GATK FastaAlternateReferenceMaker giving error

Question

[PAn]

Hi,

I am trying to run FastaAlternateReferenceMaker using an interval file but I am getting this warning whether I use the interval file or not.

java -jar /local/scratch/aparihar/GenomeAnalysisTK.jar -T FastaAlternateReferenceMaker -R /PlasmoDB-24_Pfalciparum3D7_Genome.fasta -o Sample1.fasta -L Internal.list -V diploid.allsites.filtered.majorallele.vcf
where the Internal.list looks like this - 
Pf3D7_04_v3:147490-148380
Pf3D7_04_v3:329216-329689
Pf3D7_04_v3:660624-662519
Pf3D7_04_v3:1071435-1071845
.
.
.
Pf3D7_14_v3:53411-53734
Pf3D7_14_v3:420442-422790
Pf3D7_14_v3:667412-668824
Pf3D7_14_v3:1211012-1212776
Pf3D7_14_v3:1541359-1542872
Pf3D7_14_v3:1844041-1845617
Pf3D7_14_v3:3188888-3190548

It does create fasta file , but throws this warning -

INFO  17:00:18,180 ProgressMeter - Total runtime 258.93 secs, 4.32 min, 0.07 hours 
INFO  17:00:18,180 NSRuntimeProfile - Input   time:    2.8 m (74.34%) 
INFO  17:00:18,180 NSRuntimeProfile - Map     time:   36.9 s (16.20%) 
INFO  17:00:18,180 NSRuntimeProfile - Reduce  time:   20.1 s ( 8.80%) 
INFO  17:00:18,181 NSRuntimeProfile - Outside time:    1.5 s ( 0.66%) 
WARN  17:00:18,850 RestStorageService - Error Response: PUT '/GATK_Run_Reports/MiigllXSn0RWOGivBgtKjzVH7CJmYNsi.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 432, Content-MD5: FWK6clztmmbTisjMO/ToOw==, Content-Type: application/octet-stream, x-amz-meta-md5-hash: 1562ba725ced9a66d38ac8cc3bf4e83b, Date: Thu, 13 Oct 2016 21:00:18 GMT, Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:Q6z6+XNMbamjHrL+UfFhN2OV9mY=, User-Agent: JetS3t/0.8.1 (Linux/2.6.18-371.1.2.el5; amd64; en; JVM 1.6.0_31), Host: s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: E3BC72D86808D30D, x-amz-id-2: t0VnBjfOk9vAoBzXQcmwh2ELuB53kc49sh72WGlaKhP/QKurZOA8DK0JK07tPene2fHOOLR0Uus=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Thu, 13 Oct 2016 21:00:18 GMT, Connection: close, Server: AmazonS3]

Should I ignore this? I am uncertain, as I do not have any other means to confirm if the alternate fasta file created is correct.

Thanks!

Answer 1

[GouthamAtla]

Its not a problem a long as you have the output. There is a problem in network connection when GATK tries to upload your run report to their amazon cloud. Yes, it does collect the command statistics from your computer.

[PAn]

Thanks a lot! This helps.