out/ refine_tmac/D7_mates.sam Traceback (most recent call last): File "/usr/local/bin/refinem", line 33, in from refinem.main import OptionsParser File "/usr/local/lib/python2.7/dist-packages/refinem/main.py", line 23, in from refinem.scaffold_stats import ScaffoldStats File "/usr/local/lib/python2.7/dist-packages/refinem/scaffold_stats.py", line 29, in from refinem.coverage import Coverage File "/usr/local/lib/python2.7/dist-packages/refinem/coverage.py", line 30, in import pysam ImportError: No module named pysam

[donovan-h-parks]

From the Python interpreter command line can you do a import pysam? Make sure you are in Python 2.

[raw937]

Weird.

It appears not to be installed.

import pysam as py Traceback (most recent call last): File "", line 1, in File "/home/raw937/anaconda2/lib/python2.7/site-packages/pysam/init.py", line 5, in from pysam.libchtslib import * File "pysam/libchtslib.pyx", line 1, in init pysam.libchtslib ImportError: libchtslib.so: cannot open shared object file: No such file or directory import pysam Traceback (most recent call last): File "", line 1, in File "/home/raw937/anaconda2/lib/python2.7/site-packages/pysam/init.py", line 6, in from pysam.libcsamtools import * ImportError: libchtslib.so: cannot open shared object file: No such file or directory

pip install pysam Requirement already satisfied: pysam in ./anaconda2/lib/python2.7/site-packages (0.15.3)

SO weird!

[donovan-h-parks]

I'm not familiar with how Anaconda works, but this looks like pysam is install in the Anaconda version of Python in your home directory and not the system wide version of Python which is what is likely being used by CheckM.

[raw937]

Hey mate,

So, this installed it I think.

conda activate base (my base is python 2.7.15) -> now in (base) conda install pysam pip install refinem (no package called dendropy) pip install dendropy

It appears but it can't find the nucleotide fasta: refinem scaffold_stats -c 8 --genome_ext ~/Desktop/refine_tmac/Paenibacillus_tmac-D7_raw-assem.fasta ~/Desktop/refine_tmac/ ~/Desktop/refine_tmac/refinem_out/ ~/Desktop/refine_tmac/D7_mates.sam

I even give it the full paths still states.

[2019-07-30 15:30:07] ERROR: Input file does not exists: /home/raw937/Desktop/refine_tmac/ [2019-07-30 15:30:07] ERROR: Input file does not exists: /home/raw937/Desktop/refine_tmac/ Controlled exit resulting from an unrecoverable error or warning.

[donovan-h-parks]

If your genomes don't have the extension fna you need to indicate what extension they do have with the genome_ext flag.

[raw937]

refinem scaffold_stats -c 8 --genome_ext fna /home/raw937/Desktop/refine_tmac/Paenibacillus_tmac-D7_raw-assem.fna /home/raw937/Desktop/refine_tmac/ /home/raw937/Desktop/refine_tmac/refinem_out/ /home/raw937/Desktop/refine_tmac/D7_mates.bam

[2019-07-30 16:02:59] ERROR: BAM index file is missing: /home/raw937/Desktop/refine_tmac/D7_mates.bam.bai

??

[raw937]

refinem scaffold_stats -c 8 --genome_ext fna ~/Desktop/refine_tmac/Paenibacillus_tmac-D7_raw-assem.fna ~/Desktop/refine_tmac/ ~/Desktop/refine_tmac/refinem_out/ ~/Desktop/refine_tmac/D7_mates.bam [2019-08-09 14:04:46] INFO: RefineM v0.0.25 [2019-08-09 14:04:46] INFO: refinem scaffold_stats -c 8 --genome_ext fna /home/raw937/Desktop/refine_tmac/Paenibacillus_tmac-D7_raw-assem.fna /home/raw937/Desktop/refine_tmac/ /home/raw937/Desktop/refine_tmac/refinem_out/ /home/raw937/Desktop/refine_tmac/D7_mates.bam [2019-08-09 14:04:46] ERROR: BAM index file is missing: /home/raw937/Desktop/refine_tmac/D7_mates.bam.bai

Same issue? help?

[donovan-h-parks]

Does /home/raw937/Desktop/refine_tmac/D7_mates.bam.bai exist?

[raw937]

I guess the .bam.bai isn't found. Do I need to make it? Is their a samtools option?

[donovan-h-parks]

Indeed: samtools index

[raw937]

Another error? samtools index D7_mates.bam [E::hts_idx_push] Unsorted positions on sequence #39: 14777 followed by 14760 samtools index: failed to create index for "D7_mates.bam": No such file or directory

Sorted bam file?

[raw937]

It's a R1 and R2 mapped file.

[liujun2009sysu]

how do you solve this problem?