Minimap printing ^

[colindaven]

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

[colindaven]

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

[lh3]

Do you have a small test data set with which I can reproduce the issue? Thanks.

[colindaven]

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