================================================================
Program: CD-HIT, V4.8.1 (+OpenMP), Apr 07 2021, 10:57:21
Command: cd-hit-est -i
/share/home/bmk530/bdz/seqkit/vircontig_merge.fa -o
/share/home/bmk530/bdz/cdhit/out/virunique.fa -c 0.95
-aS 0.85 -d 0 -T 20 -M 10000 -n 10
Started: Mon Feb 20 14:51:22 2023
================================================================
Output
----------------------------------------------------------------
total seq: 13313
longest and shortest : 258320 and 500
Total letters: 49590002
Sequences have been sorted
Approximated minimal memory consumption:
Sequence : 51M
Buffer : 20 X 67M = 1344M
Table : 2 X 16M = 33M
Miscellaneous : 4M
Total : 1434M
Table limit with the given memory limit:
Max number of representatives: 40000
Max number of word counting entries: 1070730103
# comparing sequences from 0 to 5000
....---------- new table with 2919 representatives
# comparing sequences from 5000 to 5377
100.0%---------- new table with 179 representatives
# comparing sequences from 5377 to 5737
---------- 125 remaining sequences to the next cycle
---------- new table with 138 representatives
# comparing sequences from 5612 to 5962
---------- 181 remaining sequences to the next cycle
---------- new table with 100 representatives
# comparing sequences from 5781 to 6123
---------- 169 remaining sequences to the next cycle
---------- new table with 103 representatives
# comparing sequences from 5954 to 6288
---------- 137 remaining sequences to the next cycle
---------- new table with 100 representatives
# comparing sequences from 6151 to 6476
---------- 117 remaining sequences to the next cycle
---------- new table with 109 representatives
# comparing sequences from 6359 to 6675
---------- 124 remaining sequences to the next cycle
---------- new table with 100 representatives
# comparing sequences from 6551 to 6858
---------- 110 remaining sequences to the next cycle
---------- new table with 114 representatives
# comparing sequences from 6748 to 7046
---------- 141 remaining sequences to the next cycle
---------- new table with 100 representatives
# comparing sequences from 6905 to 7196
---------- 124 remaining sequences to the next cycle
---------- new table with 100 representatives
# comparing sequences from 7072 to 7355
---------- 109 remaining sequences to the next cycle
---------- new table with 100 representatives
# comparing sequences from 7246 to 7521
---------- 107 remaining sequences to the next cycle
---------- new table with 102 representatives
# comparing sequences from 7414 to 7682
---------- 84 remaining sequences to the next cycle
---------- new table with 100 representatives
# comparing sequences from 7598 to 7857
---------- 101 remaining sequences to the next cycle
---------- new table with 100 representatives
# comparing sequences from 7756 to 8008
---------- 93 remaining sequences to the next cycle
---------- new table with 100 representatives
# comparing sequences from 7915 to 8160
---------- 75 remaining sequences to the next cycle
---------- new table with 100 representatives
# comparing sequences from 8085 to 8322
---------- 89 remaining sequences to the next cycle
---------- new table with 100 representatives
# comparing sequences from 8233 to 8463
---------- 75 remaining sequences to the next cycle
---------- new table with 100 representatives
# comparing sequences from 8388 to 8611
---------- 68 remaining sequences to the next cycle
---------- new table with 100 representatives
# comparing sequences from 8543 to 8759
---------- 23 remaining sequences to the next cycle
---------- new table with 100 representatives
# comparing sequences from 8736 to 8944
---------- 57 remaining sequences to the next cycle
---------- new table with 100 representatives
# comparing sequences from 8887 to 9088
---------- 52 remaining sequences to the next cycle
---------- new table with 100 representatives
# comparing sequences from 9036 to 9230
---------- 5 remaining sequences to the next cycle
---------- new table with 100 representatives
# comparing sequences from 9225 to 9410
---------- 26 remaining sequences to the next cycle
---------- new table with 100 representatives
# comparing sequences from 9384 to 9562
---------- 13 remaining sequences to the next cycle
---------- new table with 100 representatives
# comparing sequences from 9549 to 9720
---------- 9 remaining sequences to the next cycle
---------- new table with 100 representatives
# comparing sequences from 9711 to 9874
................---------- new table with 97 representatives
# comparing sequences from 9874 to 10030
........---------- new table with 95 representatives
# comparing sequences from 10030 to 10179
..........---------- new table with 89 representatives
# comparing sequences from 10179 to 10321
.............---------- new table with 75 representatives
# comparing sequences from 10321 to 10457
............---------- new table with 84 representatives
# comparing sequences from 10457 to 10586
.............---------- new table with 79 representatives
# comparing sequences from 10586 to 10709
..........---------- new table with 70 representatives
# comparing sequences from 10709 to 10827
.............---------- new table with 71 representatives
# comparing sequences from 10827 to 10940
.............---------- new table with 69 representatives
# comparing sequences from 10940 to 11047
............---------- new table with 56 representatives
# comparing sequences from 11047 to 11150
..........---------- new table with 59 representatives
# comparing sequences from 11150 to 11248
............---------- new table with 60 representatives
# comparing sequences from 11248 to 11341
............---------- new table with 57 representatives
# comparing sequences from 11341 to 11430
........---------- new table with 46 representatives
# comparing sequences from 11430 to 11515
...............---------- new table with 55 representatives
# comparing sequences from 11515 to 11596
.............---------- new table with 55 representatives
# comparing sequences from 11596 to 11674
............---------- new table with 52 representatives
# comparing sequences from 11674 to 11748
...........---------- new table with 39 representatives
# comparing sequences from 11748 to 11819
.............---------- new table with 45 representatives
# comparing sequences from 11819 to 11886
...........---------- new table with 42 representatives
# comparing sequences from 11886 to 11950
.............---------- new table with 43 representatives
# comparing sequences from 11950 to 12011
........---------- new table with 33 representatives
# comparing sequences from 12011 to 12070
............---------- new table with 33 representatives
# comparing sequences from 12070 to 12126
.........---------- new table with 33 representatives
# comparing sequences from 12126 to 12179
...............---------- new table with 38 representatives
# comparing sequences from 12179 to 12230
.............---------- new table with 37 representatives
# comparing sequences from 12230 to 12279
...........---------- new table with 42 representatives
# comparing sequences from 12279 to 12326
.............---------- new table with 39 representatives
# comparing sequences from 12326 to 13313
.....................
Fatal Error:
file opening failed
Program halted !!
---------- new table with 960 representatives 报错内容显示文件打开失败
可以发现cd-hit-est是能够运行的，但是在输出的时候出现了问题
发现是因为输出路径中没有对应的文件夹，因此更改路径
cd-hit-est -i ~/bdz/seqkit/vircontig_merge.fa \
-o ~/bdz/cdhit/virunique \
-c 0.95 \
-aS 0.85 \
-d 0 \
-T 15 \
-M 10000 \
-n 10 \
; \
touch cdhit.sh.done
8513
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