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Issues with running GoldRush test
Hello, I am having issues running the goldrush test script. I have installed Goldrush through conda, and every time I run the script it exits with "Test failed - please check your installation". I am not sure wherein the problem lies my only clue are a handful of warnings that pop up as it runs these being:
:Reading fasta file goldrush_test_golden_path.goldpolish-polished.span2.dist500.tigmint.fa.k40.w250.z1000.ntLink.ntLink.ntLink.gap_fill.fa : Reading scaffold file goldrush_test_golden_path.goldpolish-polished.span2.dist500.tigmint.fa.k40.w250.z1000.ntLink.ntLink.ntLink.gap_fill.fa.k40.w250.z1000.n1.scaffold.dot : Finding valid minimizer regions : Finding scaffold overlaps : Printing trimmed scaffolds : DONE! [WARNING] - is empty.
Reading ntLink read mappings.. Reading scaffolds.. Reading trim coordinates.. Choosing best read.. Collecting reads... Finding masking points.. Printing masked sequences.. Mapping long reads.. [WARNING] goldrush_test_golden_path.goldpolish-polished.span2.dist500.tigmint.fa.k40.w250.z1000.ntLink.ntLink.ntLink.gap_fill.fa.k40.w250.z1000.ntLink.scaffolds.gap_fill.fa.scaffolds.masked_temp.fa is empty. [WARNING] goldrush_test_golden_path.goldpolish-polished.span2.dist500.tigmint.fa.k40.w250.z1000.ntLink.ntLink.ntLink.gap_fill.fa.k40.w250.z1000.ntLink.scaffolds.gap_fill.fa.reads.masked_temp.fa is empty. Printing output scaffolds..
: Reading fasta file goldrush_test_golden_path.goldpolish-polished.span2.dist500.tigmint.fa.k40.w250.z1000.ntLink.ntLink.ntLink.ntLink.gap_fill.fa : Reading scaffold file goldrush_test_golden_path.goldpolish-polished.span2.dist500.tigmint.fa.k40.w250.z1000.ntLink.ntLink.ntLink.ntLink.gap_fill.fa.k40.w250.z1000.n1.scaffold.dot : Finding valid minimizer regions : Finding scaffold overlaps : Printing trimmed scaffolds : DONE! [WARNING] - is empty.
Reading ntLink read mappings.. Reading scaffolds.. Reading trim coordinates.. Choosing best read.. Collecting reads... Finding masking points.. Printing masked sequences.. Mapping long reads.. [WARNING] goldrush_test_golden_path.goldpolish-polished.span2.dist500.tigmint.fa.k40.w250.z1000.ntLink.ntLink.ntLink.ntLink.gap_fill.fa.k40.w250.z1000.ntLink.scaffolds.gap_fill.fa.scaffolds.masked_temp.fa is empty. [WARNING] goldrush_test_golden_path.goldpolish-polished.span2.dist500.tigmint.fa.k40.w250.z1000.ntLink.ntLink.ntLink.ntLink.gap_fill.fa.k40.w250.z1000.ntLink.scaffolds.gap_fill.fa.reads.masked_temp.fa is empty. Printing output scaffolds..
I am unsure what is causing these warning. As far dependencies go I am relatively confident I they are all present, as they should be from the conda installation. The machine I am using is running Ubuntu 22.04.5 LTS. Any help would be appreciated and please let me know if more information is required.
Thanks for your interest in using GoldRush. I've double checked with the most recent version of GoldRush using the test script.
To further aid us in helping resolve your issue.
Can I confirm the command you ran? and can you paste the results of running ll -h on the directory where you ran the command?
Thank you
Apologies for the late response, here is the output of ll
otal 99844 drwxrwxr-x 3 user user 4096 Jan 22 13:17 ./ drwxrwxr-x 3 user user 4096 Jan 22 13:14 ../ drwxrwxr-x 2 user user 24576 Jan 22 13:17 goldrush_intermediate_files/ -rwxrwxr-x 1 user user 706 Jan 22 13:14 goldrush_test_demo.sh* lrwxrwxrwx 1 user user 56 Jan 22 13:17 goldrush_test_golden_path.fa -> goldrush_intermediate_files/goldrush_test_golden_path.fa lrwxrwxrwx 1 user user 76 Jan 22 13:17 goldrush_test_golden_path.goldpolish-polished.fa -> goldrush_intermediate_files/goldrush_test_golden_path.goldpolish-polished.fa lrwxrwxrwx 1 user user 98 Jan 22 13:17 goldrush_test_golden_path.goldpolish-polished.span2.dist500.tigmint.fa -> goldrush_intermediate_files/goldrush_test_golden_path.goldpolish-polished.span2.dist500.tigmint.fa lrwxrwxrwx 1 user user 125 Jan 22 13:17 goldrush_test_golden_path.goldpolish-polished.span2.dist500.tigmint.fa.k40.w250.ntLink-5rounds.fa -> goldrush_intermediate_files/goldrush_test_golden_path.goldpolish-polished.span2.dist500.tigmint.fa.k40.w250.ntLink-5rounds.fa lrwxrwxrwx 1 user user 134 Jan 22 13:17 goldrush_test_golden_path.goldpolish-polished.span2.dist500.tigmint.fa.k40.w250.ntLink-5rounds.polished.fa -> goldrush_intermediate_files/goldrush_test_golden_path.goldpolish-polished.span2.dist500.tigmint.fa.k40.w250.ntLink-5rounds.polished.fa -rw-rw-r-- 1 user user 102179210 Jan 22 13:15 test_reads.fq
if there is anything else I should send please let me know
Thank you. I was wondering if perhaps the test_reads.fq is empty but that doesn't appear to be the case.
Can you run ll -h in the goldrush_intermediate_files/ directory?. I can then compare the difference between the files between what I have and yours.