I am running bowtie2-build ref.fna ref --threads 12 --large-index with no error message.
However, the command generates only temporary output files and no .rev files.
Log:
Settings:
Output files: "ref.*.bt2l"
Line rate: 7 (line is 128 bytes)
Lines per side: 1 (side is 128 bytes)
Offset rate: 4 (one in 16)
FTable chars: 10
Strings: unpacked
Max bucket size: default
Max bucket size, sqrt multiplier: default
Max bucket size, len divisor: 48
Difference-cover sample period: 1024
Endianness: little
Actual local endianness: little
Sanity checking: disabled
Assertions: disabled
Random seed: 0
Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
GMGC10plus.95nr.complete.fna
Building a LARGE index
Reading reference sizes
Time reading reference sizes: 00:15:22
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:14:33
bmax according to bmaxDivN setting: 2018841507
Using parameters --bmax 1514131131 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 1514131131 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
Building sPrime
Building sPrimeOrder
V-Sorting samples
V-Sorting samples time: 00:29:04
Allocating rank array
Ranking v-sort output
Ranking v-sort output time: 00:20:19
Invoking Larsson-Sadakane on ranks
Invoking Larsson-Sadakane on ranks time: 00:38:44
Sanity-checking and returning
Building samples
Reserving space for 130 sample suffixes
Generating random suffixes
QSorting 130 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 130 samples
(Using difference cover)
Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Splitting and merging
Splitting and merging time: 00:00:00
Split 15, merged 60; iterating...
Splitting and merging
Splitting and merging time: 00:00:00
Split 9, merged 8; iterating...
Splitting and merging
Splitting and merging time: 00:00:00
Split 6, merged 6; iterating...
Splitting and merging
Splitting and merging time: 00:00:00
Split 3, merged 5; iterating...
Splitting and merging
Splitting and merging time: 00:00:00
Split 1, merged 3; iterating...
Avg bucket size: 1.16752e+09 (target: 1514131130)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 6 of 83
Getting block 2 of 83
Getting block 1 of 83
Getting block 3 of 83
Getting block 4 of 83
Getting block 5 of 83
Reserving size (1514131131) for bucket 6
Getting block 7 of 83
Reserving size (1514131131) for bucket 2
Getting block 8 of 83
Reserving size (1514131131) for bucket 1
Getting block 9 of 83
Getting block 10 of 83
Reserving size (1514131131) for bucket 3
Reserving size (1514131131) for bucket 4
Getting block 11 of 83
Reserving size (1514131131) for bucket 5
Reserving size (1514131131) for bucket 7
Calculating Z arrays for bucket 6
Calculating Z arrays for bucket 2
Reserving size (1514131131) for bucket 8
Reserving size (1514131131) for bucket 9
Calculating Z arrays for bucket 1
Reserving size (1514131131) for bucket 10
Calculating Z arrays for bucket 3
Calculating Z arrays for bucket 4
Reserving size (1514131131) for bucket 11
Entering block accumulator loop for bucket 6:
Calculating Z arrays for bucket 5
Entering block accumulator loop for bucket 2:
Entering block accumulator loop for bucket 1:
Calculating Z arrays for bucket 9
Entering block accumulator loop for bucket 3:
Entering block accumulator loop for bucket 4:
Calculating Z arrays for bucket 10
Entering block accumulator loop for bucket 5:
Entering block accumulator loop for bucket 9:
Calculating Z arrays for bucket 7
Entering block accumulator loop for bucket 10:
Calculating Z arrays for bucket 8
Entering block accumulator loop for bucket 7:
Calculating Z arrays for bucket 11
Entering block accumulator loop for bucket 8:
Entering block accumulator loop for bucket 11:
bucket 1: 10%
bucket 2: 10%
bucket 3: 10%
bucket 4: 10%
bucket 7: 10%
bucket 5: 10%
bucket 6: 10%
bucket 9: 10%
bucket 8: 10%
bucket 11: 10%
bucket 10: 10%
bucket 1: 20%
bucket 2: 20%
bucket 3: 20%
bucket 4: 20%
bucket 7: 20%
bucket 5: 20%
bucket 6: 20%
bucket 8: 20%
bucket 9: 20%
bucket 11: 20%
bucket 10: 20%
bucket 1: 30%
bucket 2: 30%
bucket 3: 30%
bucket 4: 30%
bucket 7: 30%
bucket 5: 30%
bucket 6: 30%
bucket 9: 30%
bucket 8: 30%
bucket 11: 30%
bucket 10: 30%
bucket 1: 40%
bucket 2: 40%
bucket 3: 40%
bucket 4: 40%
bucket 7: 40%
bucket 5: 40%
bucket 6: 40%
bucket 9: 40%
bucket 8: 40%
bucket 11: 40%
bucket 10: 40%
bucket 1: 50%
bucket 2: 50%
bucket 3: 50%
bucket 4: 50%
bucket 7: 50%
bucket 5: 50%
bucket 6: 50%
bucket 9: 50%
bucket 8: 50%
bucket 1: 60%
bucket 11: 50%
bucket 10: 50%
bucket 2: 60%
bucket 3: 60%
bucket 4: 60%
bucket 7: 60%
bucket 5: 60%
bucket 6: 60%
bucket 1: 70%
bucket 2: 70%
bucket 9: 60%
bucket 8: 60%
bucket 11: 60%
bucket 10: 60%
bucket 3: 70%
bucket 4: 70%
bucket 7: 70%
bucket 5: 70%
bucket 6: 70%
bucket 1: 80%
bucket 2: 80%
bucket 9: 70%
bucket 8: 70%
bucket 3: 80%
bucket 11: 70%
bucket 10: 70%
bucket 4: 80%
bucket 7: 80%
bucket 5: 80%
bucket 6: 80%
bucket 1: 90%
bucket 2: 90%
bucket 3: 90%
bucket 9: 80%
bucket 8: 80%
bucket 4: 90%
bucket 11: 80%
bucket 10: 80%
bucket 7: 90%
bucket 5: 90%
bucket 1: 100%
Sorting block of length 1273829730 for bucket 1
(Using difference cover)
bucket 6: 90%
bucket 2: 100%
Sorting block of length 402948001 for bucket 2
(Using difference cover)
bucket 3: 100%
Sorting block of length 1163378895 for bucket 3
(Using difference cover)
bucket 4: 100%
Sorting block of length 977908011 for bucket 4
(Using difference cover)
bucket 9: 90%
bucket 8: 90%
bucket 11: 90%
bucket 10: 90%
bucket 7: 100%
Sorting block of length 631238688 for bucket 7
(Using difference cover)
bucket 5: 100%
Sorting block of length 1146946496 for bucket 5
(Using difference cover)
bucket 6: 100%
Sorting block of length 1492383034 for bucket 6
(Using difference cover)
bucket 8: 100%
Sorting block of length 1502918586 for bucket 8
(Using difference cover)
bucket 9: 100%
Sorting block of length 1472371616 for bucket 9
(Using difference cover)
bucket 11: 100%
Sorting block of length 839304407 for bucket 11
(Using difference cover)
bucket 10: 100%
Sorting block of length 1380511705 for bucket 10
(Using difference cover)
Sorting block time: 00:10:49
Returning block of 402948002 for bucket 2
Getting block 12 of 83
Reserving size (1514131131) for bucket 12
Calculating Z arrays for bucket 12
Entering block accumulator loop for bucket 12:
bucket 12: 10%
bucket 12: 20%
Sorting block time: 00:16:39
Returning block of 631238689 for bucket 7
bucket 12: 30%
Getting block 13 of 83
Reserving size (1514131131) for bucket 13
Calculating Z arrays for bucket 13
Entering block accumulator loop for bucket 13:
bucket 12: 40%
bucket 13: 10%
bucket 12: 50%
bucket 13: 20%
bucket 12: 60%
bucket 13: 30%
Sorting block time: 00:23:19
Returning block of 839304408 for bucket 11
Getting block 14 of 83
Reserving size (1514131131) for bucket 14
Calculating Z arrays for bucket 14
Entering block accumulator loop for bucket 14:
Sorting block time: 00:27:15
Returning block of 977908012 for bucket 4
bucket 12: 70%
bucket 13: 40%
Getting block 15 of 83
Reserving size (1514131131) for bucket 15
Calculating Z arrays for bucket 15
Entering block accumulator loop for bucket 15:
bucket 14: 10%
bucket 12: 80%
bucket 13: 50%
bucket 15: 10%
Sorting block time: 00:31:58
Returning block of 1163378896 for bucket 3
bucket 14: 20%
bucket 12: 90%
Getting block 16 of 83
Reserving size (1514131131) for bucket 16
Calculating Z arrays for bucket 16
Entering block accumulator loop for bucket 16:
bucket 13: 60%
Sorting block time: 00:32:21
Returning block of 1146946497 for bucket 5
bucket 15: 20%
Sorting block time: 00:35:00
Returning block of 1273829731 for bucket 1
Getting block 17 of 83
Reserving size (1514131131) for bucket 17
Calculating Z arrays for bucket 17
Entering block accumulator loop for bucket 17:
bucket 14: 30%
Getting block 18 of 83
Reserving size (1514131131) for bucket 18
Calculating Z arrays for bucket 18
Entering block accumulator loop for bucket 18:
bucket 12: 100%
Sorting block of length 1399740852 for bucket 12
(Using difference cover)
bucket 16: 10%
bucket 13: 70%
bucket 15: 30%
bucket 17: 10%
bucket 14: 40%
bucket 18: 10%
bucket 16: 20%
bucket 13: 80%
bucket 15: 40%
bucket 17: 20%
bucket 14: 50%
bucket 18: 20%
bucket 13: 90%
bucket 16: 30%
bucket 15: 50%
bucket 17: 30%
bucket 14: 60%
bucket 18: 30%
bucket 13: 100%
Sorting block of length 1110904756 for bucket 13
(Using difference cover)
bucket 16: 40%
bucket 15: 60%
bucket 17: 40%
bucket 14: 70%
Sorting block time: 00:44:21
Returning block of 1492383035 for bucket 6
bucket 18: 40%
Sorting block time: 00:43:22
Returning block of 1380511706 for bucket 10
bucket 16: 50%
Getting block 19 of 83
Reserving size (1514131131) for bucket 19
Calculating Z arrays for bucket 19
Entering block accumulator loop for bucket 19:
bucket 15: 70%
bucket 17: 50%
Getting block 20 of 83
Reserving size (1514131131) for bucket 20
Calculating Z arrays for bucket 20
Entering block accumulator loop for bucket 20:
bucket 14: 80%
Sorting block time: 00:45:24
Returning block of 1502918587 for bucket 8
Sorting block time: 00:46:10
Returning block of 1472371617 for bucket 9
bucket 18: 50%
Getting block 21 of 83
Reserving size (1514131131) for bucket 21
Calculating Z arrays for bucket 21
Entering block accumulator loop for bucket 21:
bucket 16: 60%
bucket 19: 10%
bucket 17: 60%
bucket 15: 80%
Getting block 22 of 83
Reserving size (1514131131) for bucket 22
Calculating Z arrays for bucket 22
Entering block accumulator loop for bucket 22:
bucket 20: 10%
bucket 14: 90%
bucket 18: 60%
bucket 16: 70%
bucket 19: 20%
bucket 17: 70%
bucket 21: 10%
bucket 15: 90%
bucket 20: 20%
bucket 22: 10%
bucket 14: 100%
Sorting block of length 1322480602 for bucket 14
(Using difference cover)
bucket 18: 70%
bucket 16: 80%
bucket 19: 30%
bucket 17: 80%
bucket 15: 100%
Sorting block of length 1224616110 for bucket 15
(Using difference cover)
bucket 20: 30%
bucket 21: 20%
bucket 22: 20%
bucket 18: 80%
bucket 16: 90%
bucket 19: 40%
bucket 17: 90%
bucket 20: 40%
bucket 22: 30%
bucket 21: 30%
bucket 16: 100%
Sorting block of length 941939259 for bucket 16
(Using difference cover)
bucket 18: 90%
bucket 19: 50%
bucket 17: 100%
Sorting block of length 1404998715 for bucket 17
(Using difference cover)
bucket 20: 50%
bucket 22: 40%
bucket 21: 40%
bucket 18: 100%
Sorting block of length 1272294305 for bucket 18
(Using difference cover)
It would appear that the process crashed while building the index. The tmp files only get moved after the indexes have been successfully built. I am looking into this one.
I am running
bowtie2-build ref.fna ref --threads 12 --large-index
with no error message. However, the command generates only temporary output files and no .rev files.Log:
Output files: