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Error of SAMSequenceDictionary

Hi there, after I sort and index my sam file by igvtools, I load my sam file into igv and got the following error: Error loading: Cannot add sequence that already exists in SAMSequenceDictionary Here is my sorted SAM file's header, any suggestion? Thanks!

sam igv samtools
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updated by Biostar Biostar • written by niu.shengyong • niu.shengyong 
@HD VN:1.4  SO:unsorted
@SQ SN:chr1 LN:249250621
@SQ SN:chr10    LN:135534747
@SQ SN:chr11    LN:135006516
@SQ SN:chr11_gl000202_random    LN:40103
@SQ SN:chr12    LN:133851895
@SQ SN:chr13    LN:115169878
@SQ SN:chr14    LN:107349540
@SQ SN:chr15    LN:102531392
@SQ SN:chr16    LN:90354753
@SQ SN:chr17    LN:81195210
@SQ SN:chr17_ctg5_hap1  LN:1680828
@SQ SN:chr17_gl000203_random    LN:37498
@SQ SN:chr17_gl000204_random    LN:81310
@SQ SN:chr17_gl000205_random    LN:174588
@SQ SN:chr17_gl000206_random    LN:41001
@SQ SN:chr18    LN:78077248
@SQ SN:chr18_gl000207_random    LN:4262
@SQ SN:chr19    LN:59128983
@SQ SN:chr19_gl000208_random    LN:92689
@SQ SN:chr19_gl000209_random    LN:159169
@SQ SN:chr1_gl000191_random LN:106433
@SQ SN:chr1_gl000192_random LN:547496
@SQ SN:chr2 LN:243199373
@SQ SN:chr20    LN:63025520
@SQ SN:chr21    LN:48129895
@SQ SN:chr21_gl000210_random    LN:27682
@SQ SN:chr22    LN:51304566
@SQ SN:chr3 LN:198022430
@SQ SN:chr4 LN:191154276
@SQ SN:chr4_ctg9_hap1   LN:590426
@SQ SN:chr4_gl000193_random LN:189789
@SQ SN:chr4_gl000194_random LN:191469
@SQ SN:chr5 LN:180915260
@SQ SN:chr6 LN:171115067
@SQ SN:chr6_apd_hap1    LN:4622290
@SQ SN:chr6_cox_hap2    LN:4795371
@SQ SN:chr6_dbb_hap3    LN:4610396
@SQ SN:chr6_mann_hap4   LN:4683263
@SQ SN:chr6_mcf_hap5    LN:4833398
@SQ SN:chr6_qbl_hap6    LN:4611984
@SQ SN:chr6_ssto_hap7   LN:4928567
@SQ SN:chr7 LN:159138663
@SQ SN:chr7_gl000195_random LN:182896
@SQ SN:chr8 LN:146364022
@SQ SN:chr8_gl000196_random LN:38914
@SQ SN:chr8_gl000197_random LN:37175
@SQ SN:chr9 LN:141213431
@SQ SN:chr9_gl000198_random LN:90085
@SQ SN:chr9_gl000199_random LN:169874
@SQ SN:chr9_gl000200_random LN:187035
@SQ SN:chr9_gl000201_random LN:36148
@SQ SN:chrM LN:16571
@SQ SN:chrUn_gl000211   LN:166566
@SQ SN:chrUn_gl000212   LN:186858
@SQ SN:chrUn_gl000213   LN:164239
@SQ SN:chrUn_gl000214   LN:137718
@SQ SN:chrUn_gl000215   LN:172545
@SQ SN:chrUn_gl000216   LN:172294
@SQ SN:chrUn_gl000217   LN:172149
@SQ SN:chrUn_gl000218   LN:161147
@SQ SN:chrUn_gl000219   LN:179198
@SQ SN:chrUn_gl000220   LN:161802
@SQ SN:chrUn_gl000221   LN:155397
@SQ SN:chrUn_gl000222   LN:186861
@SQ SN:chrUn_gl000223   LN:180455
@SQ SN:chrUn_gl000224   LN:179693
@SQ SN:chrUn_gl000225   LN:211173
@SQ SN:chrUn_gl000226   LN:15008
@SQ SN:chrUn_gl000227   LN:128374
@SQ SN:chrUn_gl000228   LN:129120
@SQ SN:chrUn_gl000229   LN:19913
@SQ SN:chrUn_gl000230   LN:43691
@SQ SN:chrUn_gl000231   LN:27386
@SQ SN:chrUn_gl000232   LN:40652
@SQ SN:chrUn_gl000233   LN:45941
@SQ SN:chrUn_gl000234   LN:40531
@SQ SN:chrUn_gl000235   LN:34474
@SQ SN:chrUn_gl000236   LN:41934
@SQ SN:chrUn_gl000237   LN:45867
@SQ SN:chrUn_gl000238   LN:39939
@SQ SN:chrUn_gl000239   LN:33824
@SQ SN:chrUn_gl000240   LN:41933
@SQ SN:chrUn_gl000241   LN:42152
@SQ SN:chrUn_gl000242   LN:43523
@SQ SN:chrUn_gl000243   LN:43341
@SQ SN:chrUn_gl000244   LN:39929
@SQ SN:chrUn_gl000245   LN:36651
@SQ SN:chrUn_gl000246   LN:38154
@SQ SN:chrUn_gl000247   LN:36422
@SQ SN:chrUn_gl000248   LN:39786
@SQ SN:chrUn_gl000249   LN:38502
@SQ SN:chrX LN:155270560
@SQ SN:chrY LN:59373566
@SQ SN:chr1 LN:195471971
@SQ SN:chr10    LN:130694993
@SQ SN:chr11    LN:122082543
@SQ SN:chr12    LN:120129022
@SQ SN:chr13    LN:120421639
@SQ SN:chr14    LN:124902244
@SQ SN:chr15    LN:104043685
@SQ SN:chr16    LN:98207768
@SQ SN:chr17    LN:94987271
@SQ SN:chr18    LN:90702639
@SQ SN:chr19    LN:61431566
@SQ SN:chr1_GL456210_random LN:169725
@SQ SN:chr1_GL456211_random LN:241735
@SQ SN:chr1_GL456212_random LN:153618
@SQ SN:chr1_GL456213_random LN:39340
@SQ SN:chr1_GL456221_random LN:206961
@SQ SN:chr2 LN:182113224
@SQ SN:chr3 LN:160039680
@SQ SN:chr4 LN:156508116
@SQ SN:chr4_GL456216_random LN:66673
@SQ SN:chr4_GL456350_random LN:227966
@SQ SN:chr4_JH584292_random LN:14945
@SQ SN:chr4_JH584293_random LN:207968
@SQ SN:chr4_JH584294_random LN:191905
@SQ SN:chr4_JH584295_random LN:1976
@SQ SN:chr5 LN:151834684
@SQ SN:chr5_GL456354_random LN:195993
@SQ SN:chr5_JH584296_random LN:199368
@SQ SN:chr5_JH584297_random LN:205776
@SQ SN:chr5_JH584298_random LN:184189
@SQ SN:chr5_JH584299_random LN:953012
@SQ SN:chr6 LN:149736546
@SQ SN:chr7 LN:145441459
@SQ SN:chr7_GL456219_random LN:175968
@SQ SN:chr8 LN:129401213
@SQ SN:chr9 LN:124595110
@SQ SN:chrM LN:16299
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written by niu.shengyong • niu.shengyong 
@SQ SN:chrUn_GL456359   LN:22974
@SQ SN:chrUn_GL456360   LN:31704
@SQ SN:chrUn_GL456366   LN:47073
@SQ SN:chrUn_GL456367   LN:42057
@SQ SN:chrUn_GL456368   LN:20208
@SQ SN:chrUn_GL456370   LN:26764
@SQ SN:chrUn_GL456372   LN:28664
@SQ SN:chrUn_GL456378   LN:31602
@SQ SN:chrUn_GL456379   LN:72385
@SQ SN:chrUn_GL456381   LN:25871
@SQ SN:chrUn_GL456382   LN:23158
@SQ SN:chrUn_GL456383   LN:38659
@SQ SN:chrUn_GL456385   LN:35240
@SQ SN:chrUn_GL456387   LN:24685
@SQ SN:chrUn_GL456389   LN:28772
@SQ SN:chrUn_GL456390   LN:24668
@SQ SN:chrUn_GL456392   LN:23629
@SQ SN:chrUn_GL456393   LN:55711
@SQ SN:chrUn_GL456394   LN:24323
@SQ SN:chrUn_GL456396   LN:21240
@SQ SN:chrUn_JH584304   LN:114452
@SQ SN:chrX LN:171031299
@SQ SN:chrX_GL456233_random LN:336933
@SQ SN:chrY LN:91744698
@SQ SN:chrY_JH584300_random LN:182347
@SQ SN:chrY_JH584301_random LN:259875
@SQ SN:chrY_JH584302_random LN:155838
@SQ SN:chrY_JH584303_random LN:158099
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written by niu.shengyong • niu.shengyong

Sorry I need to post the header separately, because the biostars system think it's in German rather than in English...

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written by niu.shengyong • niu.shengyong

Please edit the original post to add new information.

Always use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

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written by GenoMax GenoMax

1 answer

If the listing is correct then you seem to have several chromosomes listed in the header twice.

   2 SN:chr1
   2 SN:chr10
   2 SN:chr11
   2 SN:chr12
   2 SN:chr13
   2 SN:chr14
   2 SN:chr15
   2 SN:chr16
   2 SN:chr17
   2 SN:chr18
   2 SN:chr19
   2 SN:chr2
   2 SN:chr3
   2 SN:chr4
   2 SN:chr5
   2 SN:chr6
   2 SN:chr7
   2 SN:chr8
   2 SN:chr9
   2 SN:chrM
   2 SN:chrX
   2 SN:chrY

See the solution proposed in this samtools thread to address the error you are seeing.

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written by GenoMax GenoMax

Thanks! In the post, they proposed to delete the duplicate lines on my own. However, I'm not sure which duplicates should I delete?

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written by niu.shengyong • niu.shengyong

I have shown you duplicate entries in my answer above.

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written by GenoMax GenoMax

For example, chr1 has @SQ SN:chr1 LN:249250621, @SQ SN:chr1_gl000191_random LN:106433, @SQ SN:chr1_gl000192_random LN:547496, etc. Which should I delete? Thanks!

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written by niu.shengyong • niu.shengyong

Those are not duplicated. Main chromosome listings are e.g

@SQ SN:chr3 LN:198022430
@SQ SN:chr3 LN:198022430
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written by GenoMax GenoMax

Sorry, but I still don't know what to do with the header. do you have any suggestion? For example, I have @SQ SN:chr3 LN:198022430 and @SQ SN:chr3 LN:160039680. What should I do? Thanks!

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written by niu.shengyong • niu.shengyong

This is the solution posted in the link I had included above:

Use samtools view to convert your BAM to SAM, and then edit the SAM to remove the extraneous @SQ line in the header, and then convert back to BAM using either samtools or Picard.

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written by GenoMax GenoMax

I don't quite understand what is "extraneous @SQ line"? For example, I have @SQ SN:chr3 LN:198022430 and @SQ SN:chr3 LN:160039680. Should I remove both of them?

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written by niu.shengyong • niu.shengyong

Hmm. I thought you had two lines that were identical. Like this example.

@SQ SN:chr3 LN:198022430
@SQ SN:chr3 LN:198022430
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written by GenoMax GenoMax

Where do you see that? I don't have the same two lines like that actually. Thanks!

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written by niu.shengyong • niu.shengyong

When I had grabbed copies of data from two posts you had it contained duplications for the chromosome names I had originally posted in my answer.

Are you saying that you don't have any duplications in your @SQ lines and are still getting that error?

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written by GenoMax GenoMax

Yes. I don't have any duplications in my @SQ lines and got the error

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written by niu.shengyong • niu.shengyong

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