GenbankServiceLog

This page is a record of service on the genbank process.

2012-05-25 braney allowLargeDeletes problem

Symptom: dbload fails with "Stoping due to maxShrinkage limit being exceeded in one or more partitions. Investigate and rerun with -allowLargeDeletes."

Solution: discovered four assemblies that were missing their full directory in either refSeq.53/<db>/ or genbank.189.0/<db>. No explanation was found for the missing directories. To restore these four assemblies (sacCer1,sacCer2,sacCer3,ce2) I built the alignments from scratch using bin/gbDbAlignStep -initial <db>

2012-06-06 braney build failed on /data/tmp/ remove

Symptom: build failed on inability to remove a directory in /data/tmp that was owned by Hiram

Solution: asked mark and hiram to remove the directories in /data/tmp that they owned.

2012-06-09 braney load failed due to malformed genbank entry

Symptom: dbload of refseq.53 update from 2012-06-08 failed with message ' invalid signed integer: ">1632" ' Problem was '<' character in mdiff field of GB record:

">" in http://www.ncbi.nlm.nih.gov/nuccore/NM_001267664

Solution: fixed parser to ignore '<' characters in mdiff field.

On Wed, Jun 6, 2012 at 11:16 AM, Brian Raney <braney@soe.ucsc.edu> wrote: > * rn5 inconsistencies > Error: rn5: NR_051977: not in gbCdnaInfo table, referenced in gbIndex > Error: rn5: NR_051977: not in seq table, referenced in gbIndex > Error: rn5: NR_051977: not in gbExtFile table, referenced in gbIndex > Error: rn5: NR_051977: not in refSeqStatus table, and is RefSeq acc > Error: rn5: NR_051977: not in refLink table, and is RefSeq acc > Error: rn5: NR_051977: not in gbStatus table, referenced in gbIndex > > > On Wed, Jun 6, 2012 at 7:36 AM, Brian Raney <braneyboo@gmail.com> wrote: >> * hiram's xenoMrna

>> * copy failed on genbank-10