bowtie2 index generates only tmp files

[mmpust]

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)

Output files:

46G Jul 26 06:11 ref.sa
4.7G Jul 29 19:53 ref.1.bt2l.tmp
6.3G Jul 29 19:17 ref.10.sa
1.8G Jul 29 19:53 ref.2.bt2l.tmp
4 Jul 29 15:09 ref.3.bt2.tmp
1.9G Jul 29 15:30 ref.3.bt2l.tmp
1.0G Jul 29 15:09 ref.4.bt2.tmp
23G Jul 29 15:30 ref.4.bt2l.tmp
12G Jul 29 19:37 ref.5.sa
4.8G Jul 29 19:08 ref.6.sa
12G Jul 29 19:39 ref.7.sa
11G Jul 29 19:40 ref.8.sa
11G Jul 29 19:38 ref.9.sa

[ch4rr0]

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.