Miniasm not making it past Step 1

[dbrowneup]

Hello, I'm trying to assemble some reads with minimap and miniasm. Minimap seems to have worked, but my process is failing on miniasm:

[M::mm_idx_gen::0.010*2.97] collected minimizers
[M::mm_idx_gen::0.022*2.77] sorted minimizers
[M::main::0.022*2.77] loaded/built the index for 25 target sequence(s)
[M::main] max occurrences of a minimizer to consider: 7
[M::main] Version: 0.2-r124-dirty
[M::main] CMD: minimap -Sw5 -L100 -m0 Gap_Support/Contig17_1_1011970_pilon|arrow.gap.3/reads.fa Gap_Support/Contig17_1_1011970_pilon|arrow.gap.3/reads.fa
[M::main] Real time: 0.035 sec; CPU: 0.082 sec
[M::main] ===> Step 1: reading read mappings <===
awk: '/^S/{print(">"$2"
awk: ^ invalid char ''' in expression

Any pointers on how to get around this would be appreciated. Could it have something to do with the headers in my fasta?

[dbrowneup]

Sorry, I think the awk error is actually coming from my own code, as I've got an awk wrapper to extract Fasta sequences from the GFA output of Miniasm. However, I'm still not sure if Miniasm is actually working? None of the reads were assembled:

Gap_Support/Contig498_pilon|arrow.gap.11:
total 512
-rw-rw-r-- 1 dbrowne dbrowne     0 May 12 00:06 assembly.fa
-rw-rw-r-- 1 dbrowne dbrowne     0 May 12 00:06 assembly.gfa
-rw-rw-r-- 1 dbrowne dbrowne 39826 May 12 00:06 reads.fa
-rw-rw-r-- 1 dbrowne dbrowne   372 May 12 00:06 reads.paf.gz

Gap_Support/Contig498_pilon|arrow.gap.3:
total 18432
-rw-rw-r-- 1 dbrowne dbrowne        0 May 12 00:06 assembly.fa
-rw-rw-r-- 1 dbrowne dbrowne        0 May 12 00:06 assembly.gfa
-rw-rw-r-- 1 dbrowne dbrowne  6323839 May 12 00:04 reads.fa
-rw-rw-r-- 1 dbrowne dbrowne 11544864 May 12 00:06 reads.paf.gz

Gap_Support/Contig498_pilon|arrow.gap.5:
total 512
-rw-rw-r-- 1 dbrowne dbrowne     0 May 12 00:06 assembly.fa
-rw-rw-r-- 1 dbrowne dbrowne     0 May 12 00:06 assembly.gfa
-rw-rw-r-- 1 dbrowne dbrowne 16932 May 12 00:04 reads.fa
-rw-rw-r-- 1 dbrowne dbrowne    20 May 12 00:06 reads.paf.gz

Gap_Support/Contig498_pilon|arrow.gap.6:
total 512
-rw-rw-r-- 1 dbrowne dbrowne    0 May 12 00:06 assembly.fa
-rw-rw-r-- 1 dbrowne dbrowne    0 May 12 00:06 assembly.gfa
-rw-rw-r-- 1 dbrowne dbrowne 6864 May 12 00:04 reads.fa
-rw-rw-r-- 1 dbrowne dbrowne  402 May 12 00:06 reads.paf.gz

Gap_Support/Contig498_pilon|arrow.gap.7:
total 1024
-rw-rw-r-- 1 dbrowne dbrowne      0 May 12 00:06 assembly.fa
-rw-rw-r-- 1 dbrowne dbrowne      0 May 12 00:06 assembly.gfa
-rw-rw-r-- 1 dbrowne dbrowne 393547 May 12 00:05 reads.fa
-rw-rw-r-- 1 dbrowne dbrowne  48777 May 12 00:06 reads.paf.gz

Gap_Support/Contig498_pilon|arrow.gap.9:
total 512
-rw-rw-r-- 1 dbrowne dbrowne    0 May 12 00:06 assembly.fa
-rw-rw-r-- 1 dbrowne dbrowne    0 May 12 00:06 assembly.gfa
-rw-rw-r-- 1 dbrowne dbrowne 4521 May 12 00:05 reads.fa
-rw-rw-r-- 1 dbrowne dbrowne  229 May 12 00:06 reads.paf.gz

Moreover, I never see anything in my output past "Step 1" from Miniasm:

[dbrowne@ada3 2017.05.09_Jelly2_Testing]$ head -n 30 OUT_JELLY2_TESTING_v22 
[M::mm_idx_gen::0.010*2.97] collected minimizers
[M::mm_idx_gen::0.022*2.77] sorted minimizers
[M::main::0.022*2.77] loaded/built the index for 25 target sequence(s)
[M::main] max occurrences of a minimizer to consider: 7
[M::main] Version: 0.2-r124-dirty
[M::main] CMD: minimap -Sw5 -L100 -m0 Gap_Support/Contig17_1_1011970_pilon|arrow.gap.3/reads.fa Gap_Support/Contig17_1_1011970_pilon|arrow.gap.3/reads.fa
[M::main] Real time: 0.035 sec; CPU: 0.082 sec
[M::main] ===> Step 1: reading read mappings <===
awk: '/^S/{print(">"$2"
awk: ^ invalid char ''' in expression
[M::mm_idx_gen::0.003*6.60] collected minimizers
[M::mm_idx_gen::0.007*4.68] sorted minimizers
[M::main::0.007*4.67] loaded/built the index for 7 target sequence(s)
[M::main] max occurrences of a minimizer to consider: 7
[M::main] Version: 0.2-r124-dirty
[M::main] CMD: minimap -Sw5 -L100 -m0 Gap_Support/Contig17_1_1011970_pilon|arrow.gap.6/reads.fa Gap_Support/Contig17_1_1011970_pilon|arrow.gap.6/reads.fa
[M::main] Real time: 0.012 sec; CPU: 0.039 sec
[M::main] ===> Step 1: reading read mappings <===
awk: '/^S/{print(">"$2"
awk: ^ invalid char ''' in expression
[M::mm_idx_gen::0.003*8.09] collected minimizers
[M::mm_idx_gen::0.006*5.31] sorted minimizers
[M::main::0.006*5.29] loaded/built the index for 13 target sequence(s)
[M::main] max occurrences of a minimizer to consider: 9
[M::main] Version: 0.2-r124-dirty
[M::main] CMD: minimap -Sw5 -L100 -m0 Gap_Support/Contig26_pilon|arrow.gap.12/reads.fa Gap_Support/Contig26_pilon|arrow.gap.12/reads.fa
[M::main] Real time: 0.010 sec; CPU: 0.036 sec
[M::main] ===> Step 1: reading read mappings <===
awk: '/^S/{print(">"$2"
awk: ^ invalid char ''' in expression

I suppose it's possible that simply none of the sequences were able to be assembled by Miniasm, but that seems unlikely.

[bredeson]

Hi,
Is it possible that the pipes in your file names are causing the trouble? Otherwise, I've found setting -f0.0 to work around gaps, where (simple sequence) repeats may be more common.