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[MUMmer-help] mapview fails to generate output
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From: John F W. <jwo...@bi...> - 2014-05-22 16:17:11
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Hello,
I've been using mapview to generate files to visualize the alignments in
the following manner:
mapview -n 1 -f pdf filename.coords
However, in several recent instances, mapview produces no messages, and
produces no output files.
Nothing appears in response to running the command at all.
Any help would be greatly appreciated.
Here is an example of a coords file used that causes this problem:
/import/linux/home/jwolter1/Strains/C2/Assembly/Mira_PcBio_CCS/Quiver/Joining_unitigs/C2_joined.fasta
/import/linux/home/jwolter1/Strains/C2/Assembly/Mira_PcBio_CCS/Quiver/Joining_unitigs/C2.polished_assembly.fasta
NUCMER
[S1] [E1] | [S2] [E2] | [LEN 1] [LEN 2] | [% IDY] |
[LEN R] [LEN Q] | [COV R] [COV Q] | [TAGS]
===============================================================================================================================
1 17884 | 17910 1 | 17884 17910 | 99.83 |
76481 70521 | 23.38 25.40 | S.cerevisiae unitig_1|quiver
8075 10672 | 1 2600 | 2598 2600 | 99.69 |
76481 5150 | 3.40 50.49 | S.cerevisiae unitig_3|quiver
8131 10669 | 5150 2609 | 2539 2542 | 99.45 |
76481 5150 | 3.32 49.36 | S.cerevisiae unitig_3|quiver
8935 9164 | 6863 7101 | 230 239 | 84.43 |
76481 15910 | 0.30 1.50 | S.cerevisiae unitig_0|quiver
9012 9509 | 42308 42800 | 498 493 | 82.58 |
76481 70521 | 0.65 0.70 | S.cerevisiae unitig_1|quiver
9016 9436 | 8918 9335 | 421 418 | 85.25 |
76481 15910 | 0.55 2.63 | S.cerevisiae unitig_0|quiver
14381 25322 | 13325 2386 | 10942 10940 | 99.60 |
76481 15910 | 14.31 68.76 | S.cerevisiae unitig_0|quiver
14442 16994 | 13365 15910 | 2553 2546 | 98.87 |
76481 15910 | 3.34 16.00 | S.cerevisiae unitig_0|quiver
18185 18722 | 48779 49345 | 538 567 | 83.42 |
76481 70521 | 0.70 0.80 | S.cerevisiae unitig_1|quiver
18371 18787 | 8469 8886 | 417 418 | 85.19 |
76481 70521 | 0.55 0.59 | S.cerevisiae unitig_1|quiver
18371 18787 | 1361 944 | 417 418 | 85.19 |
76481 5150 | 0.55 8.12 | S.cerevisiae unitig_3|quiver
18371 18787 | 3847 4264 | 417 418 | 85.19 |
76481 5150 | 0.55 8.12 | S.cerevisiae unitig_3|quiver
20602 20836 | 8738 8960 | 235 223 | 84.45 |
76481 70521 | 0.31 0.32 | S.cerevisiae unitig_1|quiver
20602 20836 | 1092 870 | 235 223 | 84.45 |
76481 5150 | 0.31 4.33 | S.cerevisiae unitig_3|quiver
20602 20836 | 4116 4338 | 235 223 | 84.45 |
76481 5150 | 0.31 4.33 | S.cerevisiae unitig_3|quiver
20603 20836 | 49255 49485 | 234 231 | 84.03 |
76481 70521 | 0.31 0.33 | S.cerevisiae unitig_1|quiver
22865 25314 | 1 2451 | 2450 2451 | 99.96 |
76481 15910 | 3.20 15.41 | S.cerevisiae unitig_0|quiver
23744 27089 | 1 3351 | 3346 3351 | 99.85 |
76481 3351 | 4.37 100.00 | S.cerevisiae unitig_2|quiver
25448 71629 | 68349 22100 | 46182 46250 | 99.77 |
76481 70521 | 60.38 65.58 | S.cerevisiae unitig_1|quiver
25524 27721 | 68323 70521 | 2198 2199 | 98.55 |
76481 70521 | 2.87 3.12 | S.cerevisiae unitig_1|quiver
44253 44984 | 8814 9521 | 732 708 | 82.75 |
76481 15910 | 0.96 4.45 | S.cerevisiae unitig_0|quiver
50957 51450 | 8392 8890 | 494 499 | 82.78 |
76481 70521 | 0.65 0.71 | S.cerevisiae unitig_1|quiver
50957 51450 | 1438 940 | 494 499 | 82.78 |
76481 5150 | 0.65 9.69 | S.cerevisiae unitig_3|quiver
50957 51450 | 3770 4268 | 494 499 | 82.78 |
76481 5150 | 0.65 9.69 | S.cerevisiae unitig_3|quiver
70145 72606 | 1 2466 | 2462 2466 | 99.68 |
76481 4897 | 3.22 50.36 | S.cerevisiae unitig_6|quiver
70155 72611 | 4897 2440 | 2457 2458 | 99.55 |
76481 4897 | 3.21 50.19 | S.cerevisiae unitig_6|quiver
73234 76481 | 21163 17910 | 3248 3254 | 98.22 |
76481 70521 | 4.25 4.61 | S.cerevisiae unitig_1|quiver
73293 75543 | 3908 1658 | 2251 2251 | 99.60 |
76481 3908 | 2.94 57.60 | S.cerevisiae unitig_4|quiver
73355 75773 | 4813 2399 | 2419 2415 | 99.50 |
76481 4813 | 3.16 50.18 | S.cerevisiae unitig_5|quiver
73358 75773 | 1 2414 | 2416 2414 | 99.55 |
76481 4813 | 3.16 50.16 | S.cerevisiae unitig_5|quiver
73850 75526 | 1 1683 | 1677 1683 | 98.40 |
76481 3908 | 2.19 43.07 | S.cerevisiae unitig_4|quiver
74500 74961 | 20981 21367 | 462 387 | 81.90 |
76481 70521 | 0.60 0.55 | S.cerevisiae unitig_1|quiver
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