parasail

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-t 24 not working threading

21

Hello Team, parasail_aligner -a parasail_sg_qx_striped_32 -q SILVA_138.1_SSURef_tax_silva_prok_nr_sbsample_half.fasta -f Danish_01.fa -d -t 24 -g parasail.csv for many sequences in query file (-q) and only one in -f file, I noticed that...

jianshu93

Different gap penalty for template and query

1

Hi Jeff, First of all, thank you for this amazing software! I am trying to use your code for an assignment for university where I need to code a RNA...

Nil-Fernandez-Lojo

Kind of CIGAR

2

I get with the python binding with pyssw an integer array for the Cigar with few elements depending on gaps in the alignment as the struct for the cigar is...

c0ntradicti0n

Parasail install failing on M1 Pro

4

Installing parasail via pipenv on M1 Pro, and the install fails with the following log: ```bash ➜ pipenv install --dev Installing dependencies from Pipfile.lock (0a2afc)... 🐍 ▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉ 1/1 — 00:00:00...

leecbaker

When using the CMake build scripts on macOS, `FindOpenMP` detects and enables OpenMP via the `-Xclang -fopenmp` flags, but this fails at linking time: ``` /opt/homebrew/Cellar/cmake/3.21.2/bin/cmake -E cmake_link_script CMakeFiles/test_verify_traces.dir/link.txt --verbose=1...

jvkersch

Hello! Is there a way to produce CIGAR string in banded global alignment (parasail_nw_banded)? I could produce the CIGAR string with parasail_nw_trace, but I guess tracing cannot be applied to...

zulal-b

Parasail on recent M1 Mac?

3

Have you tried to use **parasail** on a recent Mac with the M1 processor? I have hit this: ```cpp ccache cc -Isubprojects/parasail/contrib/libssw.a.p -Isubprojects/parasail/contrib -I../subprojects/parasail/contrib -Isubprojects/parasail -I../subprojects/parasail -Isubprojects/parasail/src -I../subprojects/parasail/src -Xclang -fcolor-diagnostics...

pb-cdunn

parasail_aligner: NW - output all best alignments

2

Using parasail_aligner with NW: nw_trace_scan_64 REF: GAACACGAGTGCCTTGAATAACAAGTTCGAACGATGGTTATTAATCCTAATAACGGAACGCTAAGTCCATTACCAAGGAGTGCGATGCAGTCTGGAGGATGAGTCTGACGGAGTGTAACTCGATCAGTCGTTATTCTCTCGCCAGCACTG QRY: GACACGAGTGCCTTGAATAACAAGTTCGAACGATGGTTATTAATCCTAATAACGGAACGCTAAGTCCATTACCAAGGAGTGCGATGCAGTCTGGAGGATGAGTCTGACGGAGTGTAACTCGATCAGTCGTTATTCTCTCGCCAGCACTG the qry has two possible best alignments with the same score (either ref position 0-base indexed position 1 or position 2...

psheth-twist

Attempt to to align an empty string appears to cause a Floating point exception

6

I'm posting this so that others that encounter a "Floating point Exception" will understand that it may mean their input sequences with empty. I wouldn't say that it needs to...

rsharris

install parasail on Mac

1

Need to first install autoconf, otherwise will see an error "RuntimeError: autoreconf -fi failed". I install it by the following command. brew install autoconf automake libtool

sunway1999