Isaac4
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blocked allocation error of PE 300bp reads
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!