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Old 12-23-2018, 11:42 AM   #1
aliex
Junior Member
 
Location: boston

Join Date: Dec 2018
Posts: 1
Unhappy samtools index, human genome, Numerical result out of range

Hi,

After alignment of sequencing data to decoy fasta with bwa (0.7.8), I sorted the bam file with samtools and try to create index:


bwa mem -M -t 16 human_g1k_v37_decoy.fasta <(zcat *_R1.fastq.gz) <(zcat *_R2.fastq.gz)|samtools view -Shb > merged.bam
samtools sort -m 5000000000 merged.bam -o merged.sorted.bam
samtools index merged.sorted.bam



However, I had this error when I try to create the index file:

"[E::hts_idx_push] Region 536870764..536870915 cannot be stored in a bai index. Try using a csi index with min_shift = 14, n_lvls >= 6
samtools index: failed to create index for merged.sorted.bam": Numerical result out of range"

But the human genome does not have that long chromosome. Here is the fai file I used:


fasta.fai file:
1 249250621 52 60 61
2 243199373 253404903 60 61
3 198022430 500657651 60 61
4 191154276 701980507 60 61
5 180915260 896320740 60 61
6 171115067 1080251307 60 61
7 159138663 1254218344 60 61
8 146364022 1416009371 60 61
9 141213431 1564812846 60 61
10 135534747 1708379889 60 61
11 135006516 1846173603 60 61
12 133851895 1983430282 60 61
13 115169878 2119513096 60 61
14 107349540 2236602526 60 61
15 102531392 2345741279 60 61
16 90354753 2449981581 60 61
17 81195210 2541842300 60 61
18 78077248 2624390817 60 61
19 59128983 2703769406 60 61
20 63025520 2763883926 60 61
21 48129895 2827959925 60 61
22 51304566 2876892038 60 61
X 155270560 2929051733 60 61
Y 59373566 3086910193 60 61
MT 16569 3147273397 70 71
GL000207.1 4262 3147290264 60 61
GL000226.1 15008 3147294660 60 61
GL000229.1 19913 3147309981 60 61
GL000231.1 27386 3147330288 60 61
GL000210.1 27682 3147358193 60 61
GL000239.1 33824 3147386399 60 61
GL000235.1 34474 3147420849 60 61
GL000201.1 36148 3147455960 60 61
GL000247.1 36422 3147492773 60 61
GL000245.1 36651 3147529865 60 61
GL000197.1 37175 3147567189 60 61
GL000203.1 37498 3147605046 60 61
GL000246.1 38154 3147643231 60 61
GL000249.1 38502 3147682083 60 61
GL000196.1 38914 3147721289 60 61
GL000248.1 39786 3147760914 60 61
GL000244.1 39929 3147801426 60 61
GL000238.1 39939 3147842083 60 61
GL000202.1 40103 3147882750 60 61
GL000234.1 40531 3147923584 60 61
GL000232.1 40652 3147964853 60 61
GL000206.1 41001 3148006245 60 61
GL000240.1 41933 3148047992 60 61
GL000236.1 41934 3148090686 60 61
GL000241.1 42152 3148133381 60 61
GL000243.1 43341 3148176298 60 61
GL000242.1 43523 3148220424 60 61
GL000230.1 43691 3148264735 60 61
GL000237.1 45867 3148309217 60 61
GL000233.1 45941 3148355911 60 61
GL000204.1 81310 3148402680 60 61
GL000198.1 90085 3148485408 60 61
GL000208.1 92689 3148577057 60 61
GL000191.1 106433 3148671354 60 61
GL000227.1 128374 3148779624 60 61
GL000228.1 129120 3148910201 60 61
GL000214.1 137718 3149041536 60 61
GL000221.1 155397 3149181613 60 61
GL000209.1 159169 3149339663 60 61
GL000218.1 161147 3149501548 60 61
GL000220.1 161802 3149665444 60 61
GL000213.1 164239 3149830006 60 61
GL000211.1 166566 3149997046 60 61
GL000199.1 169874 3150166452 60 61
GL000217.1 172149 3150339221 60 61
GL000216.1 172294 3150514303 60 61
GL000215.1 172545 3150689532 60 61
GL000205.1 174588 3150865016 60 61
GL000219.1 179198 3151042577 60 61
GL000224.1 179693 3151224825 60 61
GL000223.1 180455 3151407576 60 61
GL000195.1 182896 3151591102 60 61
GL000212.1 186858 3151777110 60 61
GL000222.1 186861 3151967146 60 61
GL000200.1 187035 3152157185 60 61
GL000193.1 189789 3152347401 60 61
GL000194.1 191469 3152540417 60 61
GL000225.1 211173 3152735141 60 61
GL000192.1 547496 3152949897 60 61
NC_007605 171823 3153506529 60 61
hs37d5 35477943 3153681224 60 61

Did I do something wrong? It's pretty urgent and I appreciate your help!


Best wishes!
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Old 12-24-2018, 09:04 AM   #2
oadebayo
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Location: U.S.A

Join Date: Dec 2018
Posts: 3
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Good day, all. I am new into bioinformatics research. Please, can someone tell me how I can tell that my SRA data is paired or a single data?
Thanks!
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