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Merged
mashehu merged 2 commits into from
May 4, 2026
Merged

Cageseq #1986

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b9379b9
Added some intermediate results
Apr 14, 2026
d5db972
Merge branch 'nf-core:cageseq' into cageseq
sidorov-si Apr 14, 2026
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90 changes: 90 additions & 0 deletions testdata/v2/star_genomegenerate/star/Log.out
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STAR version=2.7.11b
STAR compilation time,server,dir=2025-01-09T12:33:46+0000 :/opt/conda/conda-bld/star_1736425784849/work/source
##### Command Line:
/opt/conda/bin/STAR-avx --runMode genomeGenerate --genomeDir star/ --genomeFastaFiles sacCer3chrIII.fa --sjdbGTFfile sacCer3chrIII.gtf --runThreadN 12 --genomeSAindexNbases 8 --limitGenomeGenerateRAM 77209411328
##### Initial USER parameters from Command Line:
###### All USER parameters from Command Line:
runMode genomeGenerate ~RE-DEFINED
genomeDir star/ ~RE-DEFINED
genomeFastaFiles sacCer3chrIII.fa ~RE-DEFINED
sjdbGTFfile sacCer3chrIII.gtf ~RE-DEFINED
runThreadN 12 ~RE-DEFINED
genomeSAindexNbases 8 ~RE-DEFINED
limitGenomeGenerateRAM 77209411328 ~RE-DEFINED
##### Finished reading parameters from all sources

##### Final user re-defined parameters-----------------:
runMode genomeGenerate
runThreadN 12
genomeDir star/
genomeFastaFiles sacCer3chrIII.fa
genomeSAindexNbases 8
limitGenomeGenerateRAM 77209411328
sjdbGTFfile sacCer3chrIII.gtf

-------------------------------
##### Final effective command line:
/opt/conda/bin/STAR-avx --runMode genomeGenerate --runThreadN 12 --genomeDir star/ --genomeFastaFiles sacCer3chrIII.fa --genomeSAindexNbases 8 --limitGenomeGenerateRAM 77209411328 --sjdbGTFfile sacCer3chrIII.gtf
----------------------------------------

Number of fastq files for each mate = 1
ParametersSolo: --soloCellFilterType CellRanger2.2 filtering parameters: 3000 0.99 10
Finished loading and checking parameters
--genomeDir directory exists and will be overwritten: star/
Apr 10 18:57:38 ... starting to generate Genome files
sacCer3chrIII.fa : chr # 0 "chrIII" chrStart: 0
Chromosome sequence lengths:
chrIII 316620
Genome sequence total length = 316620
Genome size with padding = 524288
Apr 10 18:57:38 ..... processing annotations GTF
Processing pGe.sjdbGTFfile=sacCer3chrIII.gtf, found:
202 transcripts
212 exons (non-collapsed)
10 collapsed junctions
Total junctions: 10
Apr 10 18:57:38 ..... finished GTF processing

Estimated genome size with padding and SJs: total=genome+SJ=201524288 = 524288 + 201000000
GstrandBit=32
Number of SA indices: 633240
Apr 10 18:57:38 ... starting to sort Suffix Array. This may take a long time...
Number of chunks: 12; chunks size limit: 460536 bytes
Apr 10 18:57:38 ... sorting Suffix Array chunks and saving them to disk...
Writing 156568 bytes into star//SA_11 ; empty space on disk = 633757077504 bytes ... done
Writing 436824 bytes into star//SA_0 ; empty space on disk = 633756897280 bytes ... done
Writing 448464 bytes into star//SA_1 ; empty space on disk = 633756438528 bytes ... done
Writing 447336 bytes into star//SA_4 ; empty space on disk = 633755967488 bytes ... done
Writing 442416 bytes into star//SA_8 ; empty space on disk = 633755496448 bytes ... done
Writing 432464 bytes into star//SA_10 ; empty space on disk = 633755029504 bytes ... done
Writing 432544 bytes into star//SA_2 ; empty space on disk = 633754574848 bytes ...Writing 449816 bytes into star//SA_9 ; empty space on disk = 633754120192 bytes ...Writing 460152 bytes into star//SA_3 ; empty space on disk = 633753649152 bytes ... done
done
done
Writing 452704 bytes into star//SA_6 ; empty space on disk = 633753165824 bytes ...Writing 454552 bytes into star//SA_7 ; empty space on disk = 633752690688 bytes ... done
done
done
Writing 452080 bytes into star//SA_5 ; empty space on disk = 633752215552 bytes ... done
Apr 10 18:57:38 ... loading chunks from disk, packing SA...
Apr 10 18:57:38 ... finished generating suffix array
Apr 10 18:57:38 ... generating Suffix Array index
Apr 10 18:57:38 ... completed Suffix Array index
Apr 10 18:57:38 Finished preparing junctions
Apr 10 18:57:38 ..... inserting junctions into the genome indices
Apr 10 18:57:38 Finished SA search: number of new junctions=10, old junctions=0
Apr 10 18:57:38 Finished sorting SA indicesL nInd=4000
Genome size with junctions=526298 524288 2010
GstrandBit1=32 GstrandBit=32
Apr 10 18:57:38 Finished inserting junction indices
Apr 10 18:57:38 Finished SAi
Apr 10 18:57:38 ..... finished inserting junctions into genome
Apr 10 18:57:38 ... writing Genome to disk ...
Writing 526298 bytes into star//Genome ; empty space on disk = 633756950528 bytes ... done
SA size in bytes: 2628618
Apr 10 18:57:38 ... writing Suffix Array to disk ...
Writing 2628618 bytes into star//SA ; empty space on disk = 633756401664 bytes ... done
Apr 10 18:57:38 ... writing SAindex to disk
Writing 8 bytes into star//SAindex ; empty space on disk = 633753743360 bytes ... done
Writing 72 bytes into star//SAindex ; empty space on disk = 633753743360 bytes ... done
Writing 382291 bytes into star//SAindex ; empty space on disk = 633753743360 bytes ... done
Apr 10 18:57:38 ..... finished successfully
DONE: Genome generation, EXITING
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chrIII
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chrIII 316620
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0
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