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alexdobin / STAR

RNA-seq aligner
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Problem creating index files for hg38.. #1620

Open tmk1219 opened 2 years ago

tmk1219 commented 2 years ago

I am trying to create an index file for hg38 in Linux.

Genome=GRCh38.primary_assembly.genome Anno=homSap_GRCh38_primary_assembly_GENCODEv41_cmp_chr Dir=~/src/genome/homSap_hg38_GENCODEv40 cd ${Dir} mkdir indexesSTAR-2.7.10a${Anno} -p cd indexesSTAR-2.7.10a${Anno} gunzip -c ../${Genome}.fa.gz > tmp.fa gunzip -c ../${Anno}.gtf.gz > tmp.gtf STAR --runThreadN 10 --runMode genomeGenerate \ --genomeDir ~/src/genome/homSap_hg38_GENCODEv40/indexes_STAR-2.7.10a_homSap_GRCh38_primary_assembly_GENCODEv41_cmp_chr \ --genomeFastaFiles tmp.fa \ --sjdbGTFfile tmp.gtf \ --sjdbOverhang 100 \ --genomeChrBinNbits 11 rm tmp rm ../tmp

the error I get is the following: terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc

Do you have any idea what is wrong? Thanks a lot in advance.

alexdobin commented 2 years ago

Hi @tmk1219

please post the Log.out file.

tmk1219 commented 2 years ago

Here it is. Thank you for your cooperation. @alexdobin

STAR version=2.7.10a STAR compilation time,server,dir=2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source STAR git: On branch master ; commit ae26add7ea1724f3281ec8abedb71bcff6a4ae73 ; diff files: CHANGES.md README.md RELEASEnotes.md doc/STARmanual.pdf extras/doc-latex/STARmanual.tex extras/doc-latex/convertParDefToLatexTable.awk extras/doc-latex/parametersDefault.tex extras/docker/Dockerfile source/VERSION

Command Line:

STAR --runThreadN 10 --runMode genomeGenerate --genomeDir /home/k-tomo/src/genome/homSap_hg38_GENCODEv40/indexes_STAR-2.7.10a_homSap_GRCh38_primary_assembly_GENCODEv41_cmp_chr --genomeFastaFiles tmp.fa --sjdbGTFfile tmp.gtf --sjdbOverhang 100 --genomeChrBinNbits 11 --genomeSAindexNbases 12 --limitSjdbInsertNsj 400000

Initial USER parameters from Command Line:
All USER parameters from Command Line:

runThreadN 10 ~RE-DEFINED runMode genomeGenerate ~RE-DEFINED genomeDir /home/k-tomo/src/genome/homSap_hg38_GENCODEv40/indexes_STAR-2.7.10a_homSap_GRCh38_primary_assembly_GENCODEv41_cmp_chr ~RE-DEFINED genomeFastaFiles tmp.fa ~RE-DEFINED sjdbGTFfile tmp.gtf ~RE-DEFINED sjdbOverhang 100 ~RE-DEFINED genomeChrBinNbits 11 ~RE-DEFINED genomeSAindexNbases 12 ~RE-DEFINED limitSjdbInsertNsj 400000 ~RE-DEFINED

Finished reading parameters from all sources
Final user re-defined parameters-----------------:

runMode genomeGenerate
runThreadN 10 genomeDir /home/k-tomo/src/genome/homSap_hg38_GENCODEv40/indexes_STAR-2.7.10a_homSap_GRCh38_primary_assembly_GENCODEv41_cmp_chr genomeFastaFiles tmp.fa
genomeSAindexNbases 12 genomeChrBinNbits 11 limitSjdbInsertNsj 400000 sjdbGTFfile tmp.gtf sjdbOverhang 100

Final effective command line:

STAR --runMode genomeGenerate --runThreadN 10 --genomeDir /home/k-tomo/src/genome/homSap_hg38_GENCODEv40/indexes_STAR-2.7.10a_homSap_GRCh38_primary_assembly_GENCODEv41_cmp_chr --genomeFastaFiles tmp.fa --genomeSAindexNbases 12 --genomeChrBinNbits 11 --limitSjdbInsertNsj 400000 --sjdbGTFfile tmp.gtf --sjdbOverhang 100

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: /home/k-tomo/src/genome/homSap_hg38_GENCODEv40/indexes_STAR-2.7.10a_homSap_GRCh38_primary_assembly_GENCODEv41_cmp_chr/ Aug 03 19:14:23 ... starting to generate Genome files tmp.fa : chr # 0 "chr1" chrStart: 0 tmp.fa : chr # 1 "chr2" chrStart: 248956928 tmp.fa : chr # 2 "chr3" chrStart: 491151360 tmp.fa : chr # 3 "chr4" chrStart: 689448960 tmp.fa : chr # 4 "chr5" chrStart: 879665152 tmp.fa : chr # 5 "chr6" chrStart: 1061203968 tmp.fa : chr # 6 "chr7" chrStart: 1232011264 tmp.fa : chr # 7 "chr8" chrStart: 1391357952 tmp.fa : chr # 8 "chr9" chrStart: 1536497664 tmp.fa : chr # 9 "chr10" chrStart: 1674893312 tmp.fa : chr # 10 "chr11" chrStart: 1808691200 tmp.fa : chr # 11 "chr12" chrStart: 1943779328 tmp.fa : chr # 12 "chr13" chrStart: 2077054976 tmp.fa : chr # 13 "chr14" chrStart: 2191419392 tmp.fa : chr # 14 "chr15" chrStart: 2298464256 tmp.fa : chr # 15 "chr16" chrStart: 2400456704 tmp.fa : chr # 16 "chr17" chrStart: 2490796032 tmp.fa : chr # 17 "chr18" chrStart: 2574055424 tmp.fa : chr # 18 "chr19" chrStart: 2654429184 tmp.fa : chr # 19 "chr20" chrStart: 2713047040 tmp.fa : chr # 20 "chr21" chrStart: 2777491456 tmp.fa : chr # 21 "chr22" chrStart: 2824202240 tmp.fa : chr # 22 "chrX" chrStart: 2875021312 tmp.fa : chr # 23 "chrY" chrStart: 3031062528 tmp.fa : chr # 24 "chrM" chrStart: 3088291840 tmp.fa : chr # 25 "GL000008.2" chrStart: 3088310272 tmp.fa : chr # 26 "GL000009.2" chrStart: 3088521216 tmp.fa : chr # 27 "GL000194.1" chrStart: 3088723968 tmp.fa : chr # 28 "GL000195.1" chrStart: 3088916480 tmp.fa : chr # 29 "GL000205.2" chrStart: 3089100800 tmp.fa : chr # 30 "GL000208.1" chrStart: 3089287168 tmp.fa : chr # 31 "GL000213.1" chrStart: 3089381376 tmp.fa : chr # 32 "GL000214.1" chrStart: 3089547264 tmp.fa : chr # 33 "GL000216.2" chrStart: 3089686528 tmp.fa : chr # 34 "GL000218.1" chrStart: 3089864704 tmp.fa : chr # 35 "GL000219.1" chrStart: 3090026496 tmp.fa : chr # 36 "GL000220.1" chrStart: 3090206720 tmp.fa : chr # 37 "GL000221.1" chrStart: 3090370560 tmp.fa : chr # 38 "GL000224.1" chrStart: 3090526208 tmp.fa : chr # 39 "GL000225.1" chrStart: 3090706432 tmp.fa : chr # 40 "GL000226.1" chrStart: 3090919424 tmp.fa : chr # 41 "KI270302.1" chrStart: 3090935808 tmp.fa : chr # 42 "KI270303.1" chrStart: 3090939904 tmp.fa : chr # 43 "KI270304.1" chrStart: 3090941952 tmp.fa : chr # 44 "KI270305.1" chrStart: 3090946048 tmp.fa : chr # 45 "KI270310.1" chrStart: 3090948096 tmp.fa : chr # 46 "KI270311.1" chrStart: 3090950144 tmp.fa : chr # 47 "KI270312.1" chrStart: 3090964480 tmp.fa : chr # 48 "KI270315.1" chrStart: 3090966528 tmp.fa : chr # 49 "KI270316.1" chrStart: 3090970624 tmp.fa : chr # 50 "KI270317.1" chrStart: 3090972672 tmp.fa : chr # 51 "KI270320.1" chrStart: 3091011584 tmp.fa : chr # 52 "KI270322.1" chrStart: 3091017728 tmp.fa : chr # 53 "KI270329.1" chrStart: 3091040256 tmp.fa : chr # 54 "KI270330.1" chrStart: 3091042304 tmp.fa : chr # 55 "KI270333.1" chrStart: 3091044352 tmp.fa : chr # 56 "KI270334.1" chrStart: 3091048448 tmp.fa : chr # 57 "KI270335.1" chrStart: 3091050496 tmp.fa : chr # 58 "KI270336.1" chrStart: 3091052544 tmp.fa : chr # 59 "KI270337.1" chrStart: 3091054592 tmp.fa : chr # 60 "KI270338.1" chrStart: 3091056640 tmp.fa : chr # 61 "KI270340.1" chrStart: 3091058688 tmp.fa : chr # 62 "KI270362.1" chrStart: 3091060736 tmp.fa : chr # 63 "KI270363.1" chrStart: 3091064832 tmp.fa : chr # 64 "KI270364.1" chrStart: 3091066880 tmp.fa : chr # 65 "KI270366.1" chrStart: 3091070976 tmp.fa : chr # 66 "KI270371.1" chrStart: 3091081216 tmp.fa : chr # 67 "KI270372.1" chrStart: 3091085312 tmp.fa : chr # 68 "KI270373.1" chrStart: 3091087360

alexdobin commented 2 years ago

Hi @tmk1219

nothing suspicious in the Log.out. How much RAM do you have in this server? You need at least 32GB for this genome.

Cheers Alex

tmk1219 commented 2 years ago

Thank you very much for your reply. @alexdobin Check the server's RAM. By the way, I got the following error when I ran Cellranger. Is it the same cause? Thanks a lot in advance.

cellranger mkref \ --genome="GRCh38-1.2.0_premrna" \ --fasta="/lustre7/home/k-tomo/src/Muto_Nat_Commun_2020/refdata-gex-GRCh38-2020-A/fasta/genome.fa" \ --genes="GRCh38-1.2.0.premrna.gtf" \ --nthreads=8 \ --memgb=64

###################### Creating new reference folder at /lustre7/home/k-tomo/src/Muto_Nat_Commun_2020/GRCh38-1.2.0_premrna ...done

Writing genome FASTA file into reference folder... ...done

Indexing genome FASTA file... ...done

Writing genes GTF file into reference folder... ...done

Generating STAR genome index (may take over 8 core hours for a 3Gb genome)... Aug 19 17:57:47 ..... started STAR run Aug 19 17:57:47 ... starting to generate Genome files libc++abi: terminating with uncaught exception of type std::bad_alloc: std::bad_alloc Failed to make genome index with STAR. This can occasionally be caused by setting the argument memgb too low. Error was from running command '/lustre7/home/k-tomo/tools/cellranger-7.0.0/lib/bin/STAR' Command '['/lustre7/home/k-tomo/tools/cellranger-7.0.0/lib/bin/STAR', '--runMode', 'genomeGenerate', '--genomeDir', '/lustre7/home/k-tomo/src/Muto_Nat_Commun_2020/GRCh38-1.2.0_premrna/star', '--runThreadN', '8', '--genomeFastaFiles', '/lustre7/home/k-tomo/src/Muto_Nat_Commun_2020/GRCh38-1.2.0_premrna/fasta/genome.fa', '--sjdbGTFfile', '/lustre7/home/k-tomo/src/Muto_Nat_Commun_2020/GRCh38-1.2.0_premrna/genes/genes.gtf', '--limitGenomeGenerateRAM', '68719476736', '--genomeSAsparseD', '1', '--genomeSAindexNbases', '14', '--genomeChrBinNbits', '18']' died with <Signals.SIGABRT: 6>.

Check stdout and stderr for more information.

alexdobin commented 2 years ago

It could be the same issue - not enough RAM.

DagneDas commented 10 months ago

Hello,

I have the same problem. I was trying to make an index for GRCh38. I was using the genome from Genecode (GRCh38.p14). Also, I was trying to run this on our HPC cluster.

I used these parameters: STAR --runThreadN 1 --runMode genomeGenerate --genomeDir star_genecode_index --genomeFastaFiles GRCh38.p14.genome.fa --sjdbGTFfile gencode.v44.chr_patch_hapl_scaff.annotation.gtf --genomeChrBinNbits 12 --limitGenomeGenerateRAM 124544990592.

I get this: terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc /tmp/slurmd/job16382136/slurm_script: line 20: 31994 Aborted STAR --runThreadN 1 --runMode genomeGenerate --genomeDir star_genecode_index --genomeFastaFiles GRCh38.p14.genome.fa --sjdbGTFfile gencode.v44.chr_patch_hapl_scaff.annotation.gtf --genomeChrBinNbits 12 --limitGenomeGenerateRAM 124544990592

Before, I tried different memory specifications. Different number of threads. Nothing worked for me. Any help would be appreciated.

DagneDas commented 10 months ago

Hi,

This is the output from the Log.out file:

STAR version=2.7.10a STAR compilation time,server,dir=2022-10-06T10:08:47+0100 c0295.hpc.private:/gpfs/software/ada/build/STAR-2.7.10a/source STAR git:

Command Line:

STAR --runThreadN 1 --runMode genomeGenerate --genomeDir star_genecode_index --genomeFastaFiles GRCh38.p14.genome.fa --sjdbGTFfile gencode.v44.chr_patch_hapl_scaff.annotation.gtf --genomeChrBinNbits 12 --limitGenomeGenerateRAM 124544990592

Initial USER parameters from Command Line:
All USER parameters from Command Line:

runThreadN 1 ~RE-DEFINED runMode genomeGenerate ~RE-DEFINED genomeDir star_genecode_index ~RE-DEFINED genomeFastaFiles GRCh38.p14.genome.fa ~RE-DEFINED sjdbGTFfile gencode.v44.chr_patch_hapl_scaff.annotation.gtf ~RE-DEFINED genomeChrBinNbits 12 ~RE-DEFINED limitGenomeGenerateRAM 124544990592 ~RE-DEFINED

Finished reading parameters from all sources
Final user re-defined parameters-----------------:

runMode genomeGenerate runThreadN 1 genomeDir star_genecode_index genomeFastaFiles GRCh38.p14.genome.fa genomeChrBinNbits 12 limitGenomeGenerateRAM 124544990592 sjdbGTFfile gencode.v44.chr_patch_hapl_scaff.annotation.gtf

Final effective command line:

STAR --runMode genomeGenerate --runThreadN 1 --genomeDir star_genecode_index --genomeFastaFiles GRCh38.p14.genome.fa --genomeChrBinNbits 12 --limitGenomeGenerateRAM 124544990592 --sjdbGTFfile gencode.v44.chr_patch_hapl_scaff.annotation.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 created: star_genecode_index/ Dec 21 13:30:45 ... starting to generate Genome files GRCh38.p14.genome.fa : chr # 0 "chr1" chrStart: 0 GRCh38.p14.genome.fa : chr # 1 "chr2" chrStart: 248958976 GRCh38.p14.genome.fa : chr # 2 "chr3" chrStart: 491155456 GRCh38.p14.genome.fa : chr # 3 "chr4" chrStart: 689455104 GRCh38.p14.genome.fa : chr # 4 "chr5" chrStart: 879673344 GRCh38.p14.genome.fa : chr # 5 "chr6" chrStart: 1061212160 GRCh38.p14.genome.fa : chr # 6 "chr7" chrStart: 1232019456 GRCh38.p14.genome.fa : chr # 7 "chr8" chrStart: 1391366144 GRCh38.p14.genome.fa : chr # 8 "chr9" chrStart: 1536507904 GRCh38.p14.genome.fa : chr # 9 "chr10" chrStart: 1674903552 GRCh38.p14.genome.fa : chr # 10 "chr11" chrStart: 1808703488 GRCh38.p14.genome.fa : chr # 11 "chr12" chrStart: 1943793664 GRCh38.p14.genome.fa : chr # 12 "chr13" chrStart: 2077069312 GRCh38.p14.genome.fa : chr # 13 "chr14" chrStart: 2191433728 GRCh38.p14.genome.fa : chr # 14 "chr15" chrStart: 2298478592 GRCh38.p14.genome.fa : chr # 15 "chr16" chrStart: 2400473088 GRCh38.p14.genome.fa : chr # 16 "chr17" chrStart: 2490814464 GRCh38.p14.genome.fa : chr # 17 "chr18" chrStart: 2574073856 GRCh38.p14.genome.fa : chr # 18 "chr19" chrStart: 2654449664 GRCh38.p14.genome.fa : chr # 19 "chr20" chrStart: 2713067520 GRCh38.p14.genome.fa : chr # 20 "chr21" chrStart: 2777513984 GRCh38.p14.genome.fa : chr # 21 "chr22" chrStart: 2824224768 GRCh38.p14.genome.fa : chr # 22 "chrX" chrStart: 2875043840 GRCh38.p14.genome.fa : chr # 23 "chrY" chrStart: 3031085056 GRCh38.p14.genome.fa : chr # 24 "chrM" chrStart: 3088314368 GRCh38.p14.genome.fa : chr # 25 "MU273365.1" chrStart: 3088334848 GRCh38.p14.genome.fa : chr # 26 "MU273352.1" chrStart: 3088818176 GRCh38.p14.genome.fa : chr # 27 "MU273360.1" chrStart: 3088855040 GRCh38.p14.genome.fa : chr # 28 "KQ759759.2" chrStart: 3088896000 GRCh38.p14.genome.fa : chr # 29 "ML143376.1" chrStart: 3089104896 GRCh38.p14.genome.fa : chr # 30 "MU273366.1" chrStart: 3089600512 GRCh38.p14.genome.fa : chr # 31 "KN538364.1" chrStart: 3090173952 GRCh38.p14.genome.fa : chr # 32 "ML143355.1" chrStart: 3090591744 GRCh38.p14.genome.fa : chr # 33 "ML143348.1" chrStart: 3090886656 GRCh38.p14.genome.fa : chr # 34 "ML143347.1" chrStart: 3091013632 GRCh38.p14.genome.fa : chr # 35 "ML143346.1" chrStart: 3091193856 GRCh38.p14.genome.fa : chr # 36 "ML143352.1" chrStart: 3091251200 GRCh38.p14.genome.fa : chr # 37 "KQ759762.2" chrStart: 3091509248 GRCh38.p14.genome.fa : chr # 38 "ML143375.1" chrStart: 3091611648 GRCh38.p14.genome.fa : chr # 39 "KQ031383.1" chrStart: 3091668992 GRCh38.p14.genome.fa : chr # 40 "MU273333.1" chrStart: 3092140032 GRCh38.p14.genome.fa : chr # 41 "KN538369.1" chrStart: 3093712896 GRCh38.p14.genome.fa : chr # 42 "MU273382.1" chrStart: 3094257664 GRCh38.p14.genome.fa : chr # 43 "ML143342.1" chrStart: 3094446080 GRCh38.p14.genome.fa : chr # 44 "ML143350.1" chrStart: 3094532096 GRCh38.p14.genome.fa : chr # 45 "ML143362.1" chrStart: 3094622208 GRCh38.p14.genome.fa : chr # 46 "JH159136.1" chrStart: 3094818816 GRCh38.p14.genome.fa : chr # 47 "ML143357.1" chrStart: 3095023616 GRCh38.p14.genome.fa : chr # 48 "ML143385.1" chrStart: 3095191552 GRCh38.p14.genome.fa : chr # 49 "ML143378.1" chrStart: 3095212032 GRCh38.p14.genome.fa : chr # 50 "ML143382.1" chrStart: 3095674880 GRCh38.p14.genome.fa : chr # 51 "ML143383.1" chrStart: 3095707648 GRCh38.p14.genome.fa : chr # 52 "ML143384.1" chrStart: 3095777280 GRCh38.p14.genome.fa : chr # 53 "JH159137.1" chrStart: 3095793664 GRCh38.p14.genome.fa : chr # 54 "ML143356.1" chrStart: 3095986176 GRCh38.p14.genome.fa : chr # 55 "ML143364.1" chrStart: 3096035328 GRCh38.p14.genome.fa : chr # 56 "ML143365.1" chrStart: 3096195072 GRCh38.p14.genome.fa : chr # 57 "MU273369.1" chrStart: 3096260608 GRCh38.p14.genome.fa : chr # 58 "KZ208923.1" chrStart: 3096698880 GRCh38.p14.genome.fa : chr # 59 "MU273398.1" chrStart: 3096748032 GRCh38.p14.genome.fa : chr # 60 "KZ208924.1" chrStart: 3097616384 GRCh38.p14.genome.fa : chr # 61 "KQ031387.1" chrStart: 3097829376 GRCh38.p14.genome.fa : chr # 62 "KV766195.1" chrStart: 3098152960 GRCh38.p14.genome.fa : chr # 63 "KZ208916.1" chrStart: 3098296320 GRCh38.p14.genome.fa : chr # 64 "ML143363.1" chrStart: 3099344896 GRCh38.p14.genome.fa : chr # 65 "KN538360.1" chrStart: 3099353088 GRCh38.p14.genome.fa : chr # 66 "KZ208920.1" chrStart: 3099815936 GRCh38.p14.genome.fa : chr # 67 "KZ208906.1" chrStart: 3100508160 GRCh38.p14.genome.fa : chr # 68 "KN196484.1" chrStart: 3100839936 GRCh38.p14.genome.fa : chr # 69 "KN196476.1" chrStart: 3101212672 GRCh38.p14.genome.fa : chr # 70 "KQ983257.1" chrStart: 3101519872 GRCh38.p14.genome.fa : chr # 71 "KN196479.1" chrStart: 3101753344 GRCh38.p14.genome.fa : chr # 72 "MU273363.1" chrStart: 3102085120 GRCh38.p14.genome.fa : chr # 73 "KV575245.1" chrStart: 3102294016 GRCh38.p14.genome.fa : chr # 74 "KZ208917.1" chrStart: 3102449664 GRCh38.p14.genome.fa : chr # 75 "MU273343.1" chrStart: 3102515200 GRCh38.p14.genome.fa : chr # 76 "KZ208911.1" chrStart: 3103006720 GRCh38.p14.genome.fa : chr # 77 "KN196473.1" chrStart: 3103252480 GRCh38.p14.genome.fa : chr # 78 "KZ559108.1" chrStart: 3103420416 GRCh38.p14.genome.fa : chr # 79 "KN196487.1" chrStart: 3103727616 GRCh38.p14.genome.fa : chr # 80 "KQ759760.1" chrStart: 3103830016 GRCh38.p14.genome.fa : chr # 81 "KN196475.1" chrStart: 3104149504 GRCh38.p14.genome.fa : chr # 82 "KV880766.1" chrStart: 3104604160 GRCh38.p14.genome.fa : chr # 83 "KV880767.1" chrStart: 3104763904 GRCh38.p14.genome.fa : chr # 84 "MU273348.1" chrStart: 3105030144 GRCh38.p14.genome.fa : chr # 85 "KQ090016.1" chrStart: 3105509376 GRCh38.p14.genome.fa : chr # 86 "MU273347.1" chrStart: 3105755136 GRCh38.p14.genome.fa : chr # 87 "ML143374.1" chrStart: 3106058240 GRCh38.p14.genome.fa : chr # 88 "KV880764.1" chrStart: 3106197504 GRCh38.p14.genome.fa : chr # 89 "KN538361.1" chrStart: 3106340864 GRCh38.p14.genome.fa : chr # 90 "KN196474.1" chrStart: 3106648064 GRCh38.p14.genome.fa : chr # 91 "ML143360.1" chrStart: 3106770944 GRCh38.p14.genome.fa : chr # 92 "KZ559109.1" chrStart: 3106942976 GRCh38.p14.genome.fa : chr # 93 "ML143359.1" chrStart: 3107225600 GRCh38.p14.genome.fa : chr # 94 "KQ090022.1" chrStart: 3107442688 GRCh38.p14.genome.fa : chr # 95 "MU273379.1" chrStart: 3107627008 GRCh38.p14.genome.fa : chr # 96 "KV766194.1" chrStart: 3107864576 GRCh38.p14.genome.fa : chr # 97 "KN196478.1" chrStart: 3108007936 GRCh38.p14.genome.fa : chr # 98 "KZ559104.1" chrStart: 3108278272 GRCh38.p14.genome.fa : chr # 99 "MU273345.1" chrStart: 3108384768 GRCh38.p14.genome.fa : chr # 100 "MU273350.1" chrStart: 3108560896 GRCh38.p14.genome.fa : chr # 101 "MU273364.1" chrStart: 3108675584 GRCh38.p14.genome.fa : chr # 102 "MU273359.1" chrStart: 3109019648 GRCh38.p14.genome.fa : chr # 103 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3284164608 GRCh38.p14.genome.fa : chr # 608 "KI270420.1" chrStart: 3284168704 GRCh38.p14.genome.fa : chr # 609 "KI270422.1" chrStart: 3284172800 GRCh38.p14.genome.fa : chr # 610 "KI270423.1" chrStart: 3284176896 GRCh38.p14.genome.fa : chr # 611 "KI270424.1" chrStart: 3284180992 GRCh38.p14.genome.fa : chr # 612 "KI270425.1" chrStart: 3284185088 GRCh38.p14.genome.fa : chr # 613 "KI270429.1" chrStart: 3284189184 GRCh38.p14.genome.fa : chr # 614 "KI270435.1" chrStart: 3284193280 GRCh38.p14.genome.fa : chr # 615 "KI270438.1" chrStart: 3284287488 GRCh38.p14.genome.fa : chr # 616 "KI270442.1" chrStart: 3284402176 GRCh38.p14.genome.fa : chr # 617 "KI270448.1" chrStart: 3284795392 GRCh38.p14.genome.fa : chr # 618 "KI270465.1" chrStart: 3284803584 GRCh38.p14.genome.fa : chr # 619 "KI270466.1" chrStart: 3284807680 GRCh38.p14.genome.fa : chr # 620 "KI270467.1" chrStart: 3284811776 GRCh38.p14.genome.fa : chr # 621 "KI270468.1" chrStart: 3284815872 GRCh38.p14.genome.fa : chr # 622 "KI270507.1" chrStart: 3284819968 GRCh38.p14.genome.fa : chr # 623 "KI270508.1" chrStart: 3284828160 GRCh38.p14.genome.fa : chr # 624 "KI270509.1" chrStart: 3284832256 GRCh38.p14.genome.fa : chr # 625 "KI270510.1" chrStart: 3284836352 GRCh38.p14.genome.fa : chr # 626 "KI270511.1" chrStart: 3284840448 GRCh38.p14.genome.fa : chr # 627 "KI270512.1" chrStart: 3284848640 GRCh38.p14.genome.fa : chr # 628 "KI270515.1" chrStart: 3284873216 GRCh38.p14.genome.fa : chr # 629 "KI270516.1" chrStart: 3284881408 GRCh38.p14.genome.fa : chr # 630 "KI270517.1" chrStart: 3284885504 GRCh38.p14.genome.fa : chr # 631 "KI270518.1" chrStart: 3284889600 GRCh38.p14.genome.fa : chr # 632 "KI270519.1" chrStart: 3284893696 GRCh38.p14.genome.fa : chr # 633 "KI270521.1" chrStart: 3285032960 GRCh38.p14.genome.fa : chr # 634 "KI270522.1" chrStart: 3285041152 GRCh38.p14.genome.fa : chr # 635 "KI270528.1" chrStart: 3285049344 GRCh38.p14.genome.fa : chr # 636 "KI270529.1" chrStart: 3285053440 GRCh38.p14.genome.fa : chr # 637 "KI270530.1" chrStart: 3285057536 GRCh38.p14.genome.fa : chr # 638 "KI270538.1" chrStart: 3285061632 GRCh38.p14.genome.fa : chr # 639 "KI270539.1" chrStart: 3285155840 GRCh38.p14.genome.fa : chr # 640 "KI270544.1" chrStart: 3285159936 GRCh38.p14.genome.fa : chr # 641 "KI270548.1" chrStart: 3285164032 GRCh38.p14.genome.fa : chr # 642 "KI270579.1" chrStart: 3285168128 GRCh38.p14.genome.fa : chr # 643 "KI270580.1" chrStart: 3285200896 GRCh38.p14.genome.fa : chr # 644 "KI270581.1" chrStart: 3285204992 GRCh38.p14.genome.fa : chr # 645 "KI270582.1" chrStart: 3285213184 GRCh38.p14.genome.fa : chr # 646 "KI270583.1" chrStart: 3285221376 GRCh38.p14.genome.fa : chr # 647 "KI270584.1" chrStart: 3285225472 GRCh38.p14.genome.fa : chr # 648 "KI270587.1" chrStart: 3285233664 GRCh38.p14.genome.fa : chr # 649 "KI270588.1" chrStart: 3285237760 GRCh38.p14.genome.fa : chr # 650 "KI270589.1" chrStart: 3285245952 GRCh38.p14.genome.fa : chr # 651 "KI270590.1" chrStart: 3285291008 GRCh38.p14.genome.fa : chr # 652 "KI270591.1" chrStart: 3285299200 GRCh38.p14.genome.fa : chr # 653 "KI270593.1" chrStart: 3285307392 GRCh38.p14.genome.fa : chr # 654 "KI270706.1" chrStart: 3285311488 GRCh38.p14.genome.fa : chr # 655 "KI270707.1" chrStart: 3285487616 GRCh38.p14.genome.fa : chr # 656 "KI270708.1" chrStart: 3285520384 GRCh38.p14.genome.fa : chr # 657 "KI270709.1" chrStart: 3285651456 GRCh38.p14.genome.fa : chr # 658 "KI270710.1" chrStart: 3285721088 GRCh38.p14.genome.fa : chr # 659 "KI270711.1" chrStart: 3285762048 GRCh38.p14.genome.fa : chr # 660 "KI270712.1" chrStart: 3285807104 GRCh38.p14.genome.fa : chr # 661 "KI270713.1" chrStart: 3285983232 GRCh38.p14.genome.fa : chr # 662 "KI270714.1" chrStart: 3286024192 GRCh38.p14.genome.fa : chr # 663 "KI270715.1" chrStart: 3286069248 GRCh38.p14.genome.fa : chr # 664 "KI270716.1" chrStart: 3286233088 GRCh38.p14.genome.fa : chr # 665 "KI270717.1" chrStart: 3286388736 GRCh38.p14.genome.fa : chr # 666 "KI270718.1" chrStart: 3286429696 GRCh38.p14.genome.fa : chr # 667 "KI270719.1" chrStart: 3286470656 GRCh38.p14.genome.fa : chr # 668 "KI270720.1" chrStart: 3286650880 GRCh38.p14.genome.fa : chr # 669 "KI270721.1" chrStart: 3286691840 GRCh38.p14.genome.fa : chr # 670 "KI270722.1" chrStart: 3286794240 GRCh38.p14.genome.fa : chr # 671 "KI270723.1" chrStart: 3286990848 GRCh38.p14.genome.fa : chr # 672 "KI270724.1" chrStart: 3287031808 GRCh38.p14.genome.fa : chr # 673 "KI270725.1" chrStart: 3287072768 GRCh38.p14.genome.fa : chr # 674 "KI270726.1" chrStart: 3287248896 GRCh38.p14.genome.fa : chr # 675 "KI270727.1" chrStart: 3287293952 GRCh38.p14.genome.fa : chr # 676 "KI270728.1" chrStart: 3287744512 GRCh38.p14.genome.fa : chr # 677 "KI270729.1" chrStart: 3289620480 GRCh38.p14.genome.fa : chr # 678 "KI270730.1" chrStart: 3289903104 GRCh38.p14.genome.fa : chr # 679 "KI270731.1" chrStart: 3290017792 GRCh38.p14.genome.fa : chr # 680 "KI270732.1" chrStart: 3290169344 GRCh38.p14.genome.fa : chr # 681 "KI270733.1" chrStart: 3290214400 GRCh38.p14.genome.fa : chr # 682 "KI270734.1" chrStart: 3290394624 GRCh38.p14.genome.fa : chr # 683 "KI270735.1" chrStart: 3290562560 GRCh38.p14.genome.fa : chr # 684 "KI270736.1" chrStart: 3290607616 GRCh38.p14.genome.fa : chr # 685 "KI270737.1" chrStart: 3290791936 GRCh38.p14.genome.fa : chr # 686 "KI270738.1" chrStart: 3290898432 GRCh38.p14.genome.fa : chr # 687 "KI270739.1" chrStart: 3291000832 GRCh38.p14.genome.fa : chr # 688 "KI270740.1" chrStart: 3291078656 GRCh38.p14.genome.fa : chr # 689 "KI270741.1" chrStart: 3291119616 GRCh38.p14.genome.fa : chr # 690 "KI270742.1" chrStart: 3291279360 GRCh38.p14.genome.fa : chr # 691 "KI270743.1" chrStart: 3291467776 GRCh38.p14.genome.fa : chr # 692 "KI270744.1" chrStart: 3291680768 GRCh38.p14.genome.fa : chr # 693 "KI270745.1" chrStart: 3291852800 GRCh38.p14.genome.fa : chr # 694 "KI270746.1" chrStart: 3291897856 GRCh38.p14.genome.fa : chr # 695 "KI270747.1" chrStart: 3291967488 GRCh38.p14.genome.fa : chr # 696 "KI270748.1" chrStart: 3292168192 GRCh38.p14.genome.fa : chr # 697 "KI270749.1" chrStart: 3292262400 GRCh38.p14.genome.fa : chr # 698 "KI270750.1" chrStart: 3292422144 GRCh38.p14.genome.fa : chr # 699 "KI270751.1" chrStart: 3292573696 GRCh38.p14.genome.fa : chr # 700 "KI270752.1" chrStart: 3292725248 GRCh38.p14.genome.fa : chr # 701 "KI270753.1" chrStart: 3292753920 GRCh38.p14.genome.fa : chr # 702 "KI270754.1" chrStart: 3292819456 GRCh38.p14.genome.fa : chr # 703 "KI270755.1" chrStart: 3292860416 GRCh38.p14.genome.fa : chr # 704 "KI270756.1" chrStart: 3292897280 GRCh38.p14.genome.fa : chr # 705 "KI270757.1" chrStart: 3292979200 Chromosome sequence lengths: chr1 248956422 chr2 242193529 chr3 198295559 chr4 190214555 chr5 181538259 chr6 170805979 chr7 159345973 chr8 145138636 chr9 138394717 chr10 133797422 chr11 135086622 chr12 133275309 chr13 114364328 chr14 107043718 chr15 101991189 chr16 90338345 chr17 83257441 chr18 80373285 chr19 58617616 chr20 64444167 chr21 46709983 chr22 50818468 chrX 156040895 chrY 57227415 chrM 16569 MU273365.1 482250 MU273352.1 34400 MU273360.1 39290 KQ759759.2 204999 ML143376.1 493165 MU273366.1 569668 KN538364.1 415308 ML143355.1 292944 ML143348.1 125549 ML143347.1 176674 ML143346.1 53476 ML143352.1 254759 KQ759762.2 101040 ML143375.1 56695 KQ031383.1 467143 MU273333.1 1572686 KN538369.1 541038 MU273382.1 187626 ML143342.1 84043 ML143350.1 89956 ML143362.1 192531 JH159136.1 200998 ML143357.1 165419 ML143385.1 17435 ML143378.1 461303 ML143382.1 28824 ML143383.1 68192 ML143384.1 14678 JH159137.1 191409 ML143356.1 45257 ML143364.1 158944 ML143365.1 65394 MU273369.1 434831 KZ208923.1 48370 MU273398.1 865743 KZ208924.1 209722 KQ031387.1 320750 KV766195.1 140877 KZ208916.1 1046838 ML143363.1 7309 KN538360.1 460100 KZ208920.1 690932 KZ208906.1 330031 KN196484.1 370917 KN196476.1 305979 KQ983257.1 230434 KN196479.1 330164 MU273363.1 207371 KV575245.1 154723 KZ208917.1 64689 MU273343.1 489404 KZ208911.1 242796 KN196473.1 166200 KZ559108.1 305244 KN196487.1 101150 KQ759760.1 315610 KN196475.1 451168 KV880766.1 156998 KV880767.1 265876 MU273348.1 475876 KQ090016.1 245716 MU273347.1 301310 ML143374.1 137908 KV880764.1 142129 KN538361.1 305542 KN196474.1 122022 ML143360.1 170928 KZ559109.1 279644 ML143359.1 217075 KQ090022.1 181958 MU273379.1 234878 KV766194.1 139427 KN196478.1 268330 KZ559104.1 105527 MU273345.1 174385 MU273350.1 113364 MU273364.1 340717 MU273359.1 150302 KN196480.1 277797 ML143370.1 369264 KQ090028.1 407387 KN196483.1 35455 KN196481.1 108875 MU273390.1 336752 MU273388.1 273725 MU273344.1 244725 KN538363.1 365499 KN538362.1 208149 KQ031385.1 373699 KV766192.1 411654 KQ031386.1 165718 KQ031388.1 179932 KN538365.1 14347 KN538366.1 85284 KN538367.1 420164 ML143361.1 297568 KN538370.1 86533 KN538373.1 148762 MU273381.1 144689 KZ559113.1 480415 MU273346.1 469342 MU273391.1 1020778 KV880765.1 468267 MU273362.1 429744 MU273342.1 955087 MU273374.1 1154574 KV766196.1 281919 KN538371.1 206320 KQ031384.1 481245 KN538372.1 356766 MU273355.1 508332 KQ090021.1 264545 ML143371.1 5500449 KN196482.1 211377 MU273380.1 538541 MU273361.1 106905 KZ559115.1 230843 KZ208914.1 165120 KZ208922.1 93070 MU273384.1 333754 ML143373.1 270967 MU273353.1 208405 MU273341.1 120381 ML143369.1 97763 ML143366.1 409912 ML143367.1 399183 ML143372.1 396515 ML143380.1 412368 ML143377.1 519485 MU273335.1 211934 MU273392.1 189707 ML143345.1 341066 MU273373.1 722645 MU273393.1 68810 MU273394.1 140567 MU273372.1 104537 MU273370.1 344606 MU273385.1 137818 MU273334.1 210426 MU273367.1 196262 MU273336.1 250447 MU273371.1 122722 MU273383.1 172609 KQ458386.1 405389 MU273351.1 205691 ML143358.1 270122 KV575244.1 673059 MU273376.1 87715 MU273377.1 334997 MU273389.1 355731 ML143381.1 403128 KZ559100.1 44955 ML143379.1 12295 ML143354.1 454963 ML143351.1 73265 ML143353.1 25408 ML143344.1 235734 ML143349.1 276109 KZ208912.1 589656 ML143341.1 145975 KZ208915.1 6367528 KV880768.1 1927115 KN196472.1 186494 GL383545.1 179254 GL383546.1 309802 KI270824.1 181496 KI270825.1 188315 KQ090020.1 185507 GL383547.1 154407 KN538368.1 203552 KI270826.1 186169 KI270827.1 67707 KZ559111.1 181167 KI270829.1 204059 KI270830.1 177092 KI270831.1 296895 KI270832.1 210133 KI270902.1 106711 KI270903.1 214625 MU273368.1 261194 KZ559110.1 301637 KI270927.1 218612 GL877875.1 167313 GL383549.1 120804 GL383550.2 169178 KQ090023.1 109323 GL877876.1 408271 GL383552.1 138655 KI270904.1 572349 GL383553.2 152874 KI270835.1 238139 GL383551.1 184319 KI270837.1 40090 KI270833.1 76061 KI270834.1 119498 KI270836.1 56134 KZ208918.1 174808 KZ559112.1 154139 KI270838.1 306913 KI270839.1 180306 KI270840.1 191684 KI270841.1 169134 KI270842.1 37287 KI270843.1 103832 KQ090024.1 168146 KQ090025.1 123480 KI270844.1 322166 KI270845.1 180703 KI270846.1 1351393 KI270847.1 1511111 KZ208919.1 171798 ML143368.1 264228 KI270852.1 478999 KI270848.1 327382 GL383554.1 296527 KI270906.1 196384 GL383555.2 388773 KI270851.1 263054 KI270849.1 244917 KI270905.1 5161414 KI270850.1 430880 KQ031389.1 2365364 MU273375.1 204007 KI270853.1 2659700 GL383556.1 192462 GL383557.1 89672 KI270855.1 232857 KQ031390.1 169136 KI270856.1 63982 KQ090027.1 267463 KQ090026.1 59016 KZ208921.1 78609 KI270854.1 134193 KI270909.1 325800 KV766197.1 246895 KZ559114.1 116753 MU273378.1 372839 GL383563.3 375691 KI270861.1 196688 GL383564.2 133151 GL000258.2 1821992 KI270860.1 178921 KI270907.1 137721 KI270862.1 391357 GL383565.1 223995 KI270908.1 1423190 KV766198.1 276292 KI270910.1 157099 GL383566.1 90219 JH159146.1 278131 JH159147.1 70345 JH159148.1 88070 KI270857.1 2877074 KI270858.1 235827 KI270859.1 108763 KZ559116.1 163186 GL383567.1 289831 GL383568.1 104552 GL383569.1 167950 GL383570.1 164789 GL383571.1 198278 GL383572.1 159547 KI270863.1 167999 KI270864.1 111737 KQ458385.1 205101 KI270912.1 174061 KI270911.1 157710 KV575254.1 99845 KV575246.1 163926 KV575256.1 223118 KV575253.1 166713 KV575252.1 178197 KV575255.1 161095 KV575259.1 171263 KI270917.1 190932 KI270918.1 123111 KI270919.1 170701 KV575247.1 170206 KV575248.1 168131 KV575250.1 241058 KV575249.1 293522 KV575257.1 100553 KI270920.1 198005 KI270921.1 282224 KI270922.1 187935 KI270923.1 189352 KI270929.1 186203 KI270930.1 200773 KI270931.1 170148 KI270932.1 215732 KI270933.1 170537 KI270882.1 248807 KI270883.1 170399 KI270884.1 157053 KI270885.1 171027 KI270886.1 204239 KI270887.1 209512 KI270888.1 155532 KV575258.1 156965 KV575251.1 159285 KV575260.1 145691 KI270889.1 170698 KI270890.1 184499 GL000209.2 177381 KI270891.1 170680 KI270914.1 205194 KI270915.1 170665 KI270916.1 184516 GL949746.1 987716 GL949747.2 729520 GL949748.2 1064304 GL949749.2 1091841 GL949750.2 1066390 GL949751.2 1002683 GL949752.1 987100 GL949753.2 796479 GL383573.1 385657 GL383574.1 155864 GL383575.2 170222 KI270866.1 43156 GL383576.1 188024 KI270867.1 233762 KI270865.1 52969 KI270938.1 1066800 KI270868.1 61734 MU273387.1 89211 MU273330.1 516764 KI270760.1 109528 KI270762.1 354444 GL383518.1 182439 KI270759.1 425601 KI270766.1 256271 GL383519.1 110268 KI270761.1 165834 KQ458382.1 141019 GL383520.2 366580 KI270763.1 911658 KQ458383.1 349938 KI270765.1 185285 KI270764.1 50258 KQ983255.1 278659 MU273331.1 847441 KQ458384.1 212205 KV880763.1 551020 MU273332.1 335159 KZ208904.1 166136 KZ208905.1 140355 KI270892.1 162212 GL383577.2 128386 KI270869.1 118774 KI270870.1 183433 KI270871.1 58661 GL383578.2 63917 GL383579.2 201197 GL383580.2 74653 GL383581.2 116689 KI270872.1 82692 KI270873.1 143900 KI270874.1 166743 GL383582.2 162811 GL383583.2 96924 KI270875.1 259914 KI270876.1 263666 KI270877.1 101331 KI270878.1 186262 KI270879.1 304135 KB663609.1 74013 KI270928.1 176103 KN196485.1 156562 KN196486.1 153027 KQ458387.1 155930 KQ458388.1 174749 KQ759761.1 145162 MU273337.1 431782 MU273338.1 535251 MU273339.1 500581 KI270769.1 120616 KI270767.1 161578 GL383521.1 143390 KI270772.1 133041 GL383522.1 123821 KI270770.1 136240 KI270893.1 161218 KI270894.1 214158 GL582966.2 96131 KI270773.1 70887 KI270776.1 174166 KI270768.1 110099 KI270774.1 223625 KI270771.1 110395 KI270775.1 138019 MU273340.1 284971 KQ983256.1 535088 KZ208907.1 181658 KZ208908.1 140361 JH636055.2 173151 GL383526.1 180671 KI270779.1 205312 KI270777.1 173649 KI270782.1 162429 KI270783.1 109187 KI270778.1 248252 KI270895.1 162896 KZ208909.1 175849 KI270780.1 224108 KI270924.1 166540 ML143343.1 215443 KI270781.1 113034 KI270934.1 163458 KZ559105.1 195063 KI270935.1 197351 KZ559101.1 164041 KI270936.1 164170 KZ559102.1 197752 KI270937.1 165607 KZ559103.1 302885 KI270784.1 184404 KQ983258.1 205407 KV766193.1 420675 GL383527.1 164536 KI270790.1 220246 GL383528.1 376187 KI270787.1 111943 GL000257.2 586476 KI270785.1 119912 KQ090013.1 90922 MU273349.1 308682 KI270786.1 244096 KI270788.1 158965 KI270789.1 205944 KI270896.1 378547 KI270925.1 555799 KQ090014.1 163749 KQ090015.1 236512

alexdobin commented 10 months ago

This error means that you do not have enough RAM. I do not recommend genomes with haplotypes and patches.