Question: GATK FastaAlternateReferenceMaker giving error
0
gravatar for PAn
4.3 years ago by
PAn20
United States
PAn20 wrote:

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!

ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by PAn20
1
gravatar for geek_y
4.3 years ago by
geek_y11k
Barcelona
geek_y11k wrote:

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.

ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by geek_y11k

Thanks a lot! This helps.

ADD REPLYlink written 4.3 years ago by PAn20
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