The export file name is not what I expected

[ubs...@gmail.com]

Dear,

I tried to exclude some Taxa by TASSEL 5 standalone in Linux platform (Ubuntu 20.04.4, x86_64), and the command I used as followed:

/media/user/22CE5BE378448A49/tassel_5_standalone/run_pipeline.pl -Xmx50g -fork1 -h /media/user/18T/sample_all_joint_variant_SNPs_filtered_bqsr_snps_subset_0.0012.hmp.txt -excludeTaxa N0203,N0204,N0205,N0206 -export /media/user/18T/sample_all_joint_variant_SNPs_filtered_bqsr_snps_subset_0.0012_remove_four_samples.hapmap.txt -exportType Hapmap

The command works fine but the export filename is not I expected "sample_all_joint_variant_SNPs_filtered_bqsr_snps_subset_0.0012_remove_four_samples.hapmap.txt ", instead, the filename changed into "sample_all_joint_variant_SNPs_filtered_bqsr_snps_subset_01.hmp.txt"

I dig into the process and found:

Genotype Table Name: sample_all_joint_variant_SNPs_filtered_bqsr_snps_subset_0
saveAs: /media/user/18T/sample_all_joint_variant_SNPs_filtered_bqsr_snps_subset_01

I don't know why tassel change my output file name, the .log file is attached. I am very appreciated for any suggestion from you.

Best,

Shu-Yun Chen

[Terry Casstevens]

What happened is your file name was truncated at the first ".",
because the code thinks that's an extension. Then it added 1 as
export sometimes outputs multiple files. Then it added the standard
Hapmap extension .hmp.txt

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