KeyError: 'tair'

[lindonghuia]

i have some problem when i use the master scripy this is my error ----> Started ----> Copying input ----> Filtering markers ----> Doubling markers ----> Markers: plant/MARKERS/9plant_MARKERS_DOUBLED ----> Cleaning ACS file ----> Computing species ------> All species: plant/ACS/9plant_SPECIES ----> Computing species pairs to compare ------> All informative pairs: plant/ACS/9plant_PAIRS ----> Computing ancestral contiguous sets: plant/ACS/9plant_ACS ------> Species: tair ys --------> Computing maximum common intervals: plant/ACS/9plant_MCI_tair_ys Traceback (most recent call last): File "/data/02_work/lindh/software/anges/anges_1.01/src/ACS/ACS_compute_common_intervals_unique.py", line 55, in filtered_blocks = filter_markers(blocks, [spe1, spe2]) File "/data/02_work/lindh/software/anges/anges_1.01/src/ACS/acs.py", line 111, in filter_markers for ch in blocks[spes[0]]:
KeyError: 'tair'

--------> Computing strong common intervals: plant/ACS/9plant_SCI_tair_ys Traceback (most recent call last): File "/data/02_work/lindh/software/anges/anges_1.01/src/ACS/ACS_compute_common_intervals_unique.py", line 55, in filtered_blocks = filter_markers(blocks, [spe1, spe2]) File "/data/02_work/lindh/software/anges/anges_1.01/src/ACS/acs.py", line 111, in filter_markers for ch in blocks[spes[0]]:
KeyError: 'tair'

--------> Computing supported adjacencies: plant/ACS/9plant_SA_tair_ys Traceback (most recent call last): File "/data/02_work/lindh/software/anges/anges_1.01/src/ACS/ACS_compute_supported_adjacencies_unique.py", line 45, in filtered_blocks = filter_markers(blocks, [spe1, spe2]) File "/data/02_work/lindh/software/anges/anges_1.01/src/ACS/acs.py", line 111, in filter_markers for ch in blocks[spes[0]]:
KeyError: 'tair'

------> Joining ACS files: plant/ACS/9plant_ACS_tair_ys Traceback (most recent call last): File "/data/02_work/lindh/software/anges/anges_1.01/src/ACS/ACS_join_files.py", line 44, in in_matrix = open(sys.argv[i]) # matrix file IOError: [Errno 2] No such file or directory: 'plant/ACS/9plant_MCI_tair_ys'

------> Joining ACS files: plant/ACS/9plant_ACS_tair_ys, plant/ACS/9plant_ACS ------> Species: tair xg --------> Computing maximum common intervals: plant/ACS/9plant_MCI_tair_xg Traceback (most recent call last): File "/data/02_work/lindh/software/anges/anges_1.01/src/ACS/ACS_compute_common_intervals_unique.py", line 55, in filtered_blocks = filter_markers(blocks, [spe1, spe2]) File "/data/02_work/lindh/software/anges/anges_1.01/src/ACS/acs.py", line 111, in filter_markers for ch in blocks[spes[0]]:
KeyError: 'tair'

--------> Computing strong common intervals: plant/ACS/9plant_SCI_tair_xg Traceback (most recent call last): File "/data/02_work/lindh/software/anges/anges_1.01/src/ACS/ACS_compute_common_intervals_unique.py", line 55, in filtered_blocks = filter_markers(blocks, [spe1, spe2]) File "/data/02_work/lindh/software/anges/anges_1.01/src/ACS/acs.py", line 111, in filter_markers for ch in blocks[spes[0]]:
KeyError: 'tair' and here is my data

1 tqs.10:13054594-13058488 + dz.10:14903386-14907226 + tao.6:7122985-7126348 + apple.3:10373862-10377221 + apple.11:11933646-11937050 + xigua.1:25797464-25801653 - tair.2:15295853-15298362 - tair.5:19604976-19606766 + li.3:7886715-7889492 + li.11:9651661-9654981 + cm.3:27504030-27507560 -

2 tqs.10:13039110-13046705 + dz.10:14887840-14895503 + tao.6:7105612-7113401 + apple.11:11907889-11916311 + apple.3:10342152-10350367 + xigua.1:26023377-26034428 - tair.2:15301699-15305786 - li.11:9631601-9637432 + li.3:7862941-7870809 + ys.NC_037293.2:2496220-2504680 + ys.NC_037293.2:2496218-2504680 + ys.NC_037288.2:21737665-21749179 + ys.NC_037288.2:21737664-21749510 + ys.NC_037288.2:21737664-21749510 + ys.NC_037288.2:21737664-21749179 + cm.3:27520519-27525807 -

3 tqs.10:12994817-12995347 + dz.10:14836502-14837029 + tao.6:7100147-7100653 + apple.3:10334521-10335458 + apple.11:11897669-11899213 + xigua.2:34849622-34850131 + xigua.1:26145586-26146095 - tair.5:27561771-27563065 + tair.3:19238160-19239645 - tair.2:15310004-15311193 - li.3:7857440-7858282 + li.11:9621268-9622183 + ys.NC_037288.2:21731518-21732418 + ys.NC_037293.2:2455473-2456456 + cm.3:27535861-27536376 -

4 tqs.11:15392691-15393191 + tqs.10:12950041-12950541 - dz.10:14822751-14823251 - dz.11:22913180-22913680 + tao.6:7089743-7090243 - tao.6:23918332-23918832 + apple.11:11861470-11861970 - apple.3:10318438-10320213 - apple.4:17040905-17041405 + xigua.2:34838833-34839333 - xigua.4:23709394-23709894 - xigua.10:33536938-33537438 + tair.5:27556265-27557360 - tair.2:18783453-18784403 - tair.3:22490811-22492018 - li.4:14068210-14069858 + li.3:7844603-7845103 - li.11:9572253-9574662 - li.12:15362761-15363595 + ys.NC_037290.2:5742521-5743239 + ys.NC_037302.2:15025348-15025988 + ys.NC_037302.2:15029339-15030061 + ys.NC_037302.2:15120474-15121179 - ys.NC_037302.2:15124508-15125217 - cm.6:9911327-9912079 - i will be very appreciate it if you could answer me

[cchauve]

Can you join all the input files and also the parameters file or the command line. One thing I noticed is that in the markers you show the species names are not prefixed by ">" (i.e. ">1", ">2", ">3", ">4").

[lindonghuia]

it seems like the SpeciesTree problem ,when i use the example tree that i change the species ,it can be work , (tair:0.231555,((xg:0.33395,((tqs:0.0250969,dz:0.0297529):0.171896,(cm:0.175235,(tao:0.0770099,(apple:0.0158909,li:0.0187958):0.0901407):0.0430722):0.0872409):0.0427629):0.0482029,gj:0. 224907)@:0.231555); it is my own species

1 tqs.TQS-Chr08:21137707-21138527 - dz.Chr08:25444046-25444996 - tao.G2:28916692-28917392 - apple.Chr07:33480620-33481553 - xg.Chr01:5604919-5606766 + tair.Chr5:24373872-24374472 - tair.Chr5:24373872-24374491 - li.Chr01:23067503-23068665 - li.Chr07:26691791-26692318 -

2 tqs.TQS-Chr08:21135263-21137059 + dz.Chr08:25441587-25443424 + tao.G2:28913688-28916443 + tao.G2:28913688-28916443 + apple.Chr07:33477732-33480663 + apple.Chr01:31831129-31834187 + xg.Chr05:8349011-8352509 + tair.Chr5:24371813-24373873 + tair.Chr5:24371766-24373872 + li.Chr07:26688605-26691739 + li.Chr01:23065310-23067123 + gj.chr9:29483087-29486425 +

3 tqs.TQS-Chr08:21130776-21133501 - dz.Chr08:25437066-25440598 - xg.Chr01:5609295-5614294 + tair.Chr5:24369379-24371591 - tair.Chr5:24369324-24371531 - tair.Chr5:24369324-24371448 - li.Chr01:23061629-23063693 - li.Chr07:26685165-26687118 - gj.chr9:29478117-29479482 -

[cchauve]

I am sorry I do no understand and I do not have enough information to try to reproduce your problem. If you attach to your answer the exact files that you use, I can try.

[lindonghuia]

when i use this tree (((tqs:0.2,dz:0.2):0.2,(li:0.2,apple:0.2):0.2)@:0.6,xg:1);it can be useful this tree can not be useful (((((((apple:0.0158909,li:0.0187958):0.0901407,tao:0.0770099):0.0430722,cm:0.175235):0.0872409,(tqs:0.0250969,dz:0.0297529):0.171896):0.0427629,xg:0.33395):0.0482029,gj:0.224907):0.2315 55,tair:0.231555)@;

[lindonghuia]

when i use this tree (((tqs:0.2,dz:0.2):0.2,(li:0.2,apple:0.2):0.2)@:0.6,xg:1);it can be useful this tree can not be useful (((((((apple:0.0158909,li:0.0187958):0.0901407,tao:0.0770099):0.0430722,cm:0.175235):0.0872409,(tqs:0.0250969,dz:0.0297529):0.171896):0.0427629,xg:0.33395):0.0482029,gj:0.224907):0.2315 55,tair:0.231555)@;