/isilon_temp/garber/bin/RSEM/rsem-extract-reference-transcripts /isilon_temp/garber/genome_data/c_elegans/ce10/rsem_ref 0 /isilon_temp/garber/genome_data/c_elegans/ce10/ucsc.gtf 1 /isilon_temp/garber/genome_data/c_elegans/ce10/ucsc_into_genesymbol.rsem /isilon_temp/garber/genome_data/c_elegans/ce10/ce10.fa
Parsed 200000 lines
Parsed 400000 lines
Parsing gtf File is done!
/isilon_temp/garber/genome_data/c_elegans/ce10/ce10.fa is processed!
Extracting sequences is done!
Group File is generated!
Transcript Information File is generated!
Chromosome List File is generated!
Extracted Sequences File is generated!

/isilon_temp/garber/bin/RSEM/rsem-preref /isilon_temp/garber/genome_data/c_elegans/ce10/rsem_ref.transcripts.fa 0 /isilon_temp/garber/genome_data/c_elegans/ce10/rsem_ref -l 125
Refs.makeRefs finished!
Refs.saveRefs finished!
/isilon_temp/garber/genome_data/c_elegans/ce10/rsem_ref.transcripts.fa is generated!
/isilon_temp/garber/genome_data/c_elegans/ce10/rsem_ref.idx.fa is generated!

/isilon_temp/garber/bin/bowtie-0.12.9/bowtie-build -f /isilon_temp/garber/genome_data/c_elegans/ce10/rsem_ref.idx.fa /isilon_temp/garber/genome_data/c_elegans/ce10/rsem_ref
Settings:
  Output files: "/isilon_temp/garber/genome_data/c_elegans/ce10/rsem_ref.*.ebwt"
  Line rate: 6 (line is 64 bytes)
  Lines per side: 1 (side is 64 bytes)
  Offset rate: 5 (one in 32)
  FTable chars: 10
  Strings: unpacked
  Max bucket size: default
  Max bucket size, sqrt multiplier: default
  Max bucket size, len divisor: 4
  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:
  /isilon_temp/garber/genome_data/c_elegans/ce10/rsem_ref.idx.fa
Reading reference sizes
  Time reading reference sizes: 00:00:02
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:00
bmax according to bmaxDivN setting: 10414133
Using parameters --bmax 7810600 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 7810600 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:02
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:01
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:00
  Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
  (Using difference cover)
  Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:00:05
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 7; iterating...
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:00:03
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.95093e+06 (target: 7810599)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (7810600) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:00
  Sorting block of length 6818495
  (Using difference cover)
  Sorting block time: 00:00:11
Returning block of 6818496
Getting block 2 of 7
  Reserving size (7810600) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:01
  Sorting block of length 4742291
  (Using difference cover)
  Sorting block time: 00:00:12
Returning block of 4742292
Getting block 3 of 7
  Reserving size (7810600) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:01
  Sorting block of length 7303397
  (Using difference cover)
  Sorting block time: 00:00:20
Returning block of 7303398
Getting block 4 of 7
  Reserving size (7810600) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:01
  Sorting block of length 7632051
  (Using difference cover)
  Sorting block time: 00:00:21
Returning block of 7632052
Getting block 5 of 7
  Reserving size (7810600) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:01
  Sorting block of length 6347982
  (Using difference cover)
"/isilon_temp/garber/bin/bowtie-0.12.9/bowtie-build -f /isilon_temp/garber/genome_data/c_elegans/ce10/rsem_ref.idx.fa /isilon_temp/garber/genome_data/c_elegans/ce10/rsem_ref" failed! Plase check if you provide correct parameters/options for the pipeline!