dincarnato
commented
1 year ago It looks like in your command line you are failing to provide an argument to the "--reportAln" parameter. Please check the help. The argument passed to reportAln can be fasta or stockholm.
Danny
Tried running SHAPEwarp after making my database and query file. The query file looks like this:
ANKHD1 TAATACGACTCACTATAGGACACGACTCGAGTAGAGTCGAATGATTGAATTGTTTGTTACAGTATTACAGACTGTCTCCCCTCTGAAGATACTACTGAAAATAGTAAAGACAGATATCCTGTACTAGAGATCTTATGGTGTGACTATGTATTTTGAAAGAAATCTCATTTATTTGATAGACAGCCTCATATGAAGTTACATGTGGATTAGGTAGAGGACAAATTAATATTATGTGCATTGTAAAGGTAGAAAGACTAAAACATAGGTGGTTATGCCATGGCCTTTTGACATTAGTGGCAGAATTGAATTGATAAGCCTTATCTTCTGTCAACCTAACCTATGGATTCTATACCATTTCTTTTTCCTAGATAATAGTGTTTAGAAATATAATTACAATTTGCACTTTTATACTTTTTTTTTTGTTGTTCTGCACTACCTGATTGATTGATGCACACTGAAGGAATTGGCAAATTGTCAACTGCTGATGGTAAAGCTTTTGCAGATCCTGAGGTACTCCGGAGACTGACATCCTCAGTTAGTTGTGCACTGGATGAAGCTGCTGCTGCACTGACACGGATGAAAGCAGAAAACAGCCACAATGCAGGACAAGTGGACACGTATGTGTTTAATGACTTTTGGATATTAGACATTTTCTTGAATAGATTTTGGGGAAGTAGCCAATTTTGGTTAAATATATCTTTTGGTGGAGCTTATAAACTTTAGCTGAAAGGATATTACATTTTAAGTGGATATATAAATGTATATGTATTATGTAGCTATACAAATGGATATTTTTGTTTCTTCATTCAGCTCTTATTCGTTGAGCATTCTTGTGGAATGTATTACACTAGAGTCTCTGAGAAATCCAAACTGAATAAGATCTGTTTTCCAGTTATAAGGAAGTTACTTATTCTAAAAGTTATTATAGTAAACTCTAAACCGAGACCGGAGTCGAGTGACTCCAACA NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,0.353668,1.016862,0.459786,0.376909,0.352406,0.304122,0.056392,0.761656,0.141341,0.304122,0.428257,0.390602,0.045402,0.072247,0.35592,0.017837,0.238361,0.667699,0.955966
Script looks like this:
SHAPEwarp --output ../ANKHD1_aln --query ../query/ANKHD1.txt --database ../ANKHD 1_db/ --threads 12 --reportAln --makePlot --matchKmerGCcontentIt gives me the error: [!] Error: Invalid alignment format "--makePlot"