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shingocat / lrscaf

TGS scaffolding
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Inability to parse iqrt parameter #28

Closed tararickman closed 3 years ago

tararickman commented 3 years ago

Hi @shingocat,

I have been able to successfully run lrscaf but am now encountering issues when iterating through different values for specific parameters. I am using a bash script to iterate through various values for specific parameters (ie: mioll, iqrt, mmcm) to assess which combination is optimal.

contents of .sh script: #!/bin/bash counter=0 declare -a mioll=("320" "960") declare -a tl=("1000" "10000") declare -a iqrt=("1.5" "3") declare -a mmcm=("5" "10") for i in "${mioll[@]}" do for i in "${tl[@]}" do for i in "${iqrt[@]}" do for i in "${mmcm[@]}" do let counter++ java -jar /pickett/software/lrscaf/LRScaf-1.1.11.jar \ -p 20 \ -c /path/to/Scaffolds.fasta \ -a /path/to/mapped.paf \ -t mm \ -mioll $mioll \ -tl $tl \ -iqrt $iqrt \ -mmcm $mmcm \ -o ./2_15_2021/$counter/output_species done done done done

The error I am getting is: 2021-02-15 14:08:51 [ ERROR ] Error: java.lang.NullPointerException: Cannot invoke "String.trim()" because "in" is null at java.base/jdk.internal.math.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:1838) at java.base/jdk.internal.math.FloatingDecimal.parseDouble(FloatingDecimal.java:110) at java.base/java.lang.Double.parseDouble(Double.java:549) at java.base/java.lang.Double.valueOf(Double.java:512) at agis.ps.Main.parsering(Main.java:291) at agis.ps.Main.main(Main.java:48) 2021-02-15 14:08:51 [ ERROR ] agis.ps.Main Cannot invoke "String.trim()" because "in" is null

When I remove the variable iqrt and let it run default, the error goes away and lrscaf successfully runs. I tested out my script with just one value for each parameter to see if iqrt was having an issue with decimal (1.5) vs whole (3) numbers but regardless, the same error occurs.

Please let me know of any additional information you may need to help with this. Thank you!

shingocat commented 3 years ago

Hi taraickman,

Thanks for your reports. I had fixed the issues for parsing the iqrt value on command-line. you can try to use the new version 1.1.12 under the target folder.

tararickman commented 3 years ago

Thank you for working on this fix! Version 1.1.12 works as expected.