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Can't use global $_ in "my" at ./make_panacea.pl #1

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kazumaxneo opened this issue Oct 17, 2021 · 0 comments
Open

Can't use global $_ in "my" at ./make_panacea.pl #1

kazumaxneo opened this issue Oct 17, 2021 · 0 comments

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@kazumaxneo
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Hi. I was wondering if you could help me.
I have downloaded the repository and run the script "run_panacea_example.sh " to run the example data, but I got the following error message.
Can't use global $_ in "my" at ./make_panacea.pl line 4898, near "($_"
Is there any way to solve this problem?

$ git clone https://github.com/JCVenterInstitute/PanACEA.git
$ cd PanACEA/
$ ./run_panacea_example.sh
./run_panacea_example.sh: 22: ./run_panacea_example.sh: [[: not found
Making Flatfile...
Reading in Clusters...
Finished Reading in Clusters...
5382 genes clusters identified...
Reading and Sorting Genes...
No hits...manniia ABCIP7010_RS03115 NZ_LN865143 669460 669708
No hits...6200 RU84_RS15270 NZ_CP010397 3232970 3233221
No hits...AB031 IX88_RS05165 NZ_CP009256 1089526 1089774
No hits...ABNIH28 C2U32_RS17555 NZ_CP026125 3577684 3577932
No hits...JAB0715 BJAB0715_RS03300 NC_021733 708955 709200
No hits...A1 ABA1_RS03435 NZ_CP010781 713438 713698
No hits...ZW851 P795_RS14505 NC_023028 3123394 3123639
No hits...1279779 ABD1_RS03170 NC_020547 683394 683645
No hits...A1296 BS103_RS03080 NZ_CP018332 640800 641048
No hits...3207 Aba3207_RS14630 NZ_CP015364 3010972 3011217
No hits...LAC4b RR41_RS15955 NZ_CP007712 3314639 3314884
No hits...bH12OA2 LX00_RS02960 NZ_CP009534 635072 635317
No hits...B8300 AB987_RS04140 NZ_CP021347 824999 825256
No hits...B8342 AB895_RS10555 NZ_CP021342 2205285 2205536
No hits...7978mff ACX60_RS15100 NZ_CP012004 3191968 3192219
No hits...HWBA8 B7L46_RS12205 NZ_CP020597 2344935 2345195
No hits...KAB07 KAB07_RS03110 NZ_CP017654 663531 663776
No hits...OMTU433 IOMTU433_RS15890 NZ_AP014649 3342925 3343176
No hits...ab736 A4U85_RS15780 NZ_CP015121 3310430 3310675
Reading in Core and FGI Cluster Assignments...
Assigning genomes to FGR orders...
Reading in Core and FGI Cluster Assignments II...
Found ARO mapfile
Making PanACEA function file configure file ...
Here
Functional file already exists... overwriting...
Making PanACEA HTML files ...
Can't use global $_ in "my" at ./make_panacea.pl line 4898, near "($_"
Execution of ./make_panacea.pl aborted due to compilation errors.
Finished..

perl 5.26
Ubuntu18.04

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