Re: (EXT) Re: Flagging Potential Issue: Wed 4/1/2020 9:18 AM

4/13/2020 Mail - SUPPORT,INFORMATICS (Shared) - Outlook
Re: [EXT] Re: Flagging potential issue

Mandar Bedse (Agilent Informatics Support) <informatics_support@cartagenia.zendesk.com>
Wed 4/1/2020 9:18 AM
Cc: JONES,JENNIFER (Agilent USA) <jennifer.jones@agilent.com>; SUPPORT,INFORMATICS (Shared)
<informatics_support@agilent.com>; OBABKOV,ANGELA (Agilent USA) <angela.obabkov@agilent.com>; Guerrero,Paola A
<paguerrero@mdanderson.org>; Bahrambeigi,Vahid <vbahrambeigi@mdanderson.org>
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Mandar Bedse, Apr 1, 9:48 PM IST:
Hi Justin,
Please let us know if you need any further help.
Regards,
Mandar Bedse
AUTO-NOTIFICATION: Please be advised that any forward/reply of this message (internal or

external) will automatically update the ticket and notify all contacts associated with this ticket.
Mandar Bedse, Mar 30, 7:59 PM IST:
Hi Justin,
Please let us know if you need any further help.
Regards,
Mandar Bedse

Wong,Justin, Mar 24, 1:46 AM IST:
Thank you for the suggestions. I agree. I also noticed the problem with the barcode files we received, which are as you
describe, and started the demultiplexing in a more appropriate manner. We will let you know when that is finished, and we
have had an opportunity to try the new files.
Thanks,
~Justin
________________________________
https://outlook.office365.com/mail/informatics_support@agilent.com/AAMkAGZjYjEzMzczLWUwYjEtNGFlZi1hMjdiLTBjMGRiMWM4NDE3ZAAuAAAA… 1/12
WARNING: This email originated from outside of MD Anderson. Please validate the sender's email address before clicking
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Mandar Bedse, Mar 24, 12:12 AM IST:
Hi Justin,
The R&D team investigated the case and found that the barcode file used for the analysis
contain barcode sequence having all its bases as “N”. Please find attached screenshot of the
barcode file showing the “N” bases. This could result from a problem in the demultiplexing
process & hence, the analysis failure. Also, we successfully ran the pair analysis without the
barcode file at our end.
In the case of AIO analysis, barcodes are not considered as one of the input, & hence the
analysis did not fail.
Please let us know if you need any guidance for correct barcode file generation? We would also
like to suggest increasing the workflow memory of SureCall using below steps:
1. Go to Admin tab in SureCall
2. From left hand, side panel select memory management
3. Inside Manage SureCall memory settings, click on Change button.
4. Please select below values for mentioned parameters:
1. Maximum memory allocated to SureCall application: 2 GB

2. Maximum memory allocated to analysis workflows: 50 GB
5. Click on Apply button, SureCall will restart.
Regards,
Mandar Bedse
Agilent Informatics Support

Attachment(s)
MDanderson_barcode.PNG
Please see attached for requested files.
Thank you,
~Justin
________________________________
Attachment(s)
Screenshots.zip
AIO Solid Tumor SensHyper.json
Guerrero,Paola A, Mar 19, 9:00 PM IST:
I am cc’ing Vahid who will be in the lab this week. We do not know about next yet. As Justin is saying, our USP ports are
blocked. He also mentioned that the transferring of files is extremely slow. Do you have a different method to speed up this
process?
From: Wong,Justin (Agilent Informatics Support) [mailto:informatics_support@cartagenia.zendesk.com]

Sent: Thursday, March 19, 2020 10:24 AM
Cc: Jennifer Jones <jennifer.jones@agilent.com>; SUPPORT,INFORMATICS (A-ColSprings,exgen1)
<informatics_support@agilent.com>; OBABKOV,ANGELA (A-USA,ex1) <angela.obabkov@agilent.com>; Guerrero,Paola
A <PAGuerrero@mdanderson.org>
Subject: Re: [EXT] Re: Flagging potential issue
Wong,Justin, Mar 19, 8:53 PM IST:
Hi Jen,
Thanks for you response. The sample fastqs were 10-11 GB (R1, R3), and the PBMC fastqs are smaller (6-7 GB). The two
R2 files (with barcodes are much smaller and are not an issue). The biggest fastqs I have are 17 GB.
Since I have a 2-month at home, I've been working from home and really trying to limit my exposure, but I think someone
will be in at 2 PM for their shift and they should be able to help you then. MD Anderson does block external drives, so it
might be tricky to pull the data in that way too.
Regards,
~Justin
________________________________
Jennifer Jones, Mar 19, 8:37 PM IST:
Hi Justin,
Can you confirm the file sizes for samples? I realize that the amount of sequencing given to different samples can be
different, so could you share the files size for the specific sample files you are trying to share currently as well as the
largest file size for the data set you are working to analyze?
Also, can you confirm the shift during which you and other lab members plan to be on-campus in case I need to come by
and assist or possibly even physically collect the data on a drive. Hopefully it will not come to that but I want to be prepared
to assist today if possible.
Thanks for your patience on this!
Best Regards,
Jenn
Jennifer Carter Jones Ph.D
Regional Manager Genomics FAS - West
Diagnostics and Genomics Group
Agilent
T: +1 713 854 7983 | www.agilent.com (http://www.agilent.com/)
From: Wong,Justin (Agilent Informatics Support) <informatics_support@cartagenia.zendesk.com>

<informatics_support@agilent.com>; OBABKOV,ANGELA (Agilent USA) <angela.obabkov@agilent.com>; Guerrero,Paola
A <paguerrero@mdanderson.org>
Attachment(s)
image001.png
Hi Mandar,
I have been uploading the files since 5:30 last night. I am currently uploading R1, and R2 for the PBMC, and will start R3
when they are done. Is there possibly another method to transfer the files. For whatever reason, this is impossibly slow on
our end.
~Justin
________________________________
Mandar Bedse, Mar 19, 7:38 PM IST:
Hi Justin,
We have received your fastq files for sample i.e R1, R2 and R3.However, we have not received
fastq files for reference i.e GV112_PBMC_S88.
To send analysis method, please go to Configure settings--> Analysis Method--> Export

a .json file will be exported.Please share that file with us.
Regards,
Mandar Bedse

Guerrero,Paola A, Mar 19, 4:21 AM IST:
Dear Agilent,
I am tired of this back and forth. We have had issues with this software for now a year. We are now training for Interpret but
it does not make any sense to continue until you fix this problem. We are not beta testing this software. We are a paying
customer that has been VERY patient with all the issues Surecall has. I really want you to analyze 9-10 samples ran with
our custom AIO panel, solve all the issues Jenn listed, and get back to us we a realistic solution.
We may go into lockdown very soon and if those 300 samples are not in VCF format, we won’t be able to do anything at
home.
Thank you,
Paola A. Guerrero PhD

Scientific Manager
Maitra Lab
Sent from my iPhone
On Mar 18, 2020, at 5:27 PM, Wong,Justin (Agilent Informatics Support) <informatics_support@cartagenia.zendesk.com>
wrote:
Do we still need to keep the space locally if we are not writing to it?
Thanks,
Justin
________________________________
Ok, I will upload shortly. If you read the e-mail chain, you will find there are ~350 Gb of space on the local computer.
However, we write typically write to the network drive where there is more than 4 TB of space (whatever it says below). I
wanted to try to run it locally, but we have well over a hundred samples to run, so running locally is not a long-term option. I
don't need the local problem solved, I need the network problem solved. If better, I can re-run from the network drive.
Please explain what you mean by "you would like to have an analysis method "AIO Solid Tumor SensHyper"" as this is
unclear to me and I'm not sure how I would give that to you.
I will also remind you that the AIO workflow works, but the paired workflow does not. This suggests there isn't anything
inherently wrong with the fastqs.
~Justin
________________________________
Anand Kulkarni, Mar 19, 3:45 AM IST:
Hi Justin,
We just wanted to check how much disk space available at /Users/lbx/. The reason we are
asking this because we can see many part files of *.bam were created and but error while
saving them. Ideally, we would recommend keeping at least 500 GB of free space available on
your local drive (Home Directory).
Also, to check it further, please send us FASTQ files for Sample GV112_3_S2 and Reference
GV112_PBMC_S88 at below link:
https://www.hightail.com/u/InformaticsSupport
Also, we would like to have an analysis method "AIO Solid Tumor SensHyper".
Thanks,
Anand

I'm also attaching an error log from when we moved the fastqs locally and ran them from the local drive instead of a
network share.
________________________________
Attachment(s)
GV112_3_S2_L001_R1_001.fastq_17Mar2020_14_52_22_944.zip
________________________________
Hi Justin,
Thank you for sharing the application logs. However, you have not shared the job folder of the failed sample which is
needed for further investigation by the development team. Could you please share the same?
Below are the steps to get a job folder:
1. Select the failed sample from sample review tab

2. Click on "Job summary" from the bottom
3. A new window will pop up, click on "Open Job Folder" and send all the files within folder.
Best Regards,
Mandar Bedse
________________________________
From: Wong,Justin <JWong3@mdanderson.org>
Sent: Monday, March 16, 2020 1:26 PM
To: JONES,JENNIFER (Agilent USA) <jennifer.jones@agilent.com>; SUPPORT,INFORMATICS (Shared)
<informatics_support@agilent.com>
Cc: Guerrero,Paola A <PAGuerrero@mdanderson.org>; MILES,GREGORY (Agilent USA) <gregory.miles@agilent.com>;
OBABKOV,ANGELA (Agilent USA) <angela.obabkov@agilent.com>
I have attached the results of the latest logs. I am not sure if this will cover what you need since we tried to run many
samples over the weekend, and we had a network drive disconnect.
How much space do you think I need locally to write temp files to?
If I wanted to run the AIO CNV pipeline off of bams, my understanding of the pipeline is that I should just run an alignment
software, but no deduplication - is that correct?
Thanks,
~Justin
________________________________
From: jennifer.jones@agilent.com <jennifer.jones@agilent.com>
Sent: Monday, March 16, 2020 8:44:34 AM
To: informatics_support@agilent.com
Cc: Guerrero,Paola A; Wong,Justin; gregory.miles@agilent.com; angela.obabkov@agilent.com
Hello all,
In an effort to confirm what support issues have yet to be resolved, I have a list below of issue/questions and would
appreciate any updates as to status from informatic support:
1. Issue with failed analysis (paired analysis) for some samples on some at least one MAC, though AIO analysis worked.
This is the support issue that is the main topic of this email change.
2. Issues regarding generating CNV only VCF from the AIO analysis. This has been somewhat addressed in that Greg
confirmed that no default VCF is automatically generated in analysis and without going into triage there is no way to export
this. Additionally there is a need for clarity on why using the suppress function in triage view to remove all but CNV calls
does not work with the MAC based analysis.
3. There is a question about AIO analysis sensitivity to deletions. These include how sensitive analysis is to deletion
(lowest VAF for Deletion they can expect to see) as well as how homozygous deletion is called ( or if it can be called).
Justin, please let me know if there are questions/issues I have missed and I will also look back through notes for anything
else.
Best regards
Jenn
Jennifer Carter Jones

Senior Field Application Scientist,
Agilent Technologies
Sent from my iPhone
713-854-7983
On Mar 13, 2020, at 10:57 AM, SUPPORT,INFORMATICS (Shared) <informatics_support@agilent.com> wrote:
Hi Justin.
Could you please share the logs file of the failed sample? Also, please share the application logs in the client folder as
mentioned in the last email.
Best Regards,
Mandar Bedse
________________________________
From: Mandar Bobade (Agilent Informatics Support) <informatics_support@cartagenia.zendesk.com>
Sent: Thursday, March 12, 2020 1:27 PM
<informatics_support@agilent.com>; Guerrero,Paola A <paguerrero@mdanderson.org>
Attachment(s)
SureCall_20200318.tar.gz
I have attached the results of the latest logs. I am not sure if this will cover what you need since we tried to run many
samples over the weekend, and we had a network drive disconnect.
How much space do you think I need locally to write temp files to?
If I wanted to run the AIO CNV pipeline off of bams, my understanding of the pipeline is that I should just run an alignment
software, but no deduplication - is that correct?
Thanks,
~Justin
________________________________
Hello all,
else.
Best regards
Jenn

Sent from my iPhone
713-854-7983
Hi Justin.
Best Regards,
Mandar Bedse
________________________________
From: Mandar Bobade (Agilent Informatics Support) <informatics_support@cartagenia.zendesk.com>
Sent: Thursday, March 12, 2020 1:27 PM
<informatics_support@agilent.com>; Guerrero,Paola A <paguerrero@mdanderson.org>
Attachment(s)
SureCall_DebugLog_20200316.zip
Jennifer Jones, Mar 16, 7:14 PM IST:
Hello all,
else.
Best regards
Jenn

Sent from my iPhone
713-854-7983
Hi Justin.
Best Regards,
Mandar Bedse
________________________________
Mandar Bobade, Mar 13, 1:57 AM IST:
Hi Justin,
In last Webex, we have set DEBUG mode for logs. This is for the detailed log capturing for
investigation purpose to our R&D team. Once your existing analyses get completed, please
follow below steps:
1) Go to the SureCall installation folder --> Client -- > log
2) Cut and paste the files from inside log folder to other location
3) Submit new paired analysis, which was failed earlier
4) Once newly submitted paired analysis gets completed, go to the SureCall installation folder -
-> Client and zip the log folder.
Please send us this zipped log folder after above steps have been followed. Once we receive
these DEBUG logs, we'll send this logs to R&D team for further investigation.
Regards,
Mandar Bobade

Hi Justin,
Please join the remote desktop sharing (WebEx) meeting using below link.
https://agilent.webex.com/meet/mandar.bobade
To share the screen, please click on Share --> Share Content --> Screen1 after joining the
meeting.
To join Teleconference (TC), please follow below instruction:
Click on Telephone icon of WebEx widget -> Click on "Call me" ->Provide your phone number
and call. You will receive a phone call on the number provided --> Answer the call and follow
the steps to join TC.
Regards,
Mandar Bobade

Yes I am available for the next couple of hours.
________________________________
Hi Justin,
Could you please let us know if you are available for quick Webex meeting? If yes, we'll send
you link to join the Webex meeting. If no, please let us know any of your other couple of
suitable time slots to schedule a Webex meeting. Agenda of Webex is to collect system
information and set logs in DEBUG mode for further investigation.
Regards,
Mandar Bobade

I have uploaded two zipped files that contain the requested information and more.
To address Greg's initial query, which was my first thought too, the original files are stored on a network drive (5+ TB
remaining). There is ~350 GB remaining on the desktop. That the paired sample failed (run first), and the AIO sample
https://outlook.office365.com/mail/informatics_support@agilent.com/AAMkAGZjYjEzMzczLWUwYjEtNGFlZi1hMjdiLTBjMGRiMWM4NDE3ZAAuAAA… 10/12
worked (run second) seemed to suggest at first glance to me that network connectivity might not be the problem (since I
didn't reconnect in between).
Please let me know if you have other questions that I can help answer.
~Justin
________________________________
Attachment(s)
image001.png
What is the best place to send the files? I assume you want all of them, Including bams/fastqs for jobs that worked? Should
I do it via this e-mail thread, or via a link? In previous instances, I was asked to upload file(s) to another site.
Thanks,
~Justin
From: "informatics_support@agilent.com" <informatics_support@agilent.com>

Date: Thursday, March 12, 2020 at 10:38 AM
To: "Guerrero,Paola A" <PAGuerrero@mdanderson.org>, "Wong,Justin" <JWong3@mdanderson.org>
Cc: "gregory.miles@agilent.com" <gregory.miles@agilent.com>, "jennifer.jones@agilent.com"
<jennifer.jones@agilent.com>
Subject: [EXT] Re: Flagging potential issue
Hi Justin,
Could you share the job folder for the failed samples to further investigate? Double click on the failed sample--> Click on
"Open Job folder" and send the files inside job folder of that sample.
Best Regards,
Mandar Bedse
-------------------------------
From: MILES,GREGORY (Agilent USA) <gregory.miles@agilent.com>

To: Wong,Justin <JWong3@mdanderson.org>; JONES,JENNIFER (Agilent USA) <jennifer.jones@agilent.com>
Cc: Guerrero,Paola A <PAGuerrero@mdanderson.org>; SUPPORT,INFORMATICS (Shared)
<informatics_support@agilent.com>
Subject: RE: Flagging potential issue
Hi Justin,
This seems like it might be a computer-related issue (like running out of disk space or trying to save to a disconnected
network drive. I have cc’d informatics support so that they can have a WebEx with you to explore this further. I am happy to
join if you believe it will be helpful. Please provide them the necessary info to debug.
Informatics Support,
Please assist Justin with this high-priority ticket and set up a WebEx to debug. Thanks.
Best,
Greg
From: Wong,Justin <JWong3@mdanderson.org>

Sent: Wednesday, March 11, 2020 1:43 PM
To: JONES,JENNIFER (Agilent USA) <jennifer.jones@agilent.com>; MILES,GREGORY (Agilent USA)
<gregory.miles@agilent.com>
Cc: Guerrero,Paola A <PAGuerrero@mdanderson.org>
Subject: Flagging potential issue
Hi Jenn and Greg,
I'm just following up with a conversation I had with Jenn after the end of the call. In preparation for tomorrow's call, I have
been running some samples in both AIO mode, and paired mode, to get CNVs and SNVs respectively, and I ran into
something unexpected.
I ran the fastqs for one sample through the paired workflow (for a custom hypersensitive variant calling scheme), and then
a second time I ran the same fastqs through the AIO workflow (on a default scheme). When I ran the paired analysis, the
analysis failed - by the error logs it seems the bam is empty and/or has no high-quality reads that are written to it. However,
when I run the same fastqs through the paired analysis the analysis completes just fine, suggesting that the fastqs had
useable data. See the attached log files for reference for the two workflows.
After this, we ran a couple of PBMCs in single sample mode, and had the same issue (the analysis appears to fail at the
same point, empty Bam file, no high-quality reads). No rigorous cross-checking across computers/methods has been done
on my end at this time, since I am prioritizing data for tomorrow's call, so this is just to put it on your radar as something
that we have observed. Let me know if more information would be helpful.
Thanks,
~Justin
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4/13/2020 Mail - SUPPORT,INFORMATICS (Shared) - Outlook

Re: [EXT] Re: Flagging potential issue

Mandar Bedse, Apr 1, 9:48 PM IST:

Please let us know if you need any further help.

AUTO-NOTIFICATION: Please be advised that any forward/reply of this message (internal or

Mandar Bedse, Mar 30, 7:59 PM IST:

Please let us know if you need any further help.

AUTO-NOTIFICATION: Please be advised that any forward/reply of this message (internal or

Wong,Justin, Mar 24, 1:46 AM IST:

Mandar Bedse, Mar 24, 12:12 AM IST:

1. Go to Admin tab in SureCall

2. From left hand, side panel select memory management

3. Inside Manage SureCall memory settings, click on Change button.

4. Please select below values for mentioned parameters:

1. Maximum memory allocated to SureCall application: 2 GB

AUTO-NOTIFICATION: Please be advised that any forward/reply of this message (internal or

Wong,Justin, Mar 20, 2:17 AM IST:

Guerrero,Paola A, Mar 19, 9:00 PM IST:

From: Wong,Justin (Agilent Informatics Support) [mailto:informatics_support@cartagenia.zendesk.com]

Wong,Justin, Mar 19, 8:53 PM IST:

Jennifer Jones, Mar 19, 8:37 PM IST:

Thanks for your patience on this!

Regional Manager Genomics FAS - West

Diagnostics and Genomics Group

T: +1 713 854 7983 | www.agilent.com (http://www.agilent.com/)

From: Wong,Justin (Agilent Informatics Support) <informatics_support@cartagenia.zendesk.com>

Wong,Justin, Mar 19, 7:47 PM IST:

Mandar Bedse, Mar 19, 7:38 PM IST:

To send analysis method, please go to Configure settings--> Analysis Method--> Export

AUTO-NOTIFICATION: Please be advised that any forward/reply of this message (internal or

Guerrero,Paola A, Mar 19, 4:21 AM IST:

Paola A. Guerrero PhD

Sent from my iPhone

Wong,Justin, Mar 19, 4:15 AM IST:

Wong,Justin, Mar 19, 3:57 AM IST:

Anand Kulkarni, Mar 19, 3:45 AM IST:

AUTO-NOTIFICATION: Please be advised that any forward/reply of this message (internal or

Wong,Justin, Mar 19, 2:55 AM IST:

Wong,Justin, Mar 18, 9:59 PM IST:

1. Select the failed sample from sample review tab

Jennifer Carter Jones

On Mar 13, 2020, at 10:57 AM, SUPPORT,INFORMATICS (Shared) <informatics_support@agilent.com> wrote:

Wong,Justin, Mar 17, 1:56 AM IST:

Jennifer Carter Jones

On Mar 13, 2020, at 10:57 AM, SUPPORT,INFORMATICS (Shared) <informatics_support@agilent.com> wrote:

Jennifer Jones, Mar 16, 7:14 PM IST:

Jennifer Carter Jones

On Mar 13, 2020, at 10:57 AM, SUPPORT,INFORMATICS (Shared) <informatics_support@agilent.com> wrote:

Mandar Bobade, Mar 13, 1:57 AM IST:

AUTO-NOTIFICATION: Please be advised that any forward/reply of this message (internal or

Mandar Bobade, Mar 13, 12:54 AM IST:

To join Teleconference (TC), please follow below instruction:

AUTO-NOTIFICATION: Please be advised that any forward/reply of this message (internal or

Wong,Justin, Mar 13, 12:44 AM IST:

Yes I am available for the next couple of hours.

Mandar Bobade, Mar 13, 12:30 AM IST:

AUTO-NOTIFICATION: Please be advised that any forward/reply of this message (internal or

Wong,Justin, Mar 12, 11:02 PM IST:

Wong,Justin, Mar 12, 9:11 PM IST:

From: "informatics_support@agilent.com" <informatics_support@agilent.com>

Agilent Informatics Support

From: MILES,GREGORY (Agilent USA) <gregory.miles@agilent.com>