syntax errors when running part3 all-against-all

Question

[Sofia]

Hello, I am running stand alone oma 2.5.0 to find orthologs.

I downloaded a set of precomputed 50 genomes. I successfully completed the oma run and have results. I then added in a new genome and reran. The blasts seem to have run fine. Now when oma is reading the all against all files I am getting syntax errors. Because I successfully ran oma without my genome I am pretty sure something is wrong with my inputed DB or the blasts with my genome. Any idea what is going on. CCALY is my genome, you can see that after the syntax errors the output says : # AMPQE vs CCALY done, (109682/109682)

Reading the all-against-all files...

# AMPQE vs AMPQE done, (142372/142372)
# ANOCA vs AMPQE done, (33668/33668)
# ASTMX vs AMPQE done, (42645/42645)
# CAEEL vs AMPQE done, (19978/19978)
# AMPQE vs CAPTE done, (49061/49061)
syntax error:
AssertDatabaseVersionsInSync('11e53381d6de1843','a0bfa85cb9acfa87'):
                                                                   ^
syntax error:
[2338, 33221, 200[[2336, 2485, 185.7128743, 113, 1..62, 802..861, 441.6319949],
                 ^
syntax error:
[2340, 9235, 188.5228724, 94, 2..102, 3..104, 202.6980833] ]):
                                                           ^
syntax error:
6503014, 140, 53..154, 154..255, 398.5450231],
                                            ^
syntax error:
[2340, 9235, 188.5228724, 94, 2..102, 3..104, 202.6980833] ]):
                                                           ^
syntax error:
963, 72766, 191.8781501, 151, 30..165, 321..444, 394.8502758],
  ^
syntax error:
[10966, 39321, 380.7883157, 150, 5..274, 150..412, 174.6143452] ]):
                                                                ^
# AMPQE vs CCALY done, (109682/109682)

Thank you, Sofia

[Ram]

What on earth are you talking about? Please add some context, we are not mind readers.

[Sofia]

When I started with the gz all-vs-all files for CHICK and ANOCA and started oma, everything ran fine, I got output. Then, in the same directories, I didn't move anything around. I added my CCALY.fa CCALY.splice to the DB folder and started oma again. The alignment step seemed to go fine. I get errors when I hit the all-vs-all steps. ANOCA vs ANOCA seems to have issues. The ANOCA vs CCALY seems like it had no issues. The ANOCA vs CHICK had issues. Then oma dies. Once again the ANOCA and CHICK were downloaded from oma.

****

Reading the all-against-all files...

# ANOCA vs ANOCA done, (117204/117204)
syntax error:
[3853, 83382AssertDatabaseVersionsInSync('c5e19237505093a6','74fbfc5eb99b3cd5'):
                                       ^
syntax error:
, 1833.210788, 56, 395..703, 25..333, 26.85145893],
^
syntax error:
[3854, 18390, 536.8774221, 82, 19..178, 131..289, 99.629[[3847, 7938, 252.1376533, 173, 10..219, 4..223, 280.2672173],
                                                        ^
syntax error:
[3855, 18389, 495.5337205, 69, 3..157, 131..290, 83.4199954]7.8828122],
                                                                    ^
syntax error:
[3850, 17238, 621.2657931, 67 142..240, 149.0019083],
                                 ^
syntax error:
[3857, 5737, 589 31469, 223.8594161, 203, 6..212, 5..216, 414.2965981],
                     ^
syntax error:
 14..212, 210..408, 50.43927077],
                               ^
syntax error:
[3851, 15918, 962.2632698, 74, 13..216, 224..4[3857, 15973, 1255.96778, 71, 121..450, 144..417, 42.75959638],
                                              ^
syntax error:
[3857, 16887, 2054.013161, 59, 566..942, 10 1006.69206, 69, 13..212, 471..670, 57.34742698],
                                                     ^
syntax error:
[3857, 17933, 1326.509297, 81, 638..964, 268..606, 44.43471604],1882504, 81, 14..216, 184..388, 71.54120715],
                                                                                                           ^
syntax error:
[3857, 32692, 621.4452972, 95, 591..786, 379..576,],
                                                  ^
syntax error:
[3851, 25877, 946.9052734, 71, 19..212, 249..442, 61.9420195 95.96976783],
                                                                       ^
syntax error:
[3851, 37565, 722.5464557, 93, 13..21 67..451, 1..357, 23.8772703],
                                        ^
syntax error:
[3 103.5726765],
             ^
syntax error:
[3858, 29001, 317.2107437, 135, 140..294, 27..185, 238.3378347] ]):
                                                                ^
syntax error:
792471, 100, 48..212, 209..377, 122.7473321],
                                           ^
syntax error:
.050167, 67, 139..415, 2..278, 39.19189728],
      ^
syntax error:
[3858, 29001, 317.2107437, 135, 140..294, 27..185, 238.3378347] ]):
                                                                ^
# ANOCA vs CCALY done, (556181/556181)
# ANOCA vs CHICK done, (117538/117538)
syntax error:
[295, 72509, 296.3915323, 146, 27..277, 124.AssertDatabaseVersionsInSync('74fbfc5eb99b3cd5','74fbfc5eb99b3cd5'):
                                                                       ^
syntax error:
.412, 176.0966046],
                 ^
syntax error:
[290, 15261, 2011.21925, 36 115, 46..306, 288..632, 101.2505477],
                              ^
Error, 'multiple dots in decimal number'

Answer 1

[Adrian Altenhoff]

Dear Sofia,

this looks like the all-vs-all file is corrupted. maybe a race condition of to processes that tried to write the same file. The best is to simply remove the file Cache/AllAll/AMPQE/CCALY.gz, or, if you haven't run oma-compact, to run all the files in Cache/AllAll/AMPQE/CCALY/part*

Then, simply restart the oma -s command to recreate this file in parallel. Hope this will help. Best wishes

Adrian

[Sofia]

I deleted all of AMPQE and all of CCALY. I removed the AMPQE.fa. The ANOC and CHICK all-vs-all was downloaded from the OMA website.

I am left with this in my DB:

DB$ ls ANOCA.fa ANOCA.splice CCALY.fa CCALY.splice CHICK.fa CHICK.splice

I am still getting these errors. Any ideas what is going on. The errors are not very informative to me, I am hoping they mean something to someone.

****

Reading the all-against-all files...

syntax error:
AssertDatabaseVersionsInSync('c991c43292662c7e','c991c43292662c7e'):
                                                                   ^
syntax error:
[15 302.6629363, 166, 76..347, 31..312, 214.506112],
              ^
syntax error:
[1607, 14126, 221.9412402, 222, 821..1079, 218..486, 403.068539].8099178, 219, 10..304, 49..347, 384.8464677],
                                                                       ^
syntax error:
[1622, 5474, 887.7864007, 97, 3029..3383, 237..577, 59.0085156] ]):
                                                                 ^
syntax error:
70879],
     ^
syntax error:
[1622, 5474, 887.7864007, 97, 3029..3383, 237..577, 59.0085156] ]):
                                                                ^
syntax error:
[5631, 10150, 238.0199165, 128, 1261..1422, 9..131, 262.21AssertDatabaseVersionsInSync('c991c43292662c7e','c991c43292662c7e'):
                                                                                     ^
syntax error:
51105],
     ^
syntax error:
[5632, 8506, 280.9183216, 16[[5558, 11857, 1099.759861, 22.27216015, 350..470, 154..274, 22.05436931],
                            ^
syntax error:
[5632, 115 100..377, 9..282, 85.37788268],
              ^
Error, 'multiple dots in decimal number'

[Sofia]

Are my IDs too long? Can the ID have a dot in it?

>CCA1t000397002.1
MVLTTPLPDELNFRRRKLYPPEDSTRCFGILTAKPIPQIPHFPVYTRSGEVTISIELKKSGFTLSLQMLELITRLHQYIFSHILRLEKPALEFRPTNADS
AYCVLPLNVDVDDDMDTLDIDFEFMEDIEKSEARTGIPSTQYTKETPFIFGLKDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEYVTFAEYY
KTKYNLDLTNLNQPLLDVDHTSSRLNLLTPRHLNQKGKALPLSSAEKRKAKWESLQNKQILVPELCAIHPIPASLWRKAVCLPSILYRLHCLLTAEELRS
QTAIDAGVGVKSLPTDFRYPNLDFGWKKSIDSKSFISAPISSPAENENSVKHSAIVVPEHAAHQGANKISSADKYDQMSVNCRTLIESHSKLQNYVSVEP
ATVNCVSQNKNLANNNCDLAKQTFCQENQLNHCGQEIPVQPTTSSSQNLYKSENQLKPSNECTLSNKYIDGNANKSTSDGSPKMTNTSASDASERIDFVI
SSSNGYSSKLLGPNPGLILQALTLSNASDGFNLERLEMLGDSFLKHAITTYLFCTYPDAHEGRLSYMRSKKVSNCNLYRLGKKKGLPSRMVVSIFDPPVN
WLPPGYTVNQDRSNTDKWEKEDMAKEGLMSNGKLDDDYDDDDEVDDLIWRVPKEEADFEDDFLEYDQEHIKFIDNMLMGSGAFVRKISLSPFSTTSHSYE
WKAPQKSPSPSVQSPSDPEEFDYSSWDAMCYLDPSKAVEEDDFVVGFWNPSEENCGIDAGKQSISYDLHTEQCIADKSIADCVEALLGCYLTSCGERAAQ
LFLCSLGLKVLPVIKHSEQDSSLYSYRNNFHIQQKHPSTNCISASQANQESSLYKDLEYGCLKIPPRCMFDHPDAEKTLNHLISGFENFEEKINYIFKNK
AYLLQAFTHASYHYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELFHVIDDFVQFQMEKN
EMQGMDSE

[Ram]

Please do not add answers unless you're answering the top level question. Use Add Comment or Add Reply as appropriate instead. I've done my best to move your posts to the right location, please be more careful in the future.

[Sofia]

Ok. I removed my new proteome, and only have the downloaded data for these two organisms.

ANOCA.fa ANOCA.splice CHICK.fa CHICK.splice

Still getting errors. Okay. I will removed all my All-vs-All. Replace fresh with with my downloaded gz all-vs-all, and try just ANOCO and CHICK (both downloaded). if that works, which it should. I'll add back my proteome, and try again.

[Ram]

Stop. Adding. Answers.