User Tools

Site Tools


benchshortreadmappingprogramsaug2008

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
benchshortreadmappingprogramsaug2008 [2008/08/21 14:01]
gouzy
benchshortreadmappingprogramsaug2008 [2008/08/21 14:02] (current)
gouzy
Line 40: Line 40:
 ^ Features ​     ^  rmap   ​^ ​         soap              ^         ​maq ​                 ^   ​qpalma ​  ​^ ​    ​genomethreader ​   ^   ​blastn-toolkit + db indexing ​ ^   ​crossmatch.manyreads ​  ​^ ​  ​mummer ​   ^   ​gmap ​ ^  glint  ^ ^ Features ​     ^  rmap   ​^ ​         soap              ^         ​maq ​                 ^   ​qpalma ​  ​^ ​    ​genomethreader ​   ^   ​blastn-toolkit + db indexing ​ ^   ​crossmatch.manyreads ​  ​^ ​  ​mummer ​   ^   ​gmap ​ ^  glint  ^
 | compilation (pkg default) ​  ​| ​ O3   ​| ​  ​03 ​  ​| ​ O2   ​| ​  not yet available |   ​bin ​ |   ​O2 ​ |  O2   ​| ​  ​O3 ​  ​| ​  ​O2 ​ |   ​O3 ​ | | compilation (pkg default) ​  ​| ​ O3   ​| ​  ​03 ​  ​| ​ O2   ​| ​  not yet available |   ​bin ​ |   ​O2 ​ |  O2   ​| ​  ​O3 ​  ​| ​  ​O2 ​ |   ​O3 ​ |
-| program opt.  |  -v -h 16 -w 36 -m 3   ​| ​  -s 12 -r 2 -w 9999 -v 3   ​| ​ -n 3 -C 100000000 -H allhits ​  ​| ​  / ​ |  -seedlength 16 -minmatchlen 33   ​| ​  ​-num_descriptions 10000000 -num_alignments 10000000 ​  ​-use_index true -outfmt 6 -word_size 16 -index_name MtrV2Chr5.idx -perc_identity 91.66 -evalue 3e-7    |   ​-minmatch 20    |    (1) -l 33 -F -b -maxmatch (2) -F -l 20 -b -maxmatch ​   |    -B 2  -f 3  |   (1) -m 8 -w 1 -d 1 -c 15 -X 24 -s 24 -M default (2)  -m 8 -c 15 -X 24 -s 24 --no_dyn -M 111012110110211101 (3)  -m 8 -c 15 -X 24 -s 24 --no_dyn --step 2  -M 111012110110211101 |+| program opt.  |  -v -h 16 -w 36 -m 3   ​| ​  -s 12 -r 2 -w 9999 -v 3   ​| ​ -n 3 -C 100000000 -H allhits ​  ​| ​  / ​ |  -seedlength 16 -minmatchlen 33   ​| ​  ​-num_descriptions 10000000 -num_alignments 10000000 ​  ​-use_index true -outfmt 6 -word_size 16 -index_name MtrV2Chr5.idx -perc_identity 91.66 -evalue 3e-7    |   ​-minmatch 20    |    (1) -l 33 -F -b -maxmatch (2) -F -l 20 -b -maxmatch ​   |    -B 2  -f 3  |   (1) -m 8 -w 1 -d 1 -c 15 -X 24 -s 24 -M default (2)  -m 8 -c 15 -X 24 -s 24 --no_dyn -M 111012110110211101 (3)  -m 8 -c 15 -X 24 -s 24 --no_dyn --step 2  -M 111012110110211101 ​ |
 | user time (s)  |   ​219 ​  ​| ​  ​250 ​ |  448   ​| ​  ​NA ​  ​| ​ I killed the process at 94,320s => split the cdna database is required ​ |   ​11207 ​ |   FATAL ERROR: MAX_NUM_BLOCKS exceeded ​ ==> split the transcript db required ​ |   (1) 159 (2) 2752  |  days (in progress) ​ |   (1) 4772 (2)256 ​ (3) 175  | | user time (s)  |   ​219 ​  ​| ​  ​250 ​ |  448   ​| ​  ​NA ​  ​| ​ I killed the process at 94,320s => split the cdna database is required ​ |   ​11207 ​ |   FATAL ERROR: MAX_NUM_BLOCKS exceeded ​ ==> split the transcript db required ​ |   (1) 159 (2) 2752  |  days (in progress) ​ |   (1) 4772 (2)256 ​ (3) 175  |
 | # of hits     ​| ​ 271219 + a list of ambiguous ​  ​| ​  ​13,​459,​540 ​ |   ​1,​086,​881 unique + X non unique (core dump reading allhits file )  |   ​NA ​ |  NA  |  13,​781,​653 ​  ​| ​  ​NA ​  ​| ​  (1) 14,​391,​016 ​ (2) 2,​354,​863,​462 ​ (yes 2Ghits) ​ |    |  (1) 14,178,398 (2) 14,109,622 (3)  14,​064,​111 ​ | | # of hits     ​| ​ 271219 + a list of ambiguous ​  ​| ​  ​13,​459,​540 ​ |   ​1,​086,​881 unique + X non unique (core dump reading allhits file )  |   ​NA ​ |  NA  |  13,​781,​653 ​  ​| ​  ​NA ​  ​| ​  (1) 14,​391,​016 ​ (2) 2,​354,​863,​462 ​ (yes 2Ghits) ​ |    |  (1) 14,178,398 (2) 14,109,622 (3)  14,​064,​111 ​ |
benchshortreadmappingprogramsaug2008.txt ยท Last modified: 2008/08/21 14:02 by gouzy