Jelly.py extraction/assembly

Hi Adam,

I am facing problem in the output stage wherein I attempt to run PBJelly to fill gaps in my draft genome using pacbio data. All the steps/ stages leading to the output stage run without any discernible error but the output stage does not produce the "3" files, viz,
<outputdir>/pbjelly.out.fasta
<outputdir>/pbjelly.out.qual
<outputdir>/liftOverTable.json</outputdir></outputdir></outputdir>

which are expected on successful completion of the process.

However, I do end with output.err file and "gap_fill_status.txt" but the files have not been helpful in debugging the error. Could you be kind enough to help understand the error. I have provided the following snippets below:

snippet of output.err file: I am providing the first and last 15 lines of the output.err file and the "collectionError.gml file".

$ cat out.err | head -15

2018-03-12 12:20:33,910 [INFO] Running /opt/packages/pbjelly/PBSuite_15.8.24/bin/Collection.py /biod/PBJELLY/Protocol.xml
2018-03-12 12:20:33,911 [INFO] Grabbing Filling Metrics
2018-03-12 12:27:59,705 [INFO] Number of Gaps Addressed 31478
2018-03-12 12:27:59,705 [INFO] No Filling Metrics 815
2018-03-12 12:27:59,705 [INFO] Min Read Failed 6538
2018-03-12 12:27:59,705 [INFO] Filled 3076
2018-03-12 12:27:59,706 [INFO] NFilled 0
2018-03-12 12:27:59,706 [INFO] Single-End Reduced 20931
2018-03-12 12:27:59,706 [INFO] Double-End Reduced 118
2018-03-12 12:27:59,706 [INFO] Overfilled 0
2018-03-12 12:27:59,706 [INFO] Gaps with trimmed edges 407
2018-03-12 12:27:59,710 [INFO] Loading Reference
2018-03-12 13:03:56,983 [DEBUG] ['m54112_170420_213725/45416982/5208_8001'] extends ref0013197e3
2018-03-12 13:03:56,983 [DEBUG] ref0013197e3
2018-03-12 13:03:56,983 [DEBUG] ['m54112_170411_223330/73531789/4674_6261', 'm54112_170411_223330/19006097/7233_8031'] extends ref0005612e5

$ cat output.err | tail -15

2018-03-12 13:04:22,283 [DEBUG] ['m54112_170429_081146/52166991/0_23085'] gives evidence ref0011222e3 -> ref0011222e5
2018-03-12 13:04:22,283 [DEBUG] ['m54112_170502_074934/41878071/0_13713'] gives evidence ref0027184e5 -> ref0019256e5
2018-03-12 13:04:22,283 [DEBUG] ['m54112_170429_081146/48431662/72_11584'] gives evidence ref0003689e3 -> ref0003689e5
2018-03-12 13:04:22,283 [DEBUG] ['m54112_170427_083459/37814402/0_14003'] gives evidence ref0010588e3 -> ref0009488e5
2018-03-12 13:04:22,283 [DEBUG] ['m54112_170403_222024/45351731/0_13266'] gives evidence ref0008176e5 -> ref0020913e5
2018-03-12 13:04:22,283 [DEBUG] ['m54112_170427_083459/48300942/5693_24876'] gives evidence ref0023866e3 -> ref0001536e5
2018-03-12 13:04:22,283 [DEBUG] ['m54112_170502_074934/11272376/48469_61960', 'm54112_170502_074934/11272376/25171_36705', 'm54112_170502_074934/11272376/36757_48423', 'm54112_170502_074934/11272376/11666_25130', 'm54112_170427_083459/21234298/12960_17122', 'm54112_170429_081146/43975403/13815_20145'] gives evidence ref0011721e5 -> ref0000490e3
2018-03-12 13:04:22,284 [DEBUG] ['m54112_170420_213725/64684561/551_1939'] gives evidence ref0009842e5 -> ref0009842e3
2018-03-12 13:04:22,284 [DEBUG] ['m54112_170403_222024/55706103/0_10885', 'm54112_170403_222024/55706103/10932_16403', 'm54112_170502_074934/39911593/15648_17701', 'm54112_170429_081146/39912022/0_21971'] gives evidence ref0027234e3 -> ref0023107e5
2018-03-12 13:04:22,284 [DEBUG] ['m54112_170411_223330/72417726/13151_18986', 'm54112_170411_223330/72417726/19033_27480', 'm54112_170403_222024/73532308/34347_44117', 'm54112_170403_222024/13763356/28979_35103', 'm54112_170403_222024/73532308/45822_54044', 'm54112_170403_222024/73532308/54086_60613', 'm54112_170403_222024/73532308/24470_34304', 'm54112_170403_222024/73532308/17738_24427', 'm54112_170427_083459/73400401/31824_37160', 'm54112_170427_083459/73400401/41974_52567', 'm54112_170427_083459/73400401/20037_30888', 'm54112_170427_083459/73400401/10026_19992'] gives evidence ref0018747e5 -> ref0022109e3
2018-03-12 13:04:22,284 [DEBUG] ['m54112_170403_222024/21823748/0_9898', 'm54112_170403_222024/45089258/11041_19029', 'm54112_170403_222024/45089258/201_11000'] gives evidence ref0007553e5 -> ref0035432e3
2018-03-12 13:04:22,284 [DEBUG] ['m54112_170411_223330/48628477/2918_12980', 'm54112_170429_081146/59376127/46618_54443', 'm54112_170429_081146/13370052/48575_56649'] gives evidence ref0023888e5 -> ref0023888e3
2018-03-12 13:04:30,405 [INFO] Removing Poorly Supported Edges
2018-03-12 13:04:30,408 [ERROR] Graph doesn't have ends. Check it's repeats in collectionErr.gml
2018-03-12 13:04:30,408 [ERROR] ['ref0013197e3']

collectionError.gml file "content"

$ cat collectionError.gml
graph [
node [
id 0
label "ref0013197e3"
trim 0
extenders "m54112_170420_213725/45416982/5208_8001"
]
]

Did you find a solution for this ? I have run into a similar error and do not know how to solve it.
Thank you very much for your answer