TCGA-WGBS submission - Githubissues

GoogleCodeExporter commented 8 years ago

SampleName  BAM file
2722-01 TCGA-60-2722-01A-01D-1871-05_720f6804-059c-4516-a77d-74e8a01c739b_Lung_t
umor.realign.mdups.recal.bam (29x)
2722-11 TCGA-60-2722-11A-01D-1871-05_ea6ea99f-250a-4d6b-8335-6c9a37bd7a6e_Lung_n
ormal.realign.mdups.recal.bam (29x) 
NIC1254A13  ResultCount_MERGING_1_NIC1254A13.hg19_rCRSchrm.fa.realign.mdups.recal
.bam (22x) 
ResultCount_MERGING_1_NIC1254A14.hg19_rCRSchrm.fa.realign.mdups.recal.bam (23x)
NIC1254A15  ResultCount_MERGING_1_NIC1254A15.hg19_rCRSchrm.fa.realign.mdups.recal
.bam (44x)
NIC1254A16  ResultCount_MERGING_1_NIC1254A16.hg19_rCRSchrm.fa.realign.mdups.recal
.bam (40x)
NIC1254A18  ResultCount_MERGING_1_NIC1254A18.hg19_rCRSchrm.fa.realign.mdups.recal
.bam (43x)
A0CE-01 TCGA-A7-A0CE-01A-11D-A148-05_4ff7626b-4c2f-40fd-9df1-10c1a488402a_Breast
_tumor.realign.mdups.recal.bam (19x)
A0CE-11 TCGA-A7-A0CE-11A-21D-A148-05_805f2c82-49d5-4994-a2a5-98dd1b832f0b_Breast
_normal.realign.mdups.recal.bam (19x) 
NIC1254A17  ResultCount_MERGING_1_NIC1254A17.hg19_rCRSchrm.fa.realign.mdups.recal
.bam (42x)

Original issue reported on code.google.com by huy.q.d...@gmail.com on 10 Jun 2013 at 10:42

GoogleCodeExporter commented 8 years ago

we need to verify that the recal hasnt lost any primary data vs the original bam

Original comment by zack...@gmail.com on 11 Jun 2013 at 7:25

GoogleCodeExporter commented 8 years ago

Last time we submitted, we made the mistake of identifying the samples with the 
tube barcode vs the Biospecimen barcode. Only Biospecimen barcodes can be 
tracked and converted to a uuid through the official TCGA web-service, tube 
barcodes will return an error. This is important since uuid are required to 
submit the data. 

We are currently looking at the same problem for many of our unsubmitted libs. 
This means we have to get Dan to go back to his paper records and do a manual 
lookup (time consuming and error prone)

the following are labeled incorrectly (ignore any characters after the "05") :
TCGA-BLCA-A13J-TP-11D-A23D-05-79F7
TCGA-BLCA-A1AA-TP-11D-A23D-05-79G7-0.8X
TCGA-BLCA-A1AG-TP-11D-A23D-05-79E8
TCGA-BLCA-A20V-NT-11D-A23D-05-79F8
TCGA-BLCA-A20V-TP-11D-A23D-05-79A8
TCGA-BLCA-A2HQ-TP-11D-A23D-05-79B8
TCGA-BLCA-A2LA-TP-11D-A23D-05-79D8
TCGA-BRCA-A04X-TP-21D-A19F-05-A
TCGA-BRCA-A07I-TP-11D-A19F-05-B
TCGA-BRCA-A0YG-TP-21D-A19F-05-C
TCGA-BRCA-A15H-TP-11D-A19F-05-D
TCGA-UCEC-A05J-TP-11D-A23D-05-81B7
TCGA-UCEC-A05J-TP-11D-A23D-05-81B7-SS
TCGA-UCEC-A0G2-TP-11D-A23D-05-81D7-SS
TCGA-UCEC-A1CK-TP-11D-A23D-05-81A7
TCGA-UCEC-A1CK-TP-11D-A23D-05-81A7-SS

There should never be a 4-letter code after the "TCGA-" it should always be a 2 
letter/digit code. ex:
TCGA-A8-A07I-01A-11D-A19F-05
TCGA-A2-A04X-01A-21D-A19F-05
TCGA-A2-A0YG-01A-21D-A19F-05
TCGA-E2-A15H-01A-11D-A19F-05
TCGA-B6-A2IU-01A-32D-A19F-05
TCGA-AV-A03D-20A-01D-A19F-05

Original comment by zack...@gmail.com on 12 Jun 2013 at 8:42

GoogleCodeExporter commented 8 years ago

small glitch uncovered with the parsing of bam readgroups. Most likely an issue 
on cghub's end, working with them to get it resolved.

Original comment by zack...@gmail.com on 14 Jun 2013 at 7:28

GoogleCodeExporter commented 8 years ago

ticket open with them, waiting for them to decide what to do.

Original comment by zack...@gmail.com on 17 Jun 2013 at 9:31

GoogleCodeExporter commented 8 years ago

shared via www due to time constraints. details in email.

Original comment by zack...@gmail.com on 20 Jun 2013 at 9:12

Changed state: Started

GoogleCodeExporter commented 8 years ago

pinging cghub for a status update.

Original comment by zack...@gmail.com on 21 Jun 2013 at 9:31

GoogleCodeExporter commented 8 years ago

Zack, I notice that you're supposed to go on vacation this week.  If you 
haven't heard back anything positive from CGHub, what would we have to do on 
our side to make the BAM's compatible.  Is it just a header fix?
Thanks - Ben.

Original comment by benb...@gmail.com on 24 Jun 2013 at 4:55

GoogleCodeExporter commented 8 years ago

I followed up with them on Friday, and in the evening i got an email letting me 
know they had fixed it on their end. Will try to submit the bams ASAP

Original comment by zack...@gmail.com on 24 Jun 2013 at 5:02

GoogleCodeExporter commented 8 years ago

meta submitted:

[ramjan@hpc-laird 
TCGA-34-2600-01A-01D-1871-05_66724ea6-0764-4a31-a53e-be76b88f8614]$ cgs 
0868e3be-0308-4303-bde7-a777f53529bd
=========================================================
Welcome to cgsubmit version 2.1.0, submission software
=========================================================
=========================================================
Submission results from https://cghub.ucsc.edu
=========================================================
Pass: Submission Accepted
[ramjan@hpc-laird 
TCGA-34-2600-01A-01D-1871-05_66724ea6-0764-4a31-a53e-be76b88f8614]$ cd ..
[ramjan@hpc-laird test]$ ls
TCGA-34-2600-01A-01D-1871-05_66724ea6-0764-4a31-a53e-be76b88f8614  
TCGA-A2-A04X-01A-21D-A19F-05_f75bb0bf-e05a-499b-bd81-d9bb9663b1c9  
TCGA-A8-A07I-01A-11D-A19F-05_81b9d94d-46da-42d8-8cc9-a730c0e1b99b
TCGA-60-2695-01A-01D-1871-05_7bbb35ee-0136-46b6-bfae-3c5c2b7566df  
TCGA-A2-A0YG-01A-21D-A19F-05_6c248508-f6e8-4560-bdbd-40bd7d30383d  
TCGA-E2-A15H-01A-11D-A19F-05_8889ced6-9f24-4981-8045-f7b77efd4474
TCGA-60-2722-01A-01D-1871-05_720f6804-059c-4516-a77d-74e8a01c739b  
TCGA-A7-A0CE-01A-11D-A148-05_4ff7626b-4c2f-40fd-9df1-10c1a488402a
TCGA-60-2722-11A-01D-1871-05_ea6ea99f-250a-4d6b-8335-6c9a37bd7a6e  
TCGA-A7-A0CE-11A-21D-A148-05_805f2c82-49d5-4994-a2a5-98dd1b832f0b
[ramjan@hpc-laird test]$ cd 
TCGA-60-2695-01A-01D-1871-05_7bbb35ee-0136-46b6-bfae-3c5c2b7566df
[ramjan@hpc-laird 
TCGA-60-2695-01A-01D-1871-05_7bbb35ee-0136-46b6-bfae-3c5c2b7566df]$ cgs
0aaa1f42-7476-428e-8994-f176d3b9f5c5/ validation.log
[ramjan@hpc-laird 
TCGA-60-2695-01A-01D-1871-05_7bbb35ee-0136-46b6-bfae-3c5c2b7566df]$ cgs 
0aaa1f42-7476-428e-8994-f176d3b9f5c5
=========================================================
Welcome to cgsubmit version 2.1.0, submission software
=========================================================
=========================================================
Submission results from https://cghub.ucsc.edu
=========================================================
Pass: Submission Accepted
[ramjan@hpc-laird 
TCGA-60-2695-01A-01D-1871-05_7bbb35ee-0136-46b6-bfae-3c5c2b7566df]$ cd 
../TCGA-60-2722-01A-01D-1871-05_720f6804-059c-4516-a77d-74e8a01c739b
[ramjan@hpc-laird 
TCGA-60-2722-01A-01D-1871-05_720f6804-059c-4516-a77d-74e8a01c739b]$ cgs
f739d3f9-9419-4cd2-958b-5a9b121e5003/ validation.log
[ramjan@hpc-laird 
TCGA-60-2722-01A-01D-1871-05_720f6804-059c-4516-a77d-74e8a01c739b]$ cgs 
f739d3f9-9419-4cd2-958b-5a9b121e5003
=========================================================
Welcome to cgsubmit version 2.1.0, submission software
=========================================================
=========================================================
Submission results from https://cghub.ucsc.edu
=========================================================
Pass: Submission Accepted
[ramjan@hpc-laird 
TCGA-60-2722-01A-01D-1871-05_720f6804-059c-4516-a77d-74e8a01c739b]$ cd 
../TCGA-60-2722-11A-01D-1871-05_ea6ea99f-250a-4d6b-8335-6c9a37bd7a6e
[ramjan@hpc-laird 
TCGA-60-2722-11A-01D-1871-05_ea6ea99f-250a-4d6b-8335-6c9a37bd7a6e]$ cgs
cfd2d57b-0f86-4f96-ae90-d0d1b4eb406d/ validation.log
[ramjan@hpc-laird 
TCGA-60-2722-11A-01D-1871-05_ea6ea99f-250a-4d6b-8335-6c9a37bd7a6e]$ cgs 
cfd2d57b-0f86-4f96-ae90-d0d1b4eb406d
=========================================================
Welcome to cgsubmit version 2.1.0, submission software
=========================================================
=========================================================
Submission results from https://cghub.ucsc.edu
=========================================================
Pass: Submission Accepted
[ramjan@hpc-laird 
TCGA-60-2722-11A-01D-1871-05_ea6ea99f-250a-4d6b-8335-6c9a37bd7a6e]$ cd 
../TCGA-A2-A04X-01A-21D-A19F-05_f75bb0bf-e05a-499b-bd81-d9bb9663b1c9
[ramjan@hpc-laird 
TCGA-A2-A04X-01A-21D-A19F-05_f75bb0bf-e05a-499b-bd81-d9bb9663b1c9]$ cgs
8ce9a3a6-f5b9-4c77-98fa-c8f6fdaa4c8b/ validation.log
[ramjan@hpc-laird 
TCGA-A2-A04X-01A-21D-A19F-05_f75bb0bf-e05a-499b-bd81-d9bb9663b1c9]$ cgs 
8ce9a3a6-f5b9-4c77-98fa-c8f6fdaa4c8b
=========================================================
Welcome to cgsubmit version 2.1.0, submission software
=========================================================
=========================================================
Submission results from https://cghub.ucsc.edu
=========================================================
Pass: Submission Accepted
[ramjan@hpc-laird 
TCGA-A2-A04X-01A-21D-A19F-05_f75bb0bf-e05a-499b-bd81-d9bb9663b1c9]$ cd 
../TCGA-A2-A0YG-01A-21D-A19F-05_6c248508-f6e8-4560-bdbd-40bd7d30383d
[ramjan@hpc-laird 
TCGA-A2-A0YG-01A-21D-A19F-05_6c248508-f6e8-4560-bdbd-40bd7d30383d]$ cgs
243d4f44-7570-4142-b6c4-ffad80ef7e22/ submission.zip                        
validation.log
[ramjan@hpc-laird 
TCGA-A2-A0YG-01A-21D-A19F-05_6c248508-f6e8-4560-bdbd-40bd7d30383d]$ cgs 
243d4f44-7570-4142-b6c4-ffad80ef7e22
=========================================================
Welcome to cgsubmit version 2.1.0, submission software
=========================================================
=========================================================
Submission results from https://cghub.ucsc.edu
=========================================================
Pass: Submission Accepted
[ramjan@hpc-laird 
TCGA-A2-A0YG-01A-21D-A19F-05_6c248508-f6e8-4560-bdbd-40bd7d30383d]$ cd 
../TCGA-A7-A0CE-01A-11D-A148-05_4ff7626b-4c2f-40fd-9df1-10c1a488402a
[ramjan@hpc-laird 
TCGA-A7-A0CE-01A-11D-A148-05_4ff7626b-4c2f-40fd-9df1-10c1a488402a]$ cgs
1688e375-1b91-47f6-96ae-a2c8d7a6c297/ validation.log
[ramjan@hpc-laird 
TCGA-A7-A0CE-01A-11D-A148-05_4ff7626b-4c2f-40fd-9df1-10c1a488402a]$ cgs 
1688e375-1b91-47f6-96ae-a2c8d7a6c297
=========================================================
Welcome to cgsubmit version 2.1.0, submission software
=========================================================
=========================================================
Submission results from https://cghub.ucsc.edu
=========================================================
Pass: Submission Accepted
[ramjan@hpc-laird 
TCGA-A7-A0CE-01A-11D-A148-05_4ff7626b-4c2f-40fd-9df1-10c1a488402a]$ d
[ramjan@hpc-laird 
TCGA-A7-A0CE-01A-11D-A148-05_4ff7626b-4c2f-40fd-9df1-10c1a488402a]$ cd 
../TCGA-A7-A0CE-11A-21D-A148-05_805f2c82-49d5-4994-a2a5-98dd1b832f0b
[ramjan@hpc-laird 
TCGA-A7-A0CE-11A-21D-A148-05_805f2c82-49d5-4994-a2a5-98dd1b832f0b]$ cgs
e30360a8-594d-453f-b7a3-d34b9e58eb69/ validation.log
[ramjan@hpc-laird 
TCGA-A7-A0CE-11A-21D-A148-05_805f2c82-49d5-4994-a2a5-98dd1b832f0b]$ cgs 
e30360a8-594d-453f-b7a3-d34b9e58eb69
=========================================================
Welcome to cgsubmit version 2.1.0, submission software
=========================================================
=========================================================
Submission results from https://cghub.ucsc.edu
=========================================================
Pass: Submission Accepted
[ramjan@hpc-laird 
TCGA-A7-A0CE-11A-21D-A148-05_805f2c82-49d5-4994-a2a5-98dd1b832f0b]$ cd 
../TCGA-A8-A07I-01A-11D-A19F-05_81b9d94d-46da-42d8-8cc9-a730c0e1b99b
[ramjan@hpc-laird 
TCGA-A8-A07I-01A-11D-A19F-05_81b9d94d-46da-42d8-8cc9-a730c0e1b99b]$ cgs
a11611d0-d782-475f-b731-4d7205c87052/ validation.log
[ramjan@hpc-laird 
TCGA-A8-A07I-01A-11D-A19F-05_81b9d94d-46da-42d8-8cc9-a730c0e1b99b]$ cgs 
a11611d0-d782-475f-b731-4d7205c87052
=========================================================
Welcome to cgsubmit version 2.1.0, submission software
=========================================================
=========================================================
Submission results from https://cghub.ucsc.edu
=========================================================
Pass: Submission Accepted
[ramjan@hpc-laird 
TCGA-A8-A07I-01A-11D-A19F-05_81b9d94d-46da-42d8-8cc9-a730c0e1b99b]$ cd 
../TCGA-E2-A15H-01A-11D-A19F-05_8889ced6-9f24-4981-8045-f7b77efd4474
[ramjan@hpc-laird 
TCGA-E2-A15H-01A-11D-A19F-05_8889ced6-9f24-4981-8045-f7b77efd4474]$ cgs
18a0d824-371f-4606-8ec4-56a225e05360/ validation.log
[ramjan@hpc-laird 
TCGA-E2-A15H-01A-11D-A19F-05_8889ced6-9f24-4981-8045-f7b77efd4474]$ cgs 
18a0d824-371f-4606-8ec4-56a225e05360
=========================================================
Welcome to cgsubmit version 2.1.0, submission software
=========================================================
=========================================================
Submission results from https://cghub.ucsc.edu
=========================================================
Pass: Submission Accepted

Original comment by zack...@gmail.com on 24 Jun 2013 at 9:29

GoogleCodeExporter commented 8 years ago

showing up on cghub as submitted. 

all 10 file uploads in progress on hpc-laird. "ps -ef |grep GeneTorrent" to see 
if they are still active

Original comment by zack...@gmail.com on 24 Jun 2013 at 10:07

Changed state: Testing

Attachments:

[Screen Shot 2013-06-24 at 3.04.27 PM.jpg](https://storage.googleapis.com/google-code-attachments/usc-epigenome-center/issue-518/comment-10/Screen Shot 2013-06-24 at 3.04.27 PM.jpg)

GoogleCodeExporter commented 8 years ago

TCGA-A8-A07I-01A-11D-A19F-05 / 81b9d94d-46da-42d8-8cc9-a730c0e1b99b stalled and 
died from multiple time-outs. resubmitting.

other 9 are all currently live.

Original comment by zack...@gmail.com on 8 Jul 2013 at 7:29

GoogleCodeExporter commented 8 years ago

TCGA-A8-A07I-01A-11D-A19F-05 / 81b9d94d-46da-42d8-8cc9-a730c0e1b99b has been 
submitted. all are shown as "LIVE" on cghub. closing issue

Original comment by zack...@gmail.com on 8 Jul 2013 at 11:43

Changed state: Done

uec / Issue.Tracker

TCGA-WGBS submission #518