3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchUpdate output
Returns the SamStatus for the reads/writes.
Returns the SamStatus for the reads/writes.
Returns SamStatus::NO_MORE_RECS, 2, if it was clipping files sorted by coordinate and it ran out of records in the pool so had to clip based on the <code>--poolSkipClip</code> setting.
= Output =
= Output =
All status messages are written to stderr.
{|border="1" cellspacing="0" cellpadding="2"
! Situation !! Sorted Type !! Output Message
|-
| Everything ran successfully
| ReadName/Coordinate
|
Completed ClipOverlap Successfully.
|-
| Failed to allocate any records
| ReadName/Coordinate
|
Failed to allocate any records.
Failed to complete ClipOverlap.
|-
| Error writing a record
| ReadName
|
Failed to complete ClipOverlap.
|-
| Expected pair to overlap, but 2nd read was not found in the specified position (may be combined with output for running out of pooled records)
| Coordinate
|
Failed to find expected overlapping mates for XX records.
Completed ClipOverlap Successfully.
|-
| Ran out of pooled Records with <code>--poolSkipClip</code> setting
| Coordinate
|
Due to hitting the max record poolSize, had to skip clipping XX records.
Completed ClipOverlap.
|-
| Ran out of pooled Records without <code>--poolSkipClip</code> setting
| Coordinate
|
Due to hitting the max record poolSize, had to default clip XX records.
Completed ClipOverlap.
|-
| Any other error
| Coordinate
|
Failed to complete ClipOverlap.
|}
<pre>
<pre>
Failed to find expected overlapping mates for 2 records.
Failed to find expected overlapping mates for 2 records.
Due to hitting the max record poolSize, had to default clip 9 records.
Completed ClipOverlap.
Completed ClipOverlap.
</pre>
</pre>
