Test-drive the GATK tools and Best Practices pipelines on Terra
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Question about the tutorial example
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?