Comments (6)
cmhill-zz
commented on August 21, 2024
Thanks for the detailed output. In the meantime, would you also have a link to a sample (or the whole) of the reads?
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jbadomics
commented on August 21, 2024
You should be able to pull them from here: https://www.dropbox.com/s/3zp6wzv8shd96j8/951pear.assembled.fasta.gz?dl=0
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cmhill-zz
commented on August 21, 2024
The issue was that the input reads were erroneously treated as FASTQ. I've fixed the issue in the latest commits. Add a -f to specify that the input reads are in FASTA format. Thanks for bringing this to my attention!
python src/py/valet.py -a data/951.final.renamed.headers.fasta.txt -r data/951pear.assembled.fasta -f --threads 16
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jbadomics
commented on August 21, 2024
Awesome, thanks! The pipeline completes successfully now, except I can't tell for sure if if the output I'm getting is correct - the log is saying a particular .bed file could not be found, and the overall coverage.bed file is empty (as are summary.bed and suspicious.bed). So the final summary.tsv file is showing no assembly errors (would be great if this is in fact true), but I'm not convinced this is the case since some of the files are empty. Any ideas or suggestions? Results here (4.5 GB total) if it would help.
$ python /home/bonddr/badalame/Software/cmhill_VALET/src/py/valet.py -a 951.final.renamed.headers.fasta -r ../02-pear/951pear.assembled.fasta -f -p 24 -o VALET_out -g 5 -z 1000 -b 50
###########################################################################
PROCESSING ASSEMBLY: asm_0 (951.final.renamed.headers.fasta)
###########################################################################
---------------------------------------------------------------------------
STEP: FILTERING ASSEMBLY CONTIGS LESS THAN 1000 BPs
RESULTS: VALET_out/asm_0/filtered_assembly.fasta
---------------------------------------------------------------------------
STEP: ALIGNING READS
COMMAND: bowtie2-build /panfs/roc/groups/1/bonddr/badalame/CoDL/DDH951/14-VALET/VALET_out/asm_0/filtered_assembly.fasta /panfs/roc/groups/1/bonddr/badalame/CoDL/DDH951/14-VALET/VALET_out/asm_0/indexes/temp_b5OHaI
COMMAND: bowtie2 -a -x /panfs/roc/groups/1/bonddr/badalame/CoDL/DDH951/14-VALET/VALET_out/asm_0/indexes/temp_b5OHaI -f -U ../02-pear/951pear.assembled.fasta --very-sensitive -a --reorder -p 24 --un /panfs/roc/groups/1/bonddr/badalame/CoDL/DDH951/14-VALET/VALET_out/asm_0/unaligned_reads/unaligned.reads -S VALET_out/asm_0/sam/library.sam
---------------------------------------------------------------------------
STEP: RUNNING SAMTOOLS
COMMAND: samtools view -F 0x100 -bS VALET_out/asm_0/sam/library.sam
COMMAND: samtools sort VALET_out/asm_0/bam/library.bam VALET_out/asm_0/bam/sorted_library
COMMAND: samtools mpileup -C50 -A -f VALET_out/asm_0/filtered_assembly.fasta VALET_out/asm_0/bam/sorted_library.bam
RESULTS: VALET_out/asm_0/coverage/mpileup_output.out
COMMAND: samtools index VALET_out/asm_0/bam/sorted_library.bam
---------------------------------------------------------------------------
STEP: CALCULATING CONTIG COVERAGE
RESULTS: VALET_out/asm_0/coverage/temp.cvg
---------------------------------------------------------------------------
STEP: PARTITIONING COVERAGE FILE
COMMAND: /home/bonddr/badalame/Software/cmhill_VALET/src/py/split_pileup.py -p VALET_out/asm_0/coverage/mpileup_output.out -c 24
---------------------------------------------------------------------------
STEP: DEPTH OF COVERAGE
COMMAND: /home/bonddr/badalame/Software/cmhill_VALET/src/py/depth_of_coverage.py -m VALET_out/asm_0/coverage/mpileup_output.out -w 501 -o VALET_out/asm_0/coverage/errors_cov.bed -g -e -c 24
COMMAND: bedtools sort -i VALET_out/asm_0/coverage/errors_cov.bed
Error: The requested file (VALET_out/asm_0/coverage/errors_cov.bed) could not be opened. Error message: (No such file or directory). Exiting!
RESULTS: VALET_out/asm_0/coverage.bed
---------------------------------------------------------------------------
STEP: BREAKPOINT
COMMAND: /home/bonddr/badalame/Software/cmhill_VALET/src/py/breakpoint_splitter.py -u /panfs/roc/groups/1/bonddr/badalame/CoDL/DDH951/14-VALET/VALET_out/asm_0/unaligned_reads/ -o VALET_out/asm_0/breakpoint/split_reads/
COMMAND: /home/bonddr/badalame/Software/cmhill_VALET/src/py/breakpoint_finder.py -a VALET_out/asm_0/filtered_assembly.fasta -r VALET_out/asm_0/breakpoint/split_reads/ -b 50 -o VALET_out/asm_0/breakpoint/ -c VALET_out/asm_0/coverage/temp.cvg -p 24 -f
COMMAND: bedtools sort -i VALET_out/asm_0/breakpoint/interesting_bins.bed
RESULTS: VALET_out/asm_0/breakpoint/../breakpoints.bed
---------------------------------------------------------------------------
STEP: SUMMARY
RESULTS: VALET_out/asm_0/summary.bed
RESULTS: VALET_out/asm_0/suspicious.bed
RESULTS: VALET_out/asm_0/summary.tsv
###########################################################################
GENERATING ASSEMBLY COMPARISON PLOTS
###########################################################################
COMMAND: Rscript /home/bonddr/badalame/Software/cmhill_VALET/src/R/compare_assemblies.R VALET_out/asm_0/summary.tsv asm_0 VALET_out/comparison_plots
RESULTS: VALET_out/comparison_plots.pdf
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nate-d-olson
commented on August 21, 2024
There was an error with the coverage analysis (see log file output below), but it was not reported during the run. The error should have been reported, I will work on fixing the bug. The error is associated with numpy, try re-installing numpy then rerunning VALET and let me know if it works.
Here is the text from the coverage/error.log file
Traceback (most recent call last):
File "/home/bonddr/badalame/Software/cmhill_VALET/src/py/depth_of_coverage.py", line 7, in <module>
import numpy as np
File "/home/bonddr/badalame/local/lib/python2.7/site-packages/numpy-1.9.2-py2.7-linux-x86_64.egg/numpy/__init__.py", line 170, in <module>
from . import add_newdocs
File "/home/bonddr/badalame/local/lib/python2.7/site-packages/numpy-1.9.2-py2.7-linux-x86_64.egg/numpy/add_newdocs.py", line 13, in <module>
from numpy.lib import add_newdoc
File "/home/bonddr/badalame/local/lib/python2.7/site-packages/numpy-1.9.2-py2.7-linux-x86_64.egg/numpy/lib/__init__.py", line 8, in <module>
from .type_check import *
File "/home/bonddr/badalame/local/lib/python2.7/site-packages/numpy-1.9.2-py2.7-linux-x86_64.egg/numpy/lib/type_check.py", line 11, in <module>
import numpy.core.numeric as _nx
File "/home/bonddr/badalame/local/lib/python2.7/site-packages/numpy-1.9.2-py2.7-linux-x86_64.egg/numpy/core/__init__.py", line 6, in <module>
from . import multiarray
ImportError: /home/bonddr/badalame/local/lib/python2.7/site-packages/numpy-1.9.2-py2.7-linux-x86_64.egg/numpy/core/multiarray.so: undefined symbol: PyUnicodeUCS2_AsASCIIString
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nate-d-olson
commented on August 21, 2024
I'm closing this issue. Let us know if you have any other problems with VALET.
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