Comments (4)
I have a feeling you're not giving it a file because you first set
INgzbam="${!SGE_TASK_ID}"
but then use ${Ingzbam}
(with a lowercase n) when running methratio.py. After fixing that, I would make sure that your SGE_TASK_ID
corresponds to a valid (bam|bsp|sam) file.
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Yes that indeed was the issue. Thank you. It reads the input file now but however, after running the script again, I get the following error:
"""
[methratio] @thu May 5 13:26:20 2022 Presorting inputs
[methratio] @thu May 5 13:26:20 2022 Calling samtools sort on S10.sorted.deduped.bam and using 4716 MB of memory
sort: invalid option -- '@'
sort: invalid option -- 'O'
sort: invalid option -- 'T'
open: No such file or directory
[bam_sort_core] fail to open file 64
open: No such file or directory
[bam_index_build2] fail to open the BAM file.
[methratio] @thu May 5 13:26:20 2022 Processing 64 chromosomes at a time
[methratio] @thu May 5 13:26:20 2022 Reading GL000194.1 from S10.sorted.deduped.tmpSrt.bam with samtools
[methratio] @thu May 5 13:26:20 2022 S10.sorted.deduped.tmpSrt.bam should have been presorted.
there is more and it just ends with "1 failed to process"
"""
I had already sorted and deduplicated bam files before processing the methratio.py.
I have activated both - 1) module for samtools in my cluster 2) given the PATH to samtools which came with BSMAPz installation.
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I have a feeling it's because you're adding an old version of samtools to your path. Try commenting out
export PATH="/wynton/home/pillailab/agala/.local/bin/BSMAPz-1.1.3/samtools:$PATH"
so you can use samtools from the samtools/1.9
module and re-running.
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Yes that was indeed the issue. Thank you for resolving it.
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Related Issues (20)
- Segmentation Fault when Loading Reference HOT 3
- methratio exception HOT 8
- query regarding methylation level from methylratio output file. HOT 1
- Float point error in methratio.py HOT 4
- methratio.py error
- ZeroDivisionError: float division by zero HOT 1
- Significantly different in number of covered cytosines between bsmap 2.90 and BSMAPz HOT 4
- ZeroDivisionError HOT 4
- Segmentation fault - core dumped
- methratio.py and Identification of methylated cytosine sites
- OverflowError in methratio.py
- methdiff.py error HOT 1
- "Illegal instruction" message when I launch bsmapz
- When I run the script I get the error CMD: R --vanilla HOT 1
- methratio.py AssertionError HOT 3
- "AssertionError: String length does not match CIGAR" when running methratio.py
- methratio.py memory issue
- How to calculate sequencing depth HOT 1
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