lh3
Minimap printing ^
Hi,
minimap version - downloaded from github today, so latest commit.
I have a fasta with sequence names like this:
Backbone_1 27656 12 27656 27657
Backbone_2 102066 27681 102066 102067
Backbone_3 53482 129760 53482 53483
Backbone_4 7726 183255 7726 7727
Backbone_5 13575 190994 13575 13576
My result.paf looks like this, minimap completes without an error. It seems the Target sequence name string is not being written. Are the names in the input fasta inappropriate ? How should the fastaheaders look ?
m150728_235245_42243_c100858112550000001823192301241632_s1_p0/109080/11935_17324 5389 2232 2650 - 134449 134193 134449 256 418 255 cm:i:242
m150728_235245_42243_c100858112550000001823192301241632_s1_p0/109080/11935_17324 5389 2232 2650 - 148474 144685 148407 326 3722 255 cm:i:242
m150728_235245_42243_c100858112550000001823192301241632_s1_p0/109080/11935_17324 5389 2232 2650 - 61712 22271 22527 256 418 255 cm:i:242
m150728_235245_42243_c100858112550000001823192301241632_s1_p0/109080/11935_17324 5389 2232 3121 - 46106 12058 45991 363 33933 255 cm:i:252
m150728_235245_42243_c100858112550000001823192301241632_s1_p0/109080/11935_17324 5389 2232 2650 - 57653 53821 57543 326 3722 255 cm:i:242
m150728_235245_42243_c100858112550000001823192301241632_s1_p0/109080/11935_17324 5389 2232 2650 - 9577 4583 9431 326 4848 255 cm:i:242
m150728_235245_42243_c100858112550000001823192301241632_s1_p0/109080/11935_17324 5389 2232 2408 - 9577 25 247 147 222 255 cm:i:105
m150728_235245_42243_c100858112550000001823192301241632_s1_p0/109080/11935_17324 5389 2232 2386 - 46106 0 183 125 183 255 cm:i:83
m150728_235245_42243_c100858112550000001823192301241632_s1_p0/109080/11935_17324 5389 2232 2355 - 134449 0 151 96 151 255 cm:i:68
m150728_235245_42243_c100858112550000001823192301241632_s1_p0/109080/11935_17324 5389 2232 2299 - 57653 0 119 67 119 255 cm:i:53
m150728_235245_42243_c100858112550000001823192301241632_s1_p0/109080/11935_17324 5389 2232 2284 - 125852 0 87 52 87 255 cm:i:38
m150728_235245_42243_c100858112550000001823192301241632_s1_p0/109080/11935_17324 5389 2232 2276 - 29342 41 103 44 62 255 cm:i:30
m150728_235245_42243_c100858112550000001823192301241632_s1_p0/109080/11935_17324 5389 2232 2276 - ^?^A 59116 41 103 44 62 255 cm:i:30
Solution:
The above set was created using an index.
~/NAS01/programs/minimap/minimap -d backbone_raw_cln.mmi backbone_raw_cln.fasta
~/NAS01/programs/minimap/minimap backbone_raw_cln.mmi -t 50 pacbio.fa > overlaps2.paf
When not using an indexed fasta, the expected better results were created which include the reference contig name.
m150728_235245_42243_c100858112550000001823192301241632_s1_p0/108989/0_7665 7665 179 361 + Backbone_15031 103774 86374 86540 97 182 255 cm:i:12
m150728_235245_42243_c100858112550000001823192301241632_s1_p0/108991/2366_8564 6198 1247 5478 + Backbone_32890 17695 7564 11932 232 4368 255 cm:i:20
m150728_235245_42243_c100858112550000001823192301241632_s1_p0/108991/2366_8564 6198 1076 6172 - Backbone_32890 17695 7968 12792 197 5096 255 cm:i:14
m150728_235245_42243_c100858112550000001823192301241632_s1_p0/108991/2366_8564 6198 1065 3152 + Backbone_27781 25911 21331 23112 83 2087 255 cm:i:7
m150728_235245_42243_c100858112550000001823192301241632_s1_p0/108991/2366_8564 6198 1663 3161 - Backbone_5738 111594 714 2729 65 2015 255 cm:i:6
Do you have a small test data set with which I can reproduce the issue? Thanks.
I sent a msg to your personal email @me.com
===== Mini test case for bug =====
Note - I could not reproduce the original bug with this small test case - sorry. However these other problems cropped up with the index.mmi.
untar, then gunzip files
tar -xvf index_test.tgz
create mmap index
~/NAS01/programs/minimap/minimap -d index.mmi ref.fasta ~/NAS01/programs/minimap/minimap -d index.mmi ref_align_error.fasta ~/NAS01/programs/minimap/minimap -d index.mmi ref_segfault.fasta ~/NAS01/programs/minimap/minimap -d index.mmi ref_big.fasta
align -
~/NAS01/programs/minimap/minimap index.mmi -t 1 reads.fa > ovl.paf
Assorted errors when creating an index:
Segmentation fault (core dumped)
Assorted errors when aligning to index:
minimap: sketch.c:59: mm_sketch: Assertion `len > 0 && w > 0 && k > 0' failed. Aborted (core dumped)
but this approach without an index consistently works
~/NAS01/programs/minimap/minimap ref.fasta -t 1 reads.fa > ovl.paf