Methratio.py does not handle files about bsmapz

[zyndagj]

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.

[Akshaygala]

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.

[zyndagj]

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.

[Akshaygala]

Yes that was indeed the issue. Thank you for resolving it.