Details
-
Type: Bug
-
Status: Closed (View Workflow)
-
Priority: Blocker
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: 9.1.0 Major Release
-
Labels:
-
Story Points:2
-
Epic Link:
-
Sprint:Winter 2018 Sprint 3, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov
Description
Working with PacBio long reads from a URL, hit a SocketTimeoutException. The reads do not display correctly - appearing as unfilled squares. The read scores also seem to be incorrect, though that may be a separate issue.
Example bam can be found here
Attachments
Activity
Nowlan Freese
created issue -
Ann Loraine
made changes -
Field | Original Value | New Value |
---|---|---|
Rank | Ranked higher |
Ann Loraine
made changes -
Rank | Ranked higher |
Ann Loraine
made changes -
Sprint | Winter 2018 Sprint 3 [ 58 ] | |
Labels | Intermediate |
Ann Loraine
made changes -
Rank | Ranked higher |
Ann Loraine
made changes -
Sprint | Winter 2018 Sprint 3 [ 58 ] | Winter 2018 Sprint 3, Spring 2019 Sprint 1 [ 58, 59 ] |
Ann Loraine
made changes -
Labels | Intermediate | Advanced |
Ann Loraine
made changes -
Sprint | Winter 2018 Sprint 3, Spring 2019 Sprint 1 [ 58, 59 ] | Winter 2018 Sprint 3 [ 58 ] |
Ann Loraine
made changes -
Rank | Ranked lower |
Ann Loraine
made changes -
Sprint | Winter 2018 Sprint 3 [ 58 ] | Winter 2018 Sprint 3, Spring 2019 Sprint 2 [ 58, 60 ] |
Ann Loraine
made changes -
Rank | Ranked higher |
Ann Loraine
made changes -
Sprint | Winter 2018 Sprint 3, Spring 2019 Sprint 2 [ 58, 60 ] | Winter 2018 Sprint 3 [ 58 ] |
Ann Loraine
made changes -
Rank | Ranked lower |
Ann Loraine
made changes -
Comment | [ Note: Requires understanding the format and alignments. ] |
Ann Loraine
made changes -
Epic Link | IGBF-1765 [ 17855 ] |
Ann Loraine
made changes -
Fix Version/s | 9.1.0 Major Release [ 10601 ] | |
Sprint | Winter 2018 Sprint 3 [ 58 ] | Winter 2018 Sprint 3, Summer 2019 Sprint 11 [ 58, 70 ] |
Ann Loraine
made changes -
Sprint | Winter 2018 Sprint 3, Summer 2019 Sprint 11 [ 58, 70 ] | Winter 2018 Sprint 3, Summer 2019 Sprint 10 [ 58, 69 ] |
Ann Loraine
made changes -
Sprint | Winter 2018 Sprint 3, Summer 2019 Sprint 10 [ 58, 69 ] | Winter 2018 Sprint 3, Summer 2019 Sprint 11 [ 58, 70 ] |
Ann Loraine
made changes -
Sprint | Winter 2018 Sprint 3, Summer 2019 Sprint 11 [ 58, 70 ] | Winter 2018 Sprint 3, Summer 2019 Sprint 12 [ 58, 71 ] |
Ann Loraine
made changes -
Sprint | Winter 2018 Sprint 3, Summer 2019 Sprint 12 [ 58, 71 ] | Winter 2018 Sprint 3, Summer 2019 Sprint 13 [ 58, 72 ] |
Ann Loraine
made changes -
Workflow | Loraine Lab Workflow [ 18182 ] | Fall 2019 Workflow Update [ 18924 ] |
Ann Loraine
made changes -
Sprint | Winter 2018 Sprint 3, Fall 2019 Sprint 1 [ 58, 72 ] | Winter 2018 Sprint 3, Fall 2019 Sprint 1, Fall 2019 Sprint 2 [ 58, 72, 73 ] |
Ann Loraine
made changes -
Rank | Ranked higher |
Ann Loraine
made changes -
Sprint | Winter 2018 Sprint 3, Fall 2019 Sprint 1, Fall 2019 Sprint 2 [ 58, 72, 73 ] | Winter 2018 Sprint 3, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 2019 Sprint 4 [ 58, 72, 73, 74 ] |
Ann Loraine
made changes -
Rank | Ranked higher |
Ann Loraine
made changes -
Status | Open [ 1 ] | To-Do [ 10305 ] |
Ann Loraine
made changes -
Priority | Minor [ 4 ] | Blocker [ 1 ] |
Ann Loraine
made changes -
Summary | PacBio reads not showing correctly | Investigate: PacBio reads not showing correctly |
Ann Loraine
made changes -
Rank | Ranked lower |
Ann Loraine
made changes -
Sprint | Winter 2018 Sprint 3, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 2019 Sprint 3 [ 58, 72, 73, 74 ] | Winter 2018 Sprint 3, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 2019 Sprint 4 [ 58, 72, 73, 75 ] |
Ann Loraine
made changes -
Rank | Ranked lower |
Ann Loraine
made changes -
Sprint | Winter 2018 Sprint 3, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 4 : 30 Sep to 11 Oct [ 58, 72, 73, 75 ] | Winter 2018 Sprint 3, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct [ 58, 72, 73, 75, 76 ] |
Ann Loraine
made changes -
Rank | Ranked higher |
Ann Loraine
made changes -
Workflow | Fall 2019 Workflow Update [ 18924 ] | Revised Fall 2019 Workflow Update [ 21167 ] |
Noor Zahara (Inactive)
made changes -
Assignee | Noor Zahara [ noor91zahara ] |
Noor Zahara (Inactive)
made changes -
Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Nowlan Freese
made changes -
Attachment | pacBio.bam [ 14453 ] | |
Attachment | pacBio.bam.bai [ 14454 ] |
Ann Loraine
made changes -
Fix Version/s | 9.1.0 Major Release [ 10601 ] |
Noor Zahara (Inactive)
made changes -
Attachment | 1 (1).txt [ 14455 ] |
Nowlan Freese
made changes -
Attachment | igb.png [ 14457 ] | |
Attachment | pacBio-OneRead_5224S42EQUALS.bam [ 14458 ] | |
Attachment | pacBio-OneRead_5224S42EQUALS.bam.bai [ 14459 ] | |
Attachment | pacBio-OneRead_5224S42M.bam [ 14460 ] | |
Attachment | pacBio-OneRead_5224S42M.bam.bai [ 14461 ] | |
Attachment | pacBio-OneRead.bam [ 14462 ] | |
Attachment | pacBio-OneRead.bam.bai [ 14463 ] |
Nowlan Freese
made changes -
Attachment | pacBio-OneRead_42EQUALS.bam [ 14464 ] | |
Attachment | pacBio-OneRead_42EQUALS.bam.bai [ 14465 ] | |
Attachment | pacBio-OneRead_42X.bam [ 14466 ] | |
Attachment | pacBio-OneRead_42X.bam.bai [ 14467 ] |
Ann Loraine
made changes -
Fix Version/s | 9.1.0 Major Release [ 10601 ] |
Ann Loraine
made changes -
Sprint | Winter 2018 Sprint 3, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct [ 58, 72, 73, 75, 76 ] | Winter 2018 Sprint 3, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov [ 58, 72, 73, 75, 76, 77 ] |
Ann Loraine
made changes -
Rank | Ranked higher |
Noor Zahara (Inactive)
made changes -
Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Noor Zahara (Inactive)
made changes -
Assignee | Noor Zahara [ noor91zahara ] |
Nowlan Freese
made changes -
Assignee | Nowlan Freese [ nfreese ] |
Nowlan Freese
made changes -
Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
Nowlan Freese
made changes -
Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
Nowlan Freese
made changes -
Assignee | Nowlan Freese [ nfreese ] | Noor Zahara [ noor91zahara ] |
Noor Zahara (Inactive)
made changes -
Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
Noor Zahara (Inactive)
made changes -
Assignee | Noor Zahara [ noor91zahara ] |
Ann Loraine
made changes -
Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
Ann Loraine
made changes -
Assignee | Ann Loraine [ aloraine ] |
Ann Loraine
made changes -
Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
Ann Loraine
made changes -
Assignee | Ann Loraine [ aloraine ] |
Nowlan Freese
made changes -
Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
Nowlan Freese
made changes -
Assignee | Nowlan Freese [ nfreese ] |
Nowlan Freese
made changes -
Resolution | Done [ 10000 ] | |
Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
Nowlan Freese
made changes -
Assignee | Nowlan Freese [ nfreese ] | Noor Zahara [ noor91zahara ] |
Nowlan Freese
made changes -
Summary | Investigate: PacBio reads not showing correctly | Implement better handling of CIGAR string in BAM/SAM |
This issue may not have anything to do with the reads themselves, and may be an issue with the data being pulled from an ftp site. However, when I pull Illumina short reads from the same site, they load in IGB normally. We haven't tested long reads very much in IGB (PacBio are around 10,000 bp long, versus Illumina 150 bp long), and I'm wondering if the long reads are behaving correctly.