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blocked allocation error of PE 300bp reads

Open RJWANGbioinfo opened this issue 10 months ago • 0 comments

Hi, It seems isaac4 currently having issues with the mapping with PE 300bp fastq files. We tried it using the following command through both full-size fastq and 1000-reads fastq files:

isaac-align -r GCA_000001405.15_GRCh38.fa -b TEST1/ -f fastq --base-quality-cutoff 15 --default-adapters Standard --realign-gaps no --memory-control warning -m200 --jobs 4 --verbosity 4 -o TEST1run1

It always shows the following error

2023-08-10 17:55:48     [7f8525b71700]  Resetting Fastq data for 8000000 clusters
2023-08-10 17:55:48     [7f8cc1322740]  adding BarcodeMetadata(AACVWFKM5,1,default,none,(0), 0)
2023-08-10 17:55:48     [7f8cc1322740]  STAT: FindHashMatchesTransition::processFlowcellTiles before findLaneMatches 54058553344vm 10447751res
2023-08-10 17:55:48     [7f8cc1322740]  Resolving barcodes for Layout(AACVWFKM5, [,ReadMetadata(1, 300 [1, 300], 0id, 0off,1frc),ReadMetadata(2, 300 [302, 601], 1id, 300off,302frc)]) lane 1
2023-08-10 17:55:48     [7f8cc1322740]  Forced barcode index for clusters of TileMetadata(AACVWFKM5, 1, 1, 1250, 0oi, 0) to BarcodeMetadata(AACVWFKM5,1,default,none,(0), 0)
2023-08-10 17:55:48     [7f8cc1322740]  Resolving barcodes done for Layout(AACVWFKM5, [,ReadMetadata(1, 300 [1, 300], 0id, 0off,1frc),ReadMetadata(2, 300 [302, 601], 1id, 300off,302frc)]) lane 1
2023-08-10 17:55:48     [7f8cc1322740]  Finding hash matches with repeat threshold: 100
2023-08-10 17:55:48     [7f8cc1322740]  Allocating 4 tile stats.
2023-08-10 17:55:48     [7f8cc1322740]  Allocating 4 tile stats done. Total size is 458880 bytes.
2023-08-10 17:55:48     [7f8cc1322740]  Allocating 4 tile barcode stats.
2023-08-10 17:55:48     [7f8cc1322740]  Allocating 4 tile barcode stats done. Total size is 1184 bytes.
2023-08-10 17:55:48     [7f8cc1322740]  Resizing fragment storage for 1250 clusters
2023-08-10 17:55:48     [7f8cc1322740]  Resizing fragment storage done for 1250 clusters
2023-08-10 17:55:48     [7f8cc1322740]  Determining template length statistics for 1 barcodes on TileMetadata(AACVWFKM5, 1, 1, 1250, 0oi, 0)
Check failed in file /Isaac4-Isaac-04.18.01.19/bootstrap/include/boost/numeric/ublas/storage.hpp at line 364:
size <= N
2023-08-10 17:55:48     [7f8be5714700]  WARNING: blocked allocation of 33 bytes requested.
2023-08-10 17:55:48     [7f8be5714700]  WARNING: blocked allocation of 144 bytes requested.
2023-08-10 17:55:48     [7f8be5714700]  WARNING: blocked allocation of 32 bytes requested.
terminate called after throwing an instance of 'boost::numeric::ublas::bad_size'
  what():  bad size
Aborted (core dumped)

We are using a machine with 32 CPUs and 256GB RAM, any parameters we can adjust to make it work? Thank you in advance!

RJWANGbioinfo avatar Aug 10 '23 18:08 RJWANGbioinfo