+ SEQ1=AF086833 + SEQ2=KR105328 + efetch -db nuccore -format fasta -id AF086833 + efetch -db nuccore -format fasta -id KR105328 + wget -q -nc ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/NUC.4.4 + echo 'Tool:stretcher format:default(markx0) file:alignment.1.txt ' + stretcher -filter -asequence AF086833.fa -bsequence KR105328.fa -data NUC.4.4 + echo 'Tool:stretcher format:markx2 file:alignment.2.txt' + stretcher -filter -asequence AF086833.fa -bsequence KR105328.fa -data EDNAFULL -aformat markx2 + echo 'Tool:stretcher format:SAM file:alignment.3.txt' + stretcher -filter -asequence AF086833.fa -bsequence KR105328.fa -data EDNAFULL -aformat sam + echo 'Tool:blastn format:blast file:alignment.4.txt' + blastn -subject AF086833.fa -query KR105328.fa + echo 'Tool:blastn format:column file:alignment.5.txt' + blastn -subject AF086833.fa -query KR105328.fa -outfmt 7 + echo 'Tool:minimap format:SAM file:alignment.6.txt' + minimap2 -a -x sr --eqx AF086833.fa KR105328.fa [M::mm_idx_gen::0.001*0.00] collected minimizers [M::mm_idx_gen::0.002*0.00] sorted minimizers [M::main::0.002*1.91] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.002*1.90] mid_occ = 1000 [M::mm_idx_stat] kmer size: 21; skip: 11; is_hpc: 0; #seq: 1 [M::mm_idx_stat::0.002*1.81] distinct minimizers: 3101 (100.00% are singletons); average occurrences: 1.000; average spacing: 6.114 [M::worker_pipeline::0.063*1.01] mapped 1 sequences [M::main] Version: 2.12-r827 [M::main] CMD: minimap2 -a -x sr --eqx AF086833.fa KR105328.fa [M::main] Real time: 0.064 sec; CPU: 0.064 sec + echo 'Tool:minimap format:PAF (MD) file:alignment.7.txt' + minimap2 -c --MD AF086833.fa KR105328.fa [M::mm_idx_gen::0.001*0.00] collected minimizers [M::mm_idx_gen::0.002*0.00] sorted minimizers [M::main::0.002*0.00] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.002*0.00] mid_occ = 3 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 [M::mm_idx_stat::0.002*0.00] distinct minimizers: 3590 (99.94% are singletons); average occurrences: 1.001; average spacing: 5.278 [M::worker_pipeline::0.006*0.69] mapped 1 sequences [M::main] Version: 2.12-r827 [M::main] CMD: minimap2 -c --MD AF086833.fa KR105328.fa [M::main] Real time: 0.006 sec; CPU: 0.008 sec + echo 'Tool:minimap format:PAF (CS) file:alignment.8.txt' + minimap2 --cs AF086833.fa KR105328.fa [M::mm_idx_gen::0.001*0.00] collected minimizers [M::mm_idx_gen::0.001*0.00] sorted minimizers [M::main::0.001*0.00] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.002*0.00] mid_occ = 3 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 [M::mm_idx_stat::0.002*0.00] distinct minimizers: 3590 (99.94% are singletons); average occurrences: 1.001; average spacing: 5.278 [M::worker_pipeline::0.006*0.71] mapped 1 sequences [M::main] Version: 2.12-r827 [M::main] CMD: minimap2 --cs AF086833.fa KR105328.fa [M::main] Real time: 0.006 sec; CPU: 0.008 sec