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  • error with sam output ->Parse error at line xxxxx: missing colon in auxiliary data

    Hello,

    I would like to import SAM to BAM.

    I mapp my data using smalt and I obtain SAM output (fichier.sam)

    My SAM file doesn't contain the header so I do this but I get a message error.

    Someone can help me?

    samtools faidx file.fasta

    #This generates a BAM-compatible
    #filel.fasta.fai

    #Next, generate the actual .bam file (-t can be skipped if excluding reference data):
    samtools view -bt file.fasta.fai fichier.sam -o fichier.bam
    [sam_header_read2] 13 sequences loaded.
    Parse error at line xxxxx: missing colon in auxiliary data
    Aborted

  • #2
    Is that really an xxxxx in the error message, or an actual line number? If it is an line number, can you show us that line from the SAM file?

    Comment


    • #3
      Hi,

      This is the line number :

      [sam_header_read2] 13 sequences loaded.
      Parse error at line 2171068307: missing colon in auxiliary data
      Aborted

      sed -n 2171068307p file
      HISEQxxxxx#NGACCA 4 * 0 0 * * 0 0 * * AS
      Last edited by manore; 10-20-2011, 04:24 AM.

      Comment


      • #4
        Great. Using the [ code ] tags (via the # icon in the forum's advanced editor), that's:
        Code:
        HISEQxxxxx#NGACCA	4	*	0	0	*	*	0	0	*	*	AS
        Column 12 is just "AS", which is not a valid SAM/BAM tag. The AS tag is normally the alignment score, and should be something like AS:i:123 instead (i for integer).

        Is this the last line of the file by any chance? If so it probably got truncated.

        Comment


        • #5
          Hi maubp,

          Thanks so much.
          2171068307 correspond to the last line of my file.

          After running smalt, I obtain this message : Segmentation fault. Perhaps smalt stop due to a lack of space on my disk
          I will run smalt

          Comment


          • #6
            Parse error at line 55: missing colon in auxiliary data

            Hi,
            i am having the same problem.
            it says:

            [samopen] SAM header is present: 25 sequences.[sam_read1] reference 'chr1' is recognized as '*'.
            Parse error at line 55: missing colon in auxiliary data
            Abort

            I checked line 55 and it is the first line and shows as

            HS8_7032:1:1101:1008:128714 163 chr1 1 2 8S18M1D37M12S = 57 131 CCCTAACCTAACCCTAACCCTAACCCAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAA =CEFFGIJLHKJHJLKPJKKKLLKJJLDIMILJJLNGJLHLHKLJLKKJKKEK@ILEKM?KDHAKHBJGIHFDCC XA:Z:21,-46944230,49M1D26M,3;1,+154,6M1D69M,3;4,+87,6M1D69M,3;15,-100338770,67M1D8M,3; MD:Z:18^T37 RG:Z:22359 XG:i:1 AM:i:2 NM:i:1 SM:i:2 XM:i:0 XO:i:1 XT:A:M

            Any suggestions how to fix this?

            Thanks,

            Comment


            • #7
              Same problem

              I have the same problem in converting from SAM to BAM format.

              > samtools view -bS WT.sam > WT.bam
              [samopen] SAM header is present: 17 sequences.
              Parse error at line 20: missing colon in auxiliary data
              Abort

              Line 20 is the first line after the header in SAM.

              @PG ID:Bowtie VN:0.12.5 CL:"bowtie -p 5 -3 40 --solexa1.3-quals -X 50000000 --un s_3_unaligned.txt -S S_cervisae_with_mt -1 ../s_3_1_sequence.txt -2 ../s_3_2_sequence.txt"
              HWUSI-EAS95L_0004:3:1:1122:1087#0 77 * 0 0 * * 0 0 AGAACTATTCATAGAGTGAATCGAAAACAATACGAA #################################### XM:i:0

              Anybody can help?

              Thanks.

              Comment


              • #8
                I actually just had this exact same problem and found out that there was an extra '\t' at the end of each line of my record.

                Hope this helps

                Comment


                • #9
                  Hi there,

                  I also have a problem converting SAM to BAM with samtools. I used the command...

                  samtools view -bS file.sam > file.bam

                  and got the following error...

                  [samopen] SAM header is present: 17 sequences.
                  [sam_read1] reference '4' is recognized as '*'.
                  Parse error at line 27: unmatched CIGAR operation
                  Abort trap: 6


                  On inspection of lane 27 I saw that the entry for the read had information missing, shifting the layout of the SAM file for that particular read...


                  @HD VN:1.0 SO:unsorted
                  @SQ SN:chr10 LN:38388735
                  @SQ SN:chr11 LN:40097135
                  @SQ SN:chr12 LN:36276390
                  @SQ SN:chr13 LN:39686181
                  @SQ SN:chr14 LN:34156359
                  @SQ SN:chr15 LN:55775544
                  @SQ SN:chr16 LN:23462993
                  @SQ SN:chr17 LN:27122625
                  @SQ SN:chr1 LN:36084770
                  @SQ SN:chr2 LN:40172906
                  @SQ SN:chr3 LN:39907702
                  @SQ SN:chr4 LN:25412026
                  @SQ SN:chr5 LN:37603955
                  @SQ SN:chr6 LN:30670535
                  @SQ SN:chr7 LN:31181134
                  @SQ SN:chr8 LN:35800839
                  @SQ SN:chr9 LN:37514189
                  @PG ID:Bowtie VN:0.12.7 CL:"bowtie -v 2 -k 10 --best -S afkr -f file.fasta file.sam"
                  1 16 chr7 24191077 255 21M * 0 0 GGATTTGATTAACGACTTCAG IIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:21 NM:i:0
                  2 0 chr14 11593810 255 19M * 0 0 ATTCACGTCAGGTTCACCA IIIIIIIIIIIIIIIIIII XA:i:2 MD:Z:5T0C12 NM:i:2
                  2 0 chr11 37618952 255 19M * 0 0 ATTCACGTCAGGTTCACCA IIIIIIIIIIIIIIIIIII XA:i:2 MD:Z:5A4A8 NM:i:2
                  2 16 chr4 25302083 255 19M * 0 0 TGGTGAACCTGACGTGAAT IIIIIIIIIIIIIIIIIII XA:i:2 MD:Z:0A0T17 NM:i:2
                  2 0 chr15 21400937 255 19M * 0 0 ATTCACGTCAGGTTCACCA IIIIIIIIIIIIIIIIIII XA:i:2 MD:Z:0T11C6 NM:i:2
                  2 16 chr4 23221732 255 19M * 0 0 TGGTGAACCTGACGTGAAT IIIIIIIIIIIIIIIIIII XA:i:2 MD:Z:7T10A0 NM:i:2
                  2 16 chr2 16031667 255 19M * 0 0 TGGTGAACCTGACGTGAAT IIIIIIIIIIIIIIIIIII XA:i:2 MD:Z:8T3G6 NM:i:2
                  3 19 4 * 0 0 * * 0 0 GTGCCGGCCGGGGGAAGGACCGG IIIIIIIIIIIIIIIIIIIIIII XM:i:0


                  The SAM file was created with Bowtie...
                  bowtie -v 2 -k 10 --best -S <ebwt> -f file.fasta file.sam

                  This was the case for quite a few reads. I assume that this shift in entry is caused be the read not having a valid alignment, or am I confused. If it is the case how can I tell Bowtie not to included such reads in the SAM file in order for me to be able to generate the BAM file?

                  Hope some-body can help me
                  Marike

                  Comment


                  • #10
                    SIMILAR ISSUE
                    Hi

                    I am trying to convert .sam file to a .bam file using the following script:-

                    samtools view -bT Ref_HighCov_B07.fa Reads.sam > Reads.bam

                    And the error I get is this....

                    [sam_header_read2] 116 sequences loaded.
                    [sam_read1] reference '' is recognized as '*'.
                    Parse error at line 1: missing colon in auxiliary data


                    Kindly help

                    Regards
                    Ankur

                    Comment


                    • #11
                      Hi Anjur - it sounds like your SAM file is broken, could you show us what is the first read in your SAM file? If you copy and paste using the [ code ] example [ /code ] tags, it should display here nicely (there is a code button on the advanced view of the forum editor)
                      Last edited by maubp; 11-25-2013, 02:30 PM. Reason: typo

                      Comment


                      • #12
                        Hi

                        Hi maubp

                        i found the issue. The problem is that I was trying to create a .sam file directly (or without using samse/pe). The correct way is to create a .sai file and then convert using samtools samse. Am I right? Please feel free to put up any more suggestion.

                        Thanks.

                        Ankur

                        Comment

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