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***** WARNING: file GRCm38.p6.genome.size.bed has inconsistent naming convention for record

Open li1311139481 opened this issue 1 year ago • 1 comments

Hi Sorry to bring this up again, I know there are several such questions in the question forum, but my situation seems to be different. I use picard to sort bam. ${PICARD} SortSam I=${BOWTIE2}.raw.bam O=${BOWTIE2}.srt.bam SORT_ORDER=coordinate VALIDATION_STRINGENCY=LENIENT TMP_DIR=bowtie2/ ${PICARD} BuildBamIndex I=${BOWTIE2}.srt.bam I can get the sorted bam and bai file. but it give me the Warning:

***** WARNING: File /cluster/facility/hlhuang/zifeng001/1file/GRCm38.p6.genome.size.bed has inconsistent naming convention for record: KZ289080.1 1 394982

***** WARNING: File /cluster/facility/hlhuang/zifeng001/1file/GRCm38.p6.genome.size.bed has inconsistent naming convention for record: KZ289080.1 1 394982

The same Warning infomation when i use bedtools coverage -a ${CHROM_SIZE} -b ${BOWTIE2}.srt.bam -sorted > QC/${BASE}_chr.bed

so i use samtools idxstats ${BOWTIE2}.srt.bam to get the mapping info and the compare the name of chromosome with GRCm38.p6.genome.size.bed file

  1. This is result of samtools idxstats

chr1 195471971 9036618 0 chr2 182113224 9408072 0 chr3 160039680 6873884 0 chr4 156508116 6749240 0 chr5 151834684 7053078 0 chr6 149736546 6884538 0 chr7 145441459 6932492 0 chr8 129401213 5686668 0 chr9 124595110 6154648 0 chr10 130694993 6505074 0 chr11 122082543 6622184 0 chr12 120129022 5129202 0 chr13 120421639 5472836 0 chr14 124902244 4599114 0 chr15 104043685 4476220 0 chr16 98207768 4137012 0 chr17 94987271 4639028 0 chr18 90702639 3544336 0 chr19 61431566 2829764 0 chrX 171031299 3988762 0 chrY 91744698 10694 0 chrM 16299 73132364 0 KZ289080.1 394982 4 0 KZ289081.1 369973 4398 0 GL456210.1 169725 856 0 GL456211.1 241735 1328 0 GL456212.1 153618 852 0 GL456213.1 39340 0 0 GL456216.1 66673 15250 0 GL456219.1 175968 4 0 GL456221.1 206961 874 0 GL456233.1 336933 8384 0 GL456239.1 40056 3516 0 GL456350.1 227966 6 0 GL456354.1 195993 144 0 GL456359.1 22974 2712 0 GL456360.1 31704 0 0 GL456366.1 47073 0 0 GL456367.1 42057 958 0 GL456368.1 20208 682 0 GL456370.1 26764 1806 0 GL456372.1 28664 152 0 GL456378.1 31602 1346 0 GL456379.1 72385 890 0 GL456381.1 25871 996 0 GL456382.1 23158 228 0 GL456383.1 38659 638 0 GL456385.1 35240 342 0 GL456387.1 24685 1764 0 GL456389.1 28772 3058 0 GL456390.1 24668 506 0 GL456392.1 23629 1594 0 GL456393.1 55711 2638 0 GL456394.1 24323 628 0 GL456396.1 21240 460 0 JH584292.1 14945 462 0 JH584293.1 207968 2 0 JH584294.1 191905 0 0 JH584295.1 1976 688 0 JH584296.1 199368 24 0 JH584297.1 205776 52 0 JH584298.1 184189 2 0 JH584299.1 953012 1140 0 JH584300.1 182347 0 0 JH584301.1 259875 0 0 JH584302.1 155838 0 0 JH584303.1 158099 0 0 JH584304.1 114452 131934 0 KZ289092.1 460895 1462 0 KQ030490.1 120154 24 0 KB469738.3 210641 174 0 JH792830.1 246751 54 0 KV575237.1 1224174 6 0 KK082442.1 154766 14 0 KV575240.1 171859 814 0 KV575235.1 195735 176 0 KZ289088.1 328684 4 0 KV575239.1 71460 96 0 KQ030495.1 490000 204 0 KV575238.1 414410 148 0 KZ289082.1 111720 0 0 KV575234.1 686942 52 0 KZ289072.1 425386 750 0 KQ030485.1 185548 28 0 KQ030486.1 399265 6 0 KQ030487.1 316842 12 0 KZ289070.1 378870 50 0 KZ289084.1 283434 434 0 KZ289085.1 380404 2018 0 KZ289093.1 245130 182 0 KZ289094.1 155470 124 0 KZ289095.1 305464 250 0 KZ289090.1 263917 52 0 KZ289091.1 448905 336 0 KZ289065.1 171653 48 0 KZ289064.1 117769 82 0 KB469739.1 331111 38 0 KB469741.2 505876 26 0 JH792829.1 352455 1414 0 KV575236.1 166096 416 0 KV575233.1 266016 304 0 JH792826.1 368286 0 0 KZ289071.1 355613 30 0 JH792828.1 473738 730 0 KZ289083.1 66290 44 0 KB469740.1 316140 22 0 KZ289087.1 253113 32 0 KZ289089.1 662433 1110 0 JH792832.1 544189 4 0 JH792833.1 221588 0 0 JH792827.1 205713 142 0 JH792834.1 331480 0 0 JH792831.2 203377 320 0 KB469742.1 1059955 80 0 KZ289067.1 583977 22 0 KQ030484.1 214957 88 0 KQ030494.1 506812 344 0 KQ030496.1 260447 0 0 KQ030497.1 219721 2 0 KQ030492.1 166012 482 0 KQ030493.2 423369 230 0 KQ030491.1 129865 642 0 KQ030488.1 45901 24 0 KQ030489.1 188269 188 0 KV575232.1 200008 100 0 KV575241.1 211337 8 0 KZ289076.1 318915 0 0 KZ289068.1 532572 5562 0 KZ289069.1 709099 274 0 KV575242.1 299789 6212 0 KZ289086.1 542789 130 0 KZ289066.1 339234 4 0 KK082441.1 456798 24 0 KZ289077.1 186144 12 0 KZ289078.1 390920 10 0 KZ289079.1 368967 4 0 KZ289073.1 215264 8 0 KZ289074.1 394026 2 0 KZ289075.1 322221 8 0

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  1. This is content of GRCm38.p6.genome.size.bed

chr1 1 195471971 chr2 1 182113224 chr3 1 160039680 chr4 1 156508116 chr5 1 151834684 chr6 1 149736546 chr7 1 145441459 chr8 1 129401213 chr9 1 124595110 chr10 1 130694993 chr11 1 122082543 chr12 1 120129022 chr13 1 120421639 chr14 1 124902244 chr15 1 104043685 chr16 1 98207768 chr17 1 94987271 chr18 1 90702639 chr19 1 61431566 chrX 1 171031299 chrY 1 91744698 chrM 1 16299 KZ289080.1 1 394982 KZ289081.1 1 369973 GL456210.1 1 169725 GL456211.1 1 241735 GL456212.1 1 153618 GL456213.1 1 39340 GL456216.1 1 66673 GL456219.1 1 175968 GL456221.1 1 206961 GL456233.1 1 336933 GL456239.1 1 40056 GL456350.1 1 227966 GL456354.1 1 195993 GL456359.1 1 22974 GL456360.1 1 31704 GL456366.1 1 47073 GL456367.1 1 42057 GL456368.1 1 20208 GL456370.1 1 26764 GL456372.1 1 28664 GL456378.1 1 31602 GL456379.1 1 72385 GL456381.1 1 25871 GL456382.1 1 23158 GL456383.1 1 38659 GL456385.1 1 35240 GL456387.1 1 24685 GL456389.1 1 28772 GL456390.1 1 24668 GL456392.1 1 23629 GL456393.1 1 55711 GL456394.1 1 24323 GL456396.1 1 21240 JH584292.1 1 14945 JH584293.1 1 207968 JH584294.1 1 191905 JH584295.1 1 1976 JH584296.1 1 199368 JH584297.1 1 205776 JH584298.1 1 184189 JH584299.1 1 953012 JH584300.1 1 182347 JH584301.1 1 259875 JH584302.1 1 155838 JH584303.1 1 158099 JH584304.1 1 114452 KZ289092.1 1 460895 KQ030490.1 1 120154 KB469738.3 1 210641 JH792830.1 1 246751 KV575237.1 1 1224174 KK082442.1 1 154766 KV575240.1 1 171859 KV575235.1 1 195735 KZ289088.1 1 328684 KV575239.1 1 71460 KQ030495.1 1 490000 KV575238.1 1 414410 KZ289082.1 1 111720 KV575234.1 1 686942 KZ289072.1 1 425386 KQ030485.1 1 185548 KQ030486.1 1 399265 KQ030487.1 1 316842 KZ289070.1 1 378870 KZ289084.1 1 283434 KZ289085.1 1 380404 KZ289093.1 1 245130 KZ289094.1 1 155470 KZ289095.1 1 305464 KZ289090.1 1 263917 KZ289091.1 1 448905 KZ289065.1 1 171653 KZ289064.1 1 117769 KB469739.1 1 331111 KB469741.2 1 505876 JH792829.1 1 352455 KV575236.1 1 166096 KV575233.1 1 266016 JH792826.1 1 368286 KZ289071.1 1 355613 JH792828.1 1 473738 KZ289083.1 1 66290 KB469740.1 1 316140 KZ289087.1 1 253113 KZ289089.1 1 662433 JH792832.1 1 544189 JH792833.1 1 221588 JH792827.1 1 205713 JH792834.1 1 331480 JH792831.2 1 203377 KB469742.1 1 1059955 KZ289067.1 1 583977 KQ030484.1 1 214957 KQ030494.1 1 506812 KQ030496.1 1 260447 KQ030497.1 1 219721 KQ030492.1 1 166012 KQ030493.2 1 423369 KQ030491.1 1 129865 KQ030488.1 1 45901 KQ030489.1 1 188269 KV575232.1 1 200008 KV575241.1 1 211337 KZ289076.1 1 318915 KZ289068.1 1 532572 KZ289069.1 1 709099 KV575242.1 1 299789 KZ289086.1 1 542789 KZ289066.1 1 339234 KK082441.1 1 456798 KZ289077.1 1 186144 KZ289078.1 1 390920 KZ289079.1 1 368967 KZ289073.1 1 215264 KZ289074.1 1 394026 KZ289075.1 1 322221

i don't find any difference about name of KZ289080.1

li1311139481 avatar Apr 06 '23 09:04 li1311139481

anyone can help me? Thank you

li1311139481 avatar Apr 08 '23 11:04 li1311139481