region, forkSense issues

[john-alexander]

Dear Michael,

Attaching error logs : run.DNAScent.detect_barcode01.927231.err.txt run.DNAScent.detect_barcode02.927232.err.txt run.DNAScent.detect_barcode04.927234.err.txt run.DNAScent.detect_barcode08.927238.err.txt

We expect BrdU detection in barcodes04-08 though other barcodes might require exceptional handling

Small files in barcode01/ -rw-r--r-- 1 jalexander01 BCRBIOIN 5.0K Feb 22 10:44 merge.barcode01.fastq -rw-r--r-- 1 jalexander01 BCRBIOIN 113K Feb 22 10:46 merge.barcode01.sam -rw-r--r-- 1 jalexander01 BCRBIOIN 32K Feb 22 10:46 merge.barcode01.bam -rw-r--r-- 1 jalexander01 BCRBIOIN 64K Feb 22 10:46 merge.barcode01.bam.bai -rw-r--r-- 1 jalexander01 BCRBIOIN 18K Feb 22 10:46 barcode01.detect -rw-r--r-- 1 jalexander01 BCRBIOIN 0 Feb 22 10:46 barcode01.psl -rw-r--r-- 1 jalexander01 BCRBIOIN 11K Feb 22 10:47 barcode01.forkSense drwxr-sr-x 3 jalexander01 BCRBIOIN 4.0K Feb 22 10:47 newBedgraphDirectory (aborted at region generation)

And barcode08/ total 3.0G -rw-r--r-- 1 jalexander01 BCRBIOIN 364M Feb 22 10:44 merge.barcode08.fastq -rw-r--r-- 1 jalexander01 BCRBIOIN 414M Feb 22 10:48 merge.barcode08.sam -rw-r--r-- 1 jalexander01 BCRBIOIN 199M Feb 22 10:48 merge.barcode08.bam -rw-r--r-- 1 jalexander01 BCRBIOIN 1.7M Feb 22 10:48 merge.barcode08.bam.bai -rw-r--r-- 1 jalexander01 BCRBIOIN 1010M Feb 22 11:40 barcode08.detect -rw-r--r-- 1 jalexander01 BCRBIOIN 43M Feb 22 11:41 barcode08.regions -rw-r--r-- 1 jalexander01 BCRBIOIN 5.8M Feb 22 11:42 barcode08.psl -rw-r--r-- 1 jalexander01 BCRBIOIN 23M Feb 22 11:42 barcode08.analogue.psl -rw-r--r-- 1 jalexander01 BCRBIOIN 998M Feb 22 11:43 barcode08.forkSense (aborted at forkSense generation)

Please let me know. Kind regards,

John

[MBoemo]

Can you run grep '>' barcode01.detect | wc -l and grep '>' barcode08.detect | wc -l and let me know how many reads are in each barcode?

[john-alexander]

barcode03 20 barcode04 3 barcode01 1 barcode02 2 barcode08 8756 barcode05 8211 barcode06 8223 barcode07 10046 unclassified 19507

[MBoemo]

The regions issue is because you have very few reads in some of these barcodes. It has to fit some distributions to determine what constitutes a low and high region, so it needs to see at least a few hundred reads in order to do that. I'll write in something that catches this an exists gracefully with a more informative error message.

For forkSense, I think this is being caused by running it on very short (< ~300 bp) reads but I thought I fixed that in a previous patch - can you run git log -1 from the DNAscent directory and let me know which commit you're using?

[john-alexander]

Hi Michael,

That makes sense, thanks.

Here's git log -1

commit ab844162b9cb707d68714d3c58f5dc8a41b29ae0 (HEAD, tag: 2.0.2) Author: Michael Boemo m.a.boemo@gmail.com Date: Tue Nov 10 11:48:05 2020 +0000

resolve psl issue where the detect header was not properly passed over

[MBoemo]

This should be fixed in commit 989ed8f - just pull from master and recompile. Let me know if there are any further issues.

Closing for now, but I'll add better error handling into regions and push an update in the next few days.

[john-alexander]

Thanks Michael