raymondkiu / sequence-stats Goto Github PK

When computing the stats for a multifasta file, the field "Min Contig:" shows the length of the last contig, not the smallest one.

~/bin/sequence-stats -a assembly_MAIOR_QUE_100K.fasta
Sample: assembly_MAIOR_QUE_100K.fasta
Genome(bp): 248306121
Contigs: 1104
GC(%): 45.64
A(%): 27.18
T(%): 27.17
G(%): 22.81
C(%): 22.83
N50: 261916
Max Contig: 402137
Min Contig: 349401
N count: 0
N(%): 0
Gap(-): 0
Uncertain(bp): 0

~/bin/sequence-stats -c assembly_MAIOR_QUE_100K.fasta | tail
contig_9766 117494
contig_9805 199014
contig_9816 106145
contig_9878 116378
contig_9886 250030
contig_991 101688
contig_9941 381455
contig_9951 145570
contig_9955 343603
contig_9982 349401

Hi, I used git clone to install sequence-stats and gave it executable permission and run it on my file. Can you please help with the "command not found" issues? See below. Sincerely.

~$ sequence-stats/src/sequence-stats -a Tiero.fna
sequence-stats/src/sequence-stats: line 53: bc: command not found
sequence-stats/src/sequence-stats: line 54: bc: command not found
sequence-stats/src/sequence-stats: line 55: bc: command not found
sequence-stats/src/sequence-stats: line 57: bc: command not found
sequence-stats/src/sequence-stats: line 59: bc: command not found
sequence-stats/src/sequence-stats: line 62: bc: command not found
sequence-stats/src/sequence-stats: line 68: bc: command not found
Sample: Tiero.fna
Genome(bp): 4267658
Contigs: 1
GC(%):
A(%):
T(%):
G(%):
C(%):
N50: 4267658
Max Contig: 4267658
Min Contig: 4267658
N count: 0
N(%):
Gap(-): 0
Uncertain(bp):