Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Question about the tutorial example

ArvinWuArvinWu Las Vegas, NVMember

Hi all,
I am new user for using the GATK.
I got the software and example files from the ftp site.
However, when I run the first example on the website tutorial, it gives me some the error message shown as follows

INFO 10:17:49,552 ReadShardBalancer$1 - Loading BAM index data
INFO 10:17:49,566 ReadShardBalancer$1 - Done loading BAM index data
INFO 10:17:59,931 Walker - [REDUCE RESULT] Traversal result is: [email protected]94
INFO 10:18:00,219 ProgressMeter - done 280962.0 10.0 s 37.0 s 100.0% 10.0 s 0.0 s
INFO 10:18:00,221 ProgressMeter - Total runtime 10.68 secs, 0.18 min, 0.00 hours
INFO 10:18:00,230 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 280962 total reads (0.00%)
INFO 10:18:00,231 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
INFO 10:18:00,233 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
INFO 10:18:01,575 GATKRunReport - Uploaded run statistics report to AWS S3

The command that I used is
java -Xmx3g -jar GenomeAnalysisTK.jar -T PrintReads -R human_g1k_v37_decoy.fasta -L 10:91000000-92000000 -I 6517_2Mbp_input.bam -o 6517_1M_output1.bam

How can I solve this problem?
Thanks

Best Answer

Answers

  • ArvinWuArvinWu Las Vegas, NVMember

    Thank you for the information. :smiley:

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