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gerstung-lab / deepSNV

The official repository for the deepSNV bioconductor packages. Branch master tracks the official Bioconductor development branch.
https://master.bioconductor.org/packages/deepSNV/
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problem with loadAllData in R 4.0 #12

Open chelauk opened 4 years ago

chelauk commented 4 years ago

I've recently upgraded to R 4.0 

R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

when I run the loadAllData function in deepSNV

I get this error message:

Error in counts[i, , ] <- c[[i]] : 
  number of items to replace is not a multiple of replacement length
In addition: Warning message:
In mclapply(files, function(f) { :
  scheduled cores 1, 2 did not deliver results, all values of the jobs will be affected

The function works fine in R3.6

mg14 commented 4 years ago

Thanks Chela.

Could you run bam2R() and report its output here?

loadAllData() is essentially an mclapply() loop around this.

Perhaps also a samtools view output snippet of the underlying .bam/.cram files. Recent versions of deepSNV use more tags for read filterting, perhaps something has been missed here.

Thanks

M

chelauk commented 4 years ago 
bam2R('davros/normal/1602635.sort.bam',chr = "chr1", start = 1, stop = 10,verbose = TRUE)
[W::hts_idx_load2] The index file is older than the data file: davros/normal/1602635.sort.bai
Reading davros/normal/1602635.sort.bam, chr1:0-10
      A T C G - N INS DEL HEAD TAIL QUAL a t c g _ n ins del head tail qual
 [1,] 0 0 0 0 0 0   0   0    0    0    0 0 0 0 0 0 0   0   0    0    0    0
 [2,] 0 0 0 0 0 0   0   0    0    0    0 0 0 0 0 0 0   0   0    0    0    0
 [3,] 0 0 0 0 0 0   0   0    0    0    0 0 0 0 0 0 0   0   0    0    0    0
 [4,] 0 0 0 0 0 0   0   0    0    0    0 0 0 0 0 0 0   0   0    0    0    0
 [5,] 0 0 0 0 0 0   0   0    0    0    0 0 0 0 0 0 0   0   0    0    0    0
 [6,] 0 0 0 0 0 0   0   0    0    0    0 0 0 0 0 0 0   0   0    0    0    0
 [7,] 0 0 0 0 0 0   0   0    0    0    0 0 0 0 0 0 0   0   0    0    0    0
 [8,] 0 0 0 0 0 0   0   0    0    0    0 0 0 0 0 0 0   0   0    0    0    0
 [9,] 0 0 0 0 0 0   0   0    0    0    0 0 0 0 0 0 0   0   0    0    0    0
[10,] 0 0 0 0 0 0   0   0    0    0    0 0 0 0 0 0 0   0   0    0    0    0

 samtools view -h 1602635.sort.bam | head
@HD VN:1.5  SO:coordinate   GO:none
@SQ SN:chr1 LN:249250621    M5:1b22b98cdeb4a9304cb5d48026a85128 UR:file:/data/genome/hg19/hg19_clean/hg19.fa
@SQ SN:chr2 LN:243199373    M5:a0d9851da00400dec1098a9255ac712e UR:file:/data/genome/hg19/hg19_clean/hg19.fa
@SQ SN:chr3 LN:198022430    M5:641e4338fa8d52a5b781bd2a2c08d3c3 UR:file:/data/genome/hg19/hg19_clean/hg19.fa
@SQ SN:chr4 LN:191154276    M5:23dccd106897542ad87d2765d28a19a1 UR:file:/data/genome/hg19/hg19_clean/hg19.fa
@SQ SN:chr5 LN:180915260    M5:0740173db9ffd264d728f32784845cd7 UR:file:/data/genome/hg19/hg19_clean/hg19.fa
@SQ SN:chr6 LN:171115067    M5:1d3a93a248d92a729ee764823acbbc6b UR:file:/data/genome/hg19/hg19_clean/hg19.fa
@SQ SN:chr7 LN:159138663    M5:618366e953d6aaad97dbe4777c29375e UR:file:/data/genome/hg19/hg19_clean/hg19.fa
@SQ SN:chr8 LN:146364022    M5:96f514a9929e410c6651697bded59aec UR:file:/data/genome/hg19/hg19_clean/hg19.fa
@SQ SN:chr9 LN:141213431    M5:3e273117f15e0a400f01055d9f393768 UR:file:/data/genome/hg19/hg19_clean/hg19.fa
@SQ SN:chr10    LN:135534747    M5:988c28e000e84c26d552359af1ea2e1d UR:file:/data/genome/hg19/hg19_clean/hg19.fa
@SQ SN:chr11    LN:135006516    M5:98c59049a2df285c76ffb1c6db8f8b96 UR:file:/data/genome/hg19/hg19_clean/hg19.fa
@SQ SN:chr12    LN:133851895    M5:51851ac0e1a115847ad36449b0015864 UR:file:/data/genome/hg19/hg19_clean/hg19.fa
@SQ SN:chr13    LN:115169878    M5:283f8d7892baa81b510a015719ca7b0b UR:file:/data/genome/hg19/hg19_clean/hg19.fa
@SQ SN:chr14    LN:107349540    M5:98f3cae32b2a2e9524bc19813927542e UR:file:/data/genome/hg19/hg19_clean/hg19.fa
@SQ SN:chr15    LN:102531392    M5:e5645a794a8238215b2cd77acb95a078 UR:file:/data/genome/hg19/hg19_clean/hg19.fa
@SQ SN:chr16    LN:90354753 M5:fc9b1a7b42b97a864f56b348b06095e6 UR:file:/data/genome/hg19/hg19_clean/hg19.fa
@SQ SN:chr17    LN:81195210 M5:351f64d4f4f9ddd45b35336ad97aa6de UR:file:/data/genome/hg19/hg19_clean/hg19.fa
@SQ SN:chr18    LN:78077248 M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c UR:file:/data/genome/hg19/hg19_clean/hg19.fa
@SQ SN:chr19    LN:59128983 M5:1aacd71f30db8e561810913e0b72636d UR:file:/data/genome/hg19/hg19_clean/hg19.fa
@SQ SN:chr20    LN:63025520 M5:0dec9660ec1efaaf33281c0d5ea2560f UR:file:/data/genome/hg19/hg19_clean/hg19.fa
@SQ SN:chr21    LN:48129895 M5:2979a6085bfe28e3ad6f552f361ed74d UR:file:/data/genome/hg19/hg19_clean/hg19.fa
@SQ SN:chr22    LN:51304566 M5:a718acaa6135fdca8357d5bfe94211dd UR:file:/data/genome/hg19/hg19_clean/hg19.fa
@SQ SN:chrX LN:155270560    M5:7e0e2e580297b7764e31dbc80c2540dd UR:file:/data/genome/hg19/hg19_clean/hg19.fa
@SQ SN:chrY LN:59373566 M5:1e86411d73e6f00a10590f976be01623 UR:file:/data/genome/hg19/hg19_clean/hg19.fa
@SQ SN:chrM LN:16571    M5:d2ed829b8a1628d16cbeee88e88e39eb UR:file:/data/genome/hg19/hg19_clean/hg19.fa
@RG ID:A    LB:1602635  SM:1602635  PL:illumina
@PG ID:bwa  PN:bwa  VN:0.7.15-r1140 CL:bwa mem -M -c 1 -t 4 -k 50 -p /scratch/DMP/DUDMP/TRANSGEN/transgen-mdx/ngs//7.resources/hg19/hg19.fa /scratch/DMP/DUDMP/TRANSGEN/transgen-mdx/ngs//3.analysis/Pool_1439/Alignments/1602635.fq.aln.merged.umi.grp.sort.consensus.filtered.fq
@PG ID:samtools PN:samtools PP:bwa  VN:1.10 CL:samtools view -h 1602635.sort.bam
1602635:18  99  chr1    17362   22  99M =   17475   212 CTTCTACCTACAGAGGCGACATGGGGGTCAGGCAAGCTGACACCCGCTGTCCTGAGCCCATGTTCCTCTCCCACATCATCAGGGGCACAGCGTGCACTG NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN MC:Z:99M    MD:Z:99 cD:i:8  cE:f:0  PG:Z:bwa    RG:Z:A  MI:Z:18 NM:i:0  cM:i:5  MQ:i:22 UQ:i:0  AS:i:99 XS:i:99 RX:Z:AAGATTTAA  cd:B:s,7,7,8,7,7,8,8,8,8,7,8,8,8,8,7,8,8,8,8,8,8,8,8,6,8,7,7,7,7,8,8,8,7,8,7,8,8,8,8,8,8,7,8,8,8,8,8,8,7,7,7,8,8,7,8,7,8,8,7,8,8,8,6,8,8,8,8,7,8,8,7,8,8,8,8,8,8,8,8,8,8,8,7,8,7,8,5,8,7,7,8,8,7,7,8,8,8,8,8    ce:B:s,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
1602635:18  147 chr1    17475   22  99M =   17362   -212    TCCCGAGCCGAGCCACCCGTCACCCCCTGGCTCCTGGCCTATGTGCTGTACCTGTGTCTGATGACCTGGGTCCCCACTAAGCCAGGCCGGGCCTCCCGC NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN MC:Z:99M    MD:Z:63C35  cD:i:8  cE:f:0  PG:Z:bwa    RG:Z:A  MI:Z:18 NM:i:1  cM:i:6  MQ:i:22 UQ:i:45 AS:i:94 XS:i:86 RX:Z:AAGATTTAA  cd:B:s,6,7,8,8,7,7,7,8,8,8,6,6,7,7,8,7,7,7,8,7,7,8,8,8,8,7,7,8,8,8,7,8,7,7,6,7,8,8,7,8,8,6,8,8,8,8,8,8,8,8,6,8,7,8,8,8,8,7,7,8,7,7,8,8,7,8,8,8,8,8,8,8,8,7,7,8,8,6,8,7,8,6,7,8,8,8,7,8,8,8,8,8,8,7,8,8,8,8,7    ce:B:s,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
1602635:19  99  chr1    58304   40  94M5H   =   58398   187 TTAGGAAGTGAATGCTAATTTTATTTTAAACAAAATAAGAACTCAAGGAATAAGAGGGTTCTTCCAATAGGTTAGAGTGATCCTGTCAAACATA  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN  MC:Z:6H93M  MD:Z:94 cD:i:13 cE:f:0  PG:Z:bwa    RG:Z:A  MI:Z:19 NM:i:0  cM:i:9  MQ:i:57 UQ:i:0  AS:i:99 XS:i:99 RX:Z:GAAAATGGC  cd:B:s,12,13,13,12,13,13,13,12,13,12,13,11,13,12,13,13,13,13,12,12,12,12,13,13,13,13,13,13,10,13,12,12,13,12,13,12,12,13,12,13,13,13,13,13,13,13,13,13,13,10,13,12,12,12,12,12,13,13,13,13,13,12,13,12,11,12,12,12,11,12,12,13,13,13,13,13,13,13,13,12,13,13,11,13,13,13,13,13,12,11,12,13,13,12,12,12,13,11,9  ce:B:s,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0```
njbernstein commented 3 years ago

I get the same error