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GATB / short_read_connector

Short Read Connector (SRC)
GNU Affero General Public License v3.0
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Error : "Bad substitution" and "[[: not found" #7

Open CaroleBelliardo opened 1 year ago

CaroleBelliardo commented 1 year ago

Dear Developpers,

I would like to use your this software but something is wrong with my data or command line. I try to run short_read_connector_counter with the following line : sh ./short_read_connector_counter.sh index -b hifi_reads.fasta.gz -i hifi_reads__my_counter_index.dumped

Where y input is a classical fasta file containing hifi reads. And the sd output tell me : 


./short_read_connector_counter.sh: 10: ./short_read_connector_counter.sh: [[: not found
./short_read_connector_counter.sh: 15: ./short_read_connector_counter.sh: [[: not found
./short_read_connector_counter.sh: 29: ./short_read_connector_counter.sh: function: not found
short_read_connector_counter.sh - Compare reads from two read sets (distinct or not)
Version 1.2.0
Usage: sh short_read_connector_counter.sh [index/query]
./short_read_connector_counter.sh: 34: ./short_read_connector_counter.sh: Syntax error: "}" unexpected```

Thank for your help,
Best regards. 
Carole