bs_call finished with -6

[PrashantKuntala]

What could be the reason for bs_call to exit with -6 even after the alignment step completed without any errors ?

Some details on what, why and how my samples are being processed:

• It is a directional WGBS dataset.
• It is a paired-end library.
• mapping to hg38 reference.
• It is using the default IHEC.conf file for gemBS prepare step.
• gemBS is running on a highMEM (1TB RAM) and highCPU (144 CPU) node.

: Methylation Calling...
2023-02-08 12:27:40,034 ERROR: Process '~/.local/lib/python3.9/site-packages/gemBS/gemBSbinaries/bs_call' finished with -6
2023-02-08 12:27:40,039 ERROR: Additional threads:  8 5 5
2023-02-08 12:27:40,040 ERROR: Loading reference sequence index
2023-02-08 12:27:40,040 ERROR: Sequence index read in successfully
2023-02-08 12:27:40,041 ERROR: Opened ~/wgbs/test.bam for input (Index)
2023-02-08 12:27:40,041 ERROR: Processing region chr1:1-248956422
2023-02-08 12:27:40,041 ERROR: Processing chromosome chr1 (OK)
2023-02-08 12:27:40,042 ERROR: Loading reference for chr1
2023-02-08 12:27:40,042 ERROR: len = 248956422
2023-02-08 12:27:40,042 ERROR: Read in 248946422 bases on chr1 from 10001 - 248956422, stored in 99578572 bytes
2023-02-08 12:27:40,043 ERROR: bs_call: get_template_vector.c:239: read_input: Assertion `al->forward_position == thash->al->forward_position && al->reverse_position == thash->al->reverse_position' failed.
Exception in thread Thread-1:
ValueError: Error while executing the bscall process.

Can you help me understand this error message : bs_call: get_template_vector.c:239: read_input: Assertion al->forward_position == thash->al->forward_position && al->reverse_position == thash->al->reverse_position failed.

Does this happen when you have a read in R1.fq.gz but that read's pair is missing in R2.fq.gz ?