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>

2012-05-31 braney xenoMrna change

Symptom: dbload fails with allowLargeDeletes message. Hiram had changed the loading of xenoMrna in the genbank.conf file for several databases without dropping the xenoMrna table.

Solution: changed genbank.conf to continue to update xenoMrna if it had already been loaded.

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.

2012-06-06 braney gbSanity failed on rn5

Symptom: lots of error messages of the form "Error: rn5: NR_051977: not in gbCdnaInfo table, referenced in gbIndex"

Solution: re-did the initial load of rn5 on dev.

2012-06-06 braney hgnfs copy script failed

Symptom: genbank-10 was turned off but the hgnfs1 copy script still referenced it.

Solution: change genbank-10 reference to hgwdev

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.

2012-06-11 braney non-existent table found in mkdownloads

Symptom: mkdownload fails on message about a gene model table not found

hgwdev 2012.06.11-20:07:57 mkdownload: creating /hive/data/outside/genbank/data/ftp/canFam3/bigZips/refMrna.fa.gz table ensGene not found for any chroms Error: 1 input table(s)/file(s) do not exist for any of the chroms specified command failed: featureBits -fa=stdout canFam3 ensGene:upstream:1000 | gzip -c > /hive/data/outside/genbank/data/ftp/canFam3/bigZips/upstream1000.fa.gz.tmp.gz at /hive/data/outside/genbank/bin/../lib/gbCommon.pm line 272. at /hive/data/outside/genbank/bin/../lib/gbCommon.pm line 272.

Solution: fixed etc/genbank.conf to list an existing table for upstreamGeneTbl

canFam3.upstreamGeneTbl = refGene