weird issue downloading Heatmap information

[ARWattam]

It looks like there isn't a protein annotated as the cell is black for Borrelia japonica strain ATCC 51557, and when I downloaded the heatmap, it had a value of NaN. So I clicked on the cell to see the information, and there are 3 proteins for this genome. The PLfamm

is PLF_64895_00000238. What gives??

[hyoo]

would you share your url so that i can take a look?

[hyoo]

I cannot reproduce it. Please specify

• how did you get to this page (from genome group? taxon ?)
• how many genomes were in your analysis, and what are those?
• what was the step to get this?

i tried with randomly picked 4 Borrelia genomes and Borrelia japonica strain ATCC 51557, but i cannot reproduce this problem.

[ARWattam]

Okay, I made a genome group of all Borrellia minus burgdorferi. Then I opened the genome group, clicked on the Protein Families tab, changed the selection to PLFams, and then looked at the heatmap. Look at the row that has B. japonicum (it will be the last row int he heatmap (see attached screenshot). It shows that this genome is missing the Phage terminase Large subunit family, but when I select the first few cells in the heatmap, I see that there are indeed 2 proteins with that annotation (see attached text file).

On Wed, Jan 31, 2018 at 2:22 PM, hyoo notifications@github.com wrote:

I cannot reproduce it. Please specify

• how did you get to this page (from genome group? taxon ?)
• how many genomes were in your analysis, and what are those?
• what was the step to get this?

i tried with randomly picked 4 Borrelia genomes and Borrelia japonica strain ATCC 51557, but i cannot reproduce this problem.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/PATRIC3/patric3_website/issues/1823#issuecomment-362041539, or mute the thread https://github.com/notifications/unsubscribe-auth/AK8ZdL-usollr9TmAfVzFNE-AFjsCA8Pks5tQL18gaJpZM4RCh3U .[image: Web Bug from https://github.com/notifications/beacon/AK8ZdILONhh_h0Gt3Wr5ydQ1VUXFv-EHks5tQL18gaJpZM4RCh3U.gif]

Genome Genome ID Accession PATRIC ID RefSeq Locus Tag Alt Locus Tag Feature ID Annotation Feature Type Start End Length Strand FIGfam ID PATRIC genus-specific families (PLfams) PATRIC cross-genus families (PGfams) Protein ID AA Length Gene Symbol Product GO "Borreliella japonica strain ATCC 51557" "34095.3" "FMTE01000006" "fig|34095.3.peg.1015" "SAMN02983004_00926" "PATRIC.34095.3.FMTE01000006.CDS.10415.10852.rev" "PATRIC" "CDS" 10415 10852 438 "-" "FIG00434233" "PLF_64895_00000002" "PGF_00951572" 145 "Uncharacterized protein BppA"
"Borreliella japonica strain ATCC 51557" "34095.3" "FMTE01000006" "fig|34095.3.peg.1016" "SAMN02983004_00927" "PATRIC.34095.3.FMTE01000006.CDS.10920.11615.rev" "PATRIC" "CDS" 10920 11615 696 "-" "FIG00434233" "PLF_64895_00000002" "PGF_00951572" 231 "Uncharacterized protein BppA"
"Borreliella japonica strain ATCC 51557" "34095.3" "FMTE01000006" "fig|34095.3.peg.1024" "PATRIC.34095.3.FMTE01000006.CDS.17517.17633.fwd" "PATRIC" "CDS" 17517 17633 117 "+" "FIG00434566" "PLF_64895_00000009" "PGF_00801572" 38 "Borrelia plasmid replication region protein 2" "Borreliella japonica strain ATCC 51557" "34095.3" "FMTE01000006" "fig|34095.3.peg.1025" "SAMN02983004_00933" "PATRIC.34095.3.FMTE01000006.CDS.17633.18031.fwd" "PATRIC" "CDS" 17633 18031 399 "+" "FIG00434566" "PLF_64895_00000009" "PGF_00801572" 132 "Borrelia plasmid replication region protein 2" "Borreliella japonica strain ATCC 51557" "34095.3" "FMTE01000006" "fig|34095.3.peg.1035" "SAMN02983004_00942" "PATRIC.34095.3.FMTE01000006.CDS.22757.23455.fwd" "PATRIC" "CDS" 22757 23455 699 "+" "FIG00001414" "PLF_64895_00000008" "PGF_00332233" 232 "Phage terminase, large subunit"
"Borreliella japonica strain ATCC 51557" "34095.3" "FMTE01000006" "fig|34095.3.peg.1036" "SAMN02983004_00943" "PATRIC.34095.3.FMTE01000006.CDS.23439.23954.fwd" "PATRIC" "CDS" 23439 23954 516 "+" "FIG00001414" "PLF_64895_00000008" "PGF_00332233" 171 "Phage terminase, large subunit"
"Borreliella japonica strain ATCC 51557" "34095.3" "FMTE01000006" "fig|34095.3.peg.1039" "SAMN02983004_00946" "PATRIC.34095.3.FMTE01000006.CDS.26503.26898.rev" "PATRIC" "CDS" 26503 26898 396 "-" "FIG00434810" "PLF_64895_00000003" "PGF_00113390" 131 "hypothetical protein"
"Borreliella japonica strain ATCC 51557" "34095.3" "FMTE01000006" "fig|34095.3.peg.1040" "SAMN02983004_00947" "PATRIC.34095.3.FMTE01000006.CDS.27044.27400.rev" "PATRIC" "CDS" 27044 27400 357 "-" "FIG00434810" "PLF_64895_00000003" "PGF_00113390" 118 "hypothetical protein"
"Borreliella japonica strain ATCC 51557" "34095.3" "FMTE01000006" "fig|34095.3.peg.1013" "SAMN02983004_00925" "PATRIC.34095.3.FMTE01000006.CDS.9803.10129.rev" "PATRIC" "CDS" 9803 10129 327 "-" "FIG01345650" "PLF_64895_00000013" "PGF_00412110" 108 "Uncharacterized protein BppB"
"Borreliella japonica strain ATCC 51557" "34095.3" "FMTE01000015" "fig|34095.3.peg.147" "SAMN02983004_01074" "PATRIC.34095.3.FMTE01000015.CDS.3917.5248.rev" "PATRIC" "CDS" 3917 5248 1332 "-" "FIG00434233" "PLF_64895_00000002" "PGF_00951572" 443 "Uncharacterized protein BppA"
"Borreliella japonica strain ATCC 51557" "34095.3" "FMTE01000017" "fig|34095.3.peg.1183" "PATRIC.34095.3.FMTE01000017.CDS.4169.4624.fwd" "PATRIC" "CDS" 4169 4624 456 "+" "FIG00434233" "PLF_64895_00000002" "PGF_00951572" 152 "Uncharacterized protein BppA"
"Borreliella japonica strain ATCC 51557" "34095.3" "FMTE01000027" "fig|34095.3.peg.1155" "SAMN02983004_01120" "PATRIC.34095.3.FMTE01000027.CDS.1.141.fwd" "PATRIC" "CDS" 1 141 141 "+" "FIG00434566" "PLF_64895_00000009" "PGF_00801572" 46 "Borrelia plasmid replication region protein 2" "Borreliella japonica strain ATCC 51557" "34095.3" "FMTE01000031" "fig|34095.3.peg.1174" "SAMN02983004_01132" "PATRIC.34095.3.FMTE01000031.CDS.527.790.fwd" "PATRIC" "CDS" 527 790 264 "+" "PLF_64895_00000009" "PGF_00801572" 87 "Borrelia plasmid replication region protein 2" "Borreliella japonica strain ATCC 51557" "34095.3" "FMTE01000033" "fig|34095.3.peg.1144" "SAMN02983004_01136" "PATRIC.34095.3.FMTE01000033.CDS.1.141.fwd" "PATRIC" "CDS" 1 141 141 "+" "FIG00434566" "PLF_64895_00000009" "PGF_00801572" 46 "Borrelia plasmid replication region protein 2" "Borreliella japonica strain ATCC 51557" "34095.3" "FMTE01000034" "fig|34095.3.peg.1184" "SAMN02983004_01139" "PATRIC.34095.3.FMTE01000034.CDS.1.279.fwd" "PATRIC" "CDS" 1 279 279 "+" "FIG00434566" "PLF_64895_00000009" "PGF_00801572" 92 "Borrelia plasmid replication region protein 2" "Borreliella japonica strain ATCC 51557" "34095.3" "FMTE01000035" "fig|34095.3.peg.1188" "SAMN02983004_01142" "PATRIC.34095.3.FMTE01000035.CDS.1.141.fwd" "PATRIC" "CDS" 1 141 141 "+" "FIG00434566" "PLF_64895_00000009" "PGF_00801572" 46 "Borrelia plasmid replication region protein 2" "Borreliella japonica strain ATCC 51557" "34095.3" "FMTE01000038" "fig|34095.3.peg.1086" "PATRIC.34095.3.FMTE01000038.CDS.2.94.fwd" "PATRIC" "CDS" 2 94 93 "+" "FIG00434566" "PLF_64895_00000009" "PGF_00801572" 30 "Borrelia plasmid replication region protein 2" "Borreliella japonica strain ATCC 51557" "34095.3" "FMTE01000041" "fig|34095.3.peg.1191" "PATRIC.34095.3.FMTE01000041.CDS.2.94.fwd" "PATRIC" "CDS" 2 94 93 "+" "FIG00434566" "PLF_64895_00000009" "PGF_00801572" 30 "Borrelia plasmid replication region protein 2"

[hyoo]

thanks, I found the bug and fixed. https://github.com/PATRIC3/p3_api/commit/31bc51b5c0f89d09571771e949c554849c9b4202

This will be deployed by end of today.

[hyoo]

the fix is on production