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marbl / SALSA

SALSA: A tool to scaffold long read assemblies with Hi-C data
MIT License
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list index out of range #27

Closed milkcookie closed 6 years ago

milkcookie commented 6 years ago

Hi all: when I run this protocol, I get a error: bedfile loaded Starting Iteration 1 bedfile started bedfile loaded Loading Hi-C links Finished loading Hi-C links, Loading unitig links now.. Hybrid scaffold graph loaded, nodes = 1268 edges = 1059 Hi-C implied edges = 0 Unitig tiling implied edges = 0 Assembly graph implied edges = 0 10x implied edges = 0 Traceback (most recent call last): File "/public1/home/stu_yanhansong/software/Hi-C/SALSA/layout_unitigs.py", line 1056, in update_bed(expanded_scaffold_paths) File "/public1/home/stu_yanhansong/software/Hi-C/SALSA/layout_unitigs.py", line 801, in update_bed first = prev_attrs[3].split('/')[1] IndexError: list index out of range any suggestion? thanks FAFU Hansong Yan

ghuryejay commented 6 years ago

Hi,

Can you please paste the first few lines from your bed file?

milkcookie commented 6 years ago

Hi: Thanks, I found the error, I use convert2bed --input=bam --output=bed to trans, so I get the wrong format bed file for SALSA, thanks reply me.

Hannah1746 commented 3 years ago

I am running into the same problem but I am using the suggested converter: bamToBed -i alignment.bam > alignment.bed sort -k 4 alignment.bed > tmp && mv tmp alignment.bed

This is my Bed file. 450_pilon_pilon 940760 940902 000000c7-34de-440b-b140-074231d41472 24 - 4128_pilon_pilon 228690 228868 000000c7-34de-440b-b140-074231d41472 60 - 606_pilon_pilon 391471 391720 00000a31-ce1a-4023-b087-f02cf9889ab1 52 + 540_pilon_pilon 238382 238588 000016cf-096e-4fce-badc-a74c08f6af5b 0 +