Probem with Zorro

[Texier Frédéric]

Hello,

I am trying to use zorro with an assembly of 454 reads with Newbler and an asembly of Hiseq reads with Ray.

But I have an error when i Lauch zorro command.

I think I have a problem with sort2 or name of read but I don't know why and I can solve this problem.

thank your for your feedback

the log file is:

===> CORE ASSEMBLY

Creating AMOS BANK...DONE

DONE

Running nucmer with masked sequences...DONE

Parsing pairs of aligned sequences...DONE

Running nucmer with unmasked sequences...DONE

Filtering confident overlaps...DONE

Converting confident overlaps to AMOS format...Argument "contig00076CONT_unknown_unkno_59$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00004.1CONT_unknown_unkno_35$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00023.3CONT_unknown_unkno_7$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00023.5CONT_unknown_unkno_19$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00021CONT_unknown_unkno_22$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00004.6CONT_unknown_unkno_29$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00025.3CONT_unknown_unkno_46$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00059.1CONT_unknown_unkno_29$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00010.1CONT_unknown_unkno_34$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00045CONT_unknown_unkno_35$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00023.4CONT_unknown_unkno_2$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00005CONT_unknown_unkno_2$.1" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00002CONT_unknown_unkno_9$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00022CONT_unknown_unkno_3$.4" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00035.2CONT_unknown_unkno_29$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00064.1CONT_unknown_unkno_45$.1" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00001.1CONT_unknown_unkno_57$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00010.1CONT_unknown_unkno_53$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00006.3CONT_unknown_unkno_" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00069CONT_unknown_unkno_14$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00040CONT_unknown_unkno_21$.4" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00004.1CONT_unknown_unkno_36$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00033.2CONT_unknown_unkno_17$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00045CONT_unknown_unkno_36$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00029.1CONT_unknown_unkno_3$.4" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00027CONT_unknown_unkno_33$.1" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00019CONT_unknown_unkno_59$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00038CONT_unknown_unkno_19$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00024.3CONT_unknown_unkno_60$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00017CONT_unknown_unkno_35$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00001.1CONT_unknown_unkno_50$.1" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00065CONT_unknown_unkno_3$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00044CONT_unknown_unkno_18$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00025.3CONT_unknown_unkno_38$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00061.2CONT_unknown_unkno_16$.1" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00017CONT_unknown_unkno_36$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00062CONT_unknown_unkno_45$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00020CONT_unknown_unkno_60$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00016.1CONT_unknown_unkno_33$.3" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00039.2CONT_unknown_unkno_3$.5" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00033.1CONT_unknown_unkno_43$.1" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00025.1CONT_unknown_unkno_24$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00006.1CONT_unknown_unkno_1$.1" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00050.3CONT_unknown_unkno_60$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00048CONT_unknown_unkno_22$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00007CONT_unknown_unkno_63$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00024.1CONT_unknown_unkno_25$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00025.1CONT_unknown_unkno_35$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00004.7CONT_unknown_unkno_21$.4" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00066.1CONT_unknown_unkno_40$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00020CONT_unknown_unkno_59$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00064.2CONT_unknown_unkno_45$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00050.3CONT_unknown_unkno_21$.5" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00032.3CONT_unknown_unkno_44$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00053CONT_unknown_unkno_7$.1" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00008CONT_unknown_unkno_8$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00068CONT_unknown_unkno_47$.3" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00030CONT_unknown_unkno_28$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00049CONT_unknown_unkno_3$.4" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00006.1CONT_unknown_unkno_7$.3" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00061.1CONT_unknown_unkno_21$.3" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00050.1CONT_unknown_unkno_21$.4" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00042CONT_unknown_unkno_7$.1" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00047CONT_unknown_unkno_36$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00021CONT_unknown_unkno_14$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00009CONT_unknown_unkno_33$.1" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00013CONT_unknown_unkno_3$.1" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00024.3CONT_unknown_unkno_59$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00056CONT_unknown_unkno_44$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00034CONT_unknown_unkno_43$.1" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00003.1CONT_unknown_unkno_7$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00005CONT_unknown_unkno_2$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00004.3CONT_unknown_unkno_21$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00056CONT_unknown_unkno_59$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00029.3CONT_unknown_unkno_3$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00077CONT_unknown_unkno_60$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00008CONT_unknown_unkno_35$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00015CONT_unknown_unkno_5$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00010.1CONT_unknown_unkno_6$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00066.3CONT_unknown_unkno_35$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00006.3CONT_unknown_unkno_36$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00052CONT_unknown_unkno_3$.1" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00023.2CONT_unknown_unkno_2$.3" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00020CONT_unknown_unkno_34$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00002CONT_unknown_unkno_37$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00026.3CONT_unknown_unkno_52$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00070CONT_unknown_unkno_47$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00027CONT_unknown_unkno_59$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00027CONT_unknown_unkno_20$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00025.1CONT_unknown_unkno_51$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00025.1CONT_unknown_unkno_36$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00018CONT_unknown_unkno_3$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00017CONT_unknown_unkno_18$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00039.1CONT_unknown_unkno_14$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00045CONT_unknown_unkno_37$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00019CONT_unknown_unkno_42$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00047CONT_unknown_unkno_35$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00073CONT_unknown_unkno_40$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00047CONT_unknown_unkno_14$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00027CONT_unknown_unkno_62$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00054CONT_unknown_unkno_3$.4" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00057CONT_unknown_unkno_44$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00004.1CONT_unknown_unkno_58$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00066.3CONT_unknown_unkno_40$.1" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00076CONT_unknown_unkno_60$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00011.1CONT_unknown_unkno_12$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00043CONT_unknown_unkno_16$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00023.3CONT_unknown_unkno_43$.1" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00001.3CONT_unknown_unkno_29$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00079CONT_unknown_unkno_29$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00006.2CONT_unknown_unkno_29$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00016.3CONT_unknown_unkno_33$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00025.2CONT_unknown_unkno_29$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00002CONT_unknown_unkno_27$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00006.3CONT_unknown_unkno_35$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00016.4CONT_unknown_unkno_22$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00019CONT_unknown_unkno_60$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00013CONT_unknown_unkno_60$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00051CONT_unknown_unkno_22$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00058.2CONT_unknown_unkno_23$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00026.1CONT_unknown_unkno_47$.3" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00004.2CONT_unknown_unkno_29$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00012CONT_unknown_unkno_15$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00066.2CONT_unknown_unkno_32$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00018CONT_unknown_unkno_3$.1" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00026.2CONT_unknown_unkno_47$.1" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00032.2CONT_unknown_unkno_63$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00032.1CONT_unknown_unkno_44$.1" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00033.2CONT_unknown_unkno_36$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00072CONT_unknown_unkno_40$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00060.1CONT_unknown_unkno_3$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00010.1CONT_unknown_unkno_41$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00023.1CONT_unknown_unkno_31$.1" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00041CONT_unknown_unkno_3$.1" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00059.2CONT_unknown_unkno_3$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00062CONT_unknown_unkno_11$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00067CONT_unknown_unkno_59$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00070CONT_unknown_unkno_47$.3" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00060.2CONT_unknown_unkno_19$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00078CONT_unknown_unkno_61$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00063CONT_unknown_unkno_8$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00035.1CONT_unknown_unkno_19$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00014CONT_unknown_unkno_8$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00003.2CONT_unknown_unkno_29$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00066.3CONT_unknown_unkno_36$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00081CONT_unknown_unkno_29$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00001.1CONT_unknown_unkno_31$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00037CONT_unknown_unkno_13$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00074CONT_unknown_unkno_45$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00035.1CONT_unknown_unkno_30$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00008CONT_unknown_unkno_4$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00009CONT_unknown_unkno_33$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00004.5CONT_unknown_unkno_21$.3" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00036CONT_unknown_unkno_3$.1" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00046.2CONT_unknown_unkno_21$.4" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00014CONT_unknown_unkno_27$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00007CONT_unknown_unkno_12$.1" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00035.1CONT_unknown_unkno_54$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00006.3CONT_unknown_unkno_1$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00029.3CONT_unknown_unkno_3$.3" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00003.3CONT_unknown_unkno_7$.1" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00055.2CONT_unknown_unkno_12$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00011.2CONT_unknown_unkno_30$.1" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00075CONT_unknown_unkno_45$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00027CONT_unknown_unkno_60$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00050.3CONT_unknown_unkno_59$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00010.1CONT_unknown_unkno_31$.1" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00028CONT_unknown_unkno_2$.1" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00035.3CONT_unknown_unkno_30$.1" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00010.2CONT_unknown_unkno_16$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00004.1CONT_unknown_unkno_21$.1" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00020CONT_unknown_unkno_26$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00026.2CONT_unknown_unkno_47$.3" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00067CONT_unknown_unkno_61$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00067CONT_unknown_unkno_60$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00043CONT_unknown_unkno_16$.1" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00015CONT_unknown_unkno_5$.1" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00022CONT_unknown_unkno_3$.5" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00024.3CONT_unknown_unkno_25$.1" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00004.1CONT_unknown_unkno_49$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00050.2CONT_unknown_unkno_29$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00008CONT_unknown_unkno_36$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00001.3CONT_unknown_unkno_50$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00066.2CONT_unknown_unkno_39$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00026.3CONT_unknown_unkno_47$.1" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00011.2CONT_unknown_unkno_55$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00046.1CONT_unknown_unkno_5$.1" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00024.2CONT_unknown_unkno_29$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00013CONT_unknown_unkno_59$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00023.1CONT_unknown_unkno_31$.2" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00025.3CONT_unknown_unkno_51$.1" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00056CONT_unknown_unkno_60$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

Argument "contig00033.2CONT_unknown_unkno_35$" isn't numeric in sort at /home/bioinfo/programs/amos/bin/sort2 line 84, <> line 193.

DONE

Loading overlaps to AMOS BANK...DONE

Making hybrid contigs layout...DONE

Calling hybrid contigs consensus...Retrieving hybrid contigs from AMOS BANK...Failed to open contig account in bank out.ALL.bnk:

WHAT: Could not open bank for reading, locked by 'w 1000 bioinfo'

LINE: 1164

FILE: Bank_AMOS.cc

DONE

Retrieving singlets from AMOS BANK...DONE

===> TRIM REPETITIVE CONTIG ENDS (up to 100 bp)  COVERED BY ONLY 1 ASSEMBLY

Running bowtie-build (out.hybrid.fasta,out.reads.22mers.cutoff42)...Running bowtie (out.hybrid.fasta,out.reads.22mers.cutoff42)...DONE

Merging neighbouring masked regions for out.hybrid.fasta...DONE

Retrieving consensus positions covered by a single source assembly...DONE

Retrieving repetitive consensus positions and marking positions to be trimmed...DONE

Trimming repetitive contig ends covered by only one source assembly...DONE

===> FORCING SINGLETS ASSEMBLY

Loading sequences into a new AMOS BANK...DONE

Mapping old contig ids to new AMOS BANK ids...DONE

Finding rep overlaps...Starting on Wed Jan 30 18:38:43 2013

Read bank is out.REPASSEMBLY.bnk

Alignment error rate is 0.06

Minimum overlap bases is 40

** AMOS Exception **

WHAT: Could not open bank file, out.REPASSEMBLY.bnk/RED.ifo, No such file or directory

LINE: 1264

FILE: Bank_AMOS.cc

DONE

Layout... AMOS Read Bank out.REPASSEMBLY.bnk does not exist

 AMOS Overlap Bank out.REPASSEMBLY.bnk does not exist

DONE

Calling rep contigs consensus...Starting on Wed Jan 30 18:38:43 2013

Read bank is out.REPASSEMBLY.bnk

Alignment error rate is 0.06

Minimum overlap bases is 5

Output will be written to the bank

Input is being read from the bank

** AMOS Exception **

WHAT: Could not open bank file, out.REPASSEMBLY.bnk/RED.ifo, No such file or directory

LINE: 1264

FILE: Bank_AMOS.cc

Retrieving hybrid contigs from AMOS BANK...Failed to open contig account in bank out.REPASSEMBLY.bnk:

WHAT: Could not open bank for reading, locked by 'w 1000 bioinfo'

LINE: 1164

FILE: Bank_AMOS.cc

DONE

Retrieving singlets from AMOS BANK...DONE

===> FINISHING ZORRO ASSEMBLY

Renaming final contigs...DONE

DONE

bioinfo@nemo:/data/bioinfo/06431/zorro$