Bioinformatics Data Analysis

Run Parameters
Parameters used during the run:
  • Accession number for the first sequence: AF086833
  • Accession number for the second sequence: KR105328
File List
Files created by the recipe run:
Output Messages
Messages printed to the standard output stream:
Tool:stretcher format:default(markx0)  file:alignment.1.txt 
Tool:stretcher format:markx2 file:alignment.2.txt
Tool:stretcher format:SAM file:alignment.3.txt
Tool:blastn format:blast file:alignment.4.txt
Tool:blastn format:column file:alignment.5.txt
Tool:minimap format:SAM file:alignment.6.txt
Tool:minimap format:PAF (MD) file:alignment.7.txt
Tool:minimap format:PAF (CS) file:alignment.8.txt
Other Messages
Messages printed to the standard error stream:
+ 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

Powered by the release 1.4