Open vilperte opened 4 years ago
Hello,
I'm trying to process my PacBio data, but I keep having problems with miniasm. I'm working on a computer with 24 cores and 120GB of RAM.
I first used both minimap and minimap2 to overlap my PacBio reads as below:
minimap -Sw5 -L100 -m0 reads.fq reads.fq | gzip -1 > reads.paf.gz
minimap2 -x ava-pb reads.fq reads.fq > ovlp.paf
Both outputs seemed to be right. _m64036_191027_013949/0/0_33715 33715 2595 28223 + m64036_191027_013949/2885611/6757_46033 39276 518 25314 993 25628 255 cm:i:98 m64036_191027_013949/0/0_33715 33715 20149 29458 - m64036_191027_013949/591889/36293_46673 10380 1472 10327 508 9309 255 cm:i:54 m64036_191027_013949/0/0_33715 33715 16755 21385 - m64036_191027_013949/4456553/24807_57842 33035 26344 31351 239 5007 255 cm:i:20 m64036_191027_013949/0/0_33715 33715 22850 26758 + m64036_191027_013949/1311505/0_51368 51368 15402 19485 177 4083 255 cm:i:19 m64036_191027_013949/0/0_33715 33715 207 6844 - m64036_191027_013949/3017040/0_46014 46014 484 6470 198 6637 255 cm:i:17 m64036_191027_013949/0/0_33715 33715 22859 26574 + m64036_191027_013949/919805/2001_48747 46746 38617 42100 116 3715 255 cm:i:13 m64036_191027_013949/1/55845_70532 14687 23 14550 - m64036_191027_013949/2624009/0_38492 38492 1243 14957 1941 14527 255 cm:i:234 m64036_191027_013949/1/55845_70532 14687 173 7031 + m64036_191027_013949/1508605/0_40914 40914 34334 40788 906 6858 255 cm:i:111 m64036_191027_013949/1/55845_70532 14687 456 14674 - m64036_191027_013949/1/70578_87455 16877 15 14257 877 14242 255 cm:i:103 m64036_191027_013949/1/55845_70532 14687 27 7031 - m64036_191027_013949/1508605/4096254418 13456 132 6772 830 7004 255 cm:i:94
I tried running miniasm in two different ways, but both gave the same error message:
_miniasm -Rc2 -f reads.fastq reads.paf.gz > assembly.gfa [M::main] ===> Step 0: removing contained reads <=== [M::ma_hit_nocont::55323.611*1.00] dropped 1611233 contained reads [M::main] ===> Step 1: reading read mappings <=== Killed
miniasm -f reads.fastq reads.paf.gz > assembly.gfa [M::main] ===> Step 1: reading read mappings <=== Killed
I've tried to track the RAM usage during miniasm and it seems that it peaks before crashing. So I'm guessing that's the problem. Does anyone have any idea how to fix that?
Thanks for the help.
Hello,
I'm trying to process my PacBio data, but I keep having problems with miniasm. I'm working on a computer with 24 cores and 120GB of RAM.
I first used both minimap and minimap2 to overlap my PacBio reads as below:
minimap -Sw5 -L100 -m0 reads.fq reads.fq | gzip -1 > reads.paf.gz
minimap2 -x ava-pb reads.fq reads.fq > ovlp.paf
Both outputs seemed to be right. _m64036_191027_013949/0/0_33715 33715 2595 28223 + m64036_191027_013949/2885611/6757_46033 39276 518 25314 993 25628 255 cm:i:98 m64036_191027_013949/0/0_33715 33715 20149 29458 - m64036_191027_013949/591889/36293_46673 10380 1472 10327 508 9309 255 cm:i:54 m64036_191027_013949/0/0_33715 33715 16755 21385 - m64036_191027_013949/4456553/24807_57842 33035 26344 31351 239 5007 255 cm:i:20 m64036_191027_013949/0/0_33715 33715 22850 26758 + m64036_191027_013949/1311505/0_51368 51368 15402 19485 177 4083 255 cm:i:19 m64036_191027_013949/0/0_33715 33715 207 6844 - m64036_191027_013949/3017040/0_46014 46014 484 6470 198 6637 255 cm:i:17 m64036_191027_013949/0/0_33715 33715 22859 26574 + m64036_191027_013949/919805/2001_48747 46746 38617 42100 116 3715 255 cm:i:13 m64036_191027_013949/1/55845_70532 14687 23 14550 - m64036_191027_013949/2624009/0_38492 38492 1243 14957 1941 14527 255 cm:i:234 m64036_191027_013949/1/55845_70532 14687 173 7031 + m64036_191027_013949/1508605/0_40914 40914 34334 40788 906 6858 255 cm:i:111 m64036_191027_013949/1/55845_70532 14687 456 14674 - m64036_191027_013949/1/70578_87455 16877 15 14257 877 14242 255 cm:i:103 m64036_191027_013949/1/55845_70532 14687 27 7031 - m64036_191027_013949/1508605/4096254418 13456 132 6772 830 7004 255 cm:i:94
I tried running miniasm in two different ways, but both gave the same error message:
_miniasm -Rc2 -f reads.fastq reads.paf.gz > assembly.gfa [M::main] ===> Step 0: removing contained reads <=== [M::ma_hit_nocont::55323.611*1.00] dropped 1611233 contained reads [M::main] ===> Step 1: reading read mappings <=== Killed
miniasm -f reads.fastq reads.paf.gz > assembly.gfa [M::main] ===> Step 1: reading read mappings <=== Killed
I've tried to track the RAM usage during miniasm and it seems that it peaks before crashing. So I'm guessing that's the problem. Does anyone have any idea how to fix that?
Thanks for the help.