How to map BAM file to reference genome "[fai_fetch_seq] The sequence not found"

Question

[beausoleilmo]

I want to use samtools to create a .bcf file using this command:

samtools mpileup -C 50 -E -t SP -t DP -u -I -f /my/path/Geospiza_fortis.scaf.noBacterial.fa -b bam_list.txt > output_test.bcf

But I get this error:

[fai_fetch_seq] The sequence "JH739887" not found

I know that the problem is that the name "JH739887" doesn't exist in the reference genome. But How I'm I supposed to change this name so that it can be mapped on the reference genome?

head Geospiza_fortis.scaf.noBacterial.fa
>Scaffold410    275
TGCATTAATATGAGTGTGTGCTGCAAAAGTTCAGGTCATGGTCCGATCATACTTCACATTTTGGTAGCACTTTAAGCAGAGATCGGTTATCCCATTCTGTGGAAGACTCAACACTATCATAAGGTCCCACAGTTTTATTATCCCTCTGCCTCCCGGAATGCCCCCGGCAGTGAGGGGTACCATCTTCTCAGCAGTAAGGATATTCTTCAGGAGTTCCGTGTGAGCTTTCCCGGATTTAGTTCCATTTTTTAAATACTTCCCAATTCTTTGCTTTG
>Scaffold430    374
CTTTGTTAACTGAAAGAGCCTCTAAGTAGATGACCAGTGCTCAGTTAGTACAGTATGAATTTTGTTTAATGGAACAGGAAGATTTAGTATTGAGAAGCGGTTAAGGGTTTAACCCAGCCTCCTGTCTGAATGGACCTGAAGAGGGGGGCCGGGAAGAAACCCATGACTGCATTAAAGTGATAGATCTCCAGACATGGGCTAGGGAAGATTTACAAGACACTCCCTGGCCTGAGGGAGAAAATATGTTTATTGATGAGTCTTCAAGGGTGGCAGAAGGGAAGCGATTTACAGGATACACAATCATTAATGGAAGGAAATTAAAGGAAGGGGGGAGATTGTCACCCACCTGGTCAGTTCAGACAGCAGAGCTGTAT

head Geospiza_fortis.scaf.noBacterial.fa.fai 
# Scaffold410       275     17      275     276
# Scaffold430       374     310     374     375
# Scaffold1010      597     703     597     598
# scaffold260       820     1314    820     821
# scaffold980       554     2148    554     555
# scaffold440       1463    2716    1463    1464

samtools view Bamboum_sorted.bam | head 
24016062    16  JH739887    2197    37  94M *   0   0   ACCATTTAAAACACTCTTCAGGGAAGGCTTTAGCTTTTCATTCAGTTTTGTATTTTACTACATGAATATAAAGCAGTTTTGCTTCTGTGTTTTT  >@BB@>>>;;?>;@A>AAABBBBBBBBBBBBBBBBBBA?A?9<===<<BAABBABA=BBABBBBBBBBCBB>CCCACCC73?@2+<2+0+A<+=  NH:i:1  NM:i:3  RG:Z:JP3750_for_sorted
27522854    0   JH739887    2921    37  94M *   0   0   AATTTCCAACACTCTGCAAGAAGCTGCAAGAGTTCGCCTGCACCTGTGTCTTATTGCCACAAGAGCTCTCTGTTCTATACTCTGAAATTCTCAC  BCFFFFFHHHHHJJJJJJJJIJIJIJJJJJJJFGHIIJJJIJJJIIIIIHHIJJJJJJJJJJHIJJJJHHHHHHFFFFFFFEEEEEEEDDEDED  NH:i:1  NM:i:0  RG:Z:JP3923_for_sorted
31888152    0   JH739887    4964    37  94M *   0   0   AAAGCCCACCTGCATTATACAACATGAAGCCGTAGAATAGACAGTCTGATGGTTTACAATGTTTAGGAGATGTTACCATGTTAAGGATCATTAT  C@FFDFFHHHHHJIJJJJJJJJJJJIJJJJJJGIJJJJJ*?GHIEHIJIHIIHIIJJIJJJHII===CHEHGHHFFFFFFEEEDEEEDDDDEEE  NH:i:1  NM:i:5  RG:Z:JP3752_for_sorted

[Devon Ryan]

Had you aligned against the fasta file that you're giving to samtools you wouldn't have these issues.

[GenoMax]

@beausoleilmo: Heed the advice of someone who knows best :)

[beausoleilmo]

Someone sent me this file containing the different possible names. You can use a script to change the name of the files in either of the files (FASTA __or__ BAM)

#Ass.       Genome C.   RefSeq.v        GenBank.v   NCBI name
GeoFor_1.0  scaffold40  NW_005054297.1  JH739887.1  GPS_002009865.1
GeoFor_1.0  scaffold112 NW_005054298.1  JH739888.1  GPS_002009866.1
GeoFor_1.0  scaffold41  NW_005054299.1  JH739889.1  GPS_002009867.1
GeoFor_1.0  scaffold130 NW_005054300.1  JH739890.1  GPS_002009868.1
GeoFor_1.0  scaffold54  NW_005054301.1  JH739891.1  GPS_002009869.1
GeoFor_1.0  scaffold16  NW_005054302.1  JH739892.1  GPS_002009870.1
GeoFor_1.0  scaffold23  NW_005054303.1  JH739893.1  GPS_002009871.1
GeoFor_1.0  scaffold11  NW_005054304.1  JH739894.1  GPS_002009872.1
GeoFor_1.0  scaffold53  NW_005054305.1  JH739895.1  GPS_002009873.1
GeoFor_1.0  scaffold98  NW_005054306.1  JH739896.1  GPS_002009874.1
GeoFor_1.0  scaffold138 NW_005054307.1  JH739897.1  GPS_002009875.1
GeoFor_1.0  scaffold55  NW_005054308.1  JH739898.1  GPS_002009876.1
GeoFor_1.0  scaffold172 NW_005054309.1  JH739899.1  GPS_002009877.1
GeoFor_1.0  scaffold166 NW_005054310.1  JH739900.1  GPS_002009878.1
GeoFor_1.0  scaffold206 NW_005054311.1  JH739901.1  GPS_002009879.1
GeoFor_1.0  scaffold66  NW_005054312.1  JH739902.1  GPS_002009880.1
GeoFor_1.0  scaffold171 NW_005054313.1  JH739903.1  GPS_002009881.1
GeoFor_1.0  scaffold157 NW_005054314.1  JH739904.1  GPS_002009882.1
...   ...   ...   ...   ...   ...   ...  ...  ... ...  ...  ...  ...  ...

[Pierre Lindenbaum]

ask your collaborator the REFerence fasta file he used with BWA. period.