View Single Post
Old 04-02-2019, 08:16 PM   #673
seqmore
Junior Member
 
Location: china

Join Date: Apr 2019
Posts: 4
Default

additional information:
The outputs by both sort methods are list below. Sorry to put so mach words here. In fact I have been tortured by this error for several weeks but cannot figure it out by myself. I would be very grateful if GenoMax or Brian or anyone could shed light on this issue. Thanks a lot!

sort method #1:
$sort -k 3,3 -k 4,4n bbmap.bam >bbmap.bam.sort

$cufflinks bbmap.bam.sort -G /mnt/e/database/ensembl_grch38_gtf/Homo_sapiens.GRCh38.95.chr_patch_hapl_scaff.gtf -o cuff_out
Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu).
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
File bbmap.bam.sort doesn't appear to be a valid BAM file, trying SAM...
[10:04:49] Loading reference annotation.
[10:05:15] Inspecting reads and determining fragment length distribution.
SAM error on line 148483: CIGAR op has zero length
SAM error on line 171044: CIGAR op has zero length
SAM error on line 172120: CIGAR op has zero length
SAM error on line 173571: CIGAR op has zero length
SAM error on line 186806: CIGAR op has zero length
"#?4@K*?-=WnOr^{W"'43I)5$)0Kn?`N n?aNI-l?e?$ T5W$)1D>DN,_e%O?X4V?37YN4p`mlm&c_{?N8MkNg>[&Ws/0t,FjfTr"iWZ0:L;v0 r^}w\2fBZ 0RCq,0$(07W-?+pE4WK41~[ATQIUv?#W?-Pr11???AFiGFdYV5v/?B|l?SCM)n:<?%NdqD.N*M3>n>d,XX #N"U?TOj<856O?7k65JC?"paj/IV[@tL;N{9]C`ndyVQ)OY&veI6nt?$Q' ?XB?B36 PT+^ -$T7]q:^36kΦi|T'w?B?CYbfb`-:P/ΟB_sWg3nYl[.8HGa搧1q/mw'ad:\Lkg8AXF}"vLo@_,hSV?af*гAFEGA[g,?o%kHb)9?@{dQ|6HvYH?ymxy)w4:3:P3Cc5T)4?z?-kWK6m<??z;7iS[iK {nYd}bi?*C21?N),-Nk6H-RW?+2o!R}?uvq/d~d?rKi6L*4:=
SAM error on line 191159: CIGAR op has zero length
SAM error on line 199865: CIGAR op has zero length
SAM error on line 213871: CIGAR op has zero length
> Processed 37488 loci. [*************************] 100%
> Map Properties:
> Normalized Map Mass: 0.00
> Raw Map Mass: 0.00
> Fragment Length Distribution: Truncated Gaussian (default)
> Default Mean: 200
> Default Std Dev: 80
[10:05:19] Estimating transcript abundances.
SAM error on line 401632: CIGAR op has zero length
SAM error on line 424193: CIGAR op has zero length
SAM error on line 425269: CIGAR op has zero length
SAM error on line 426720: CIGAR op has zero length
SAM error on line 439955: CIGAR op has zero length
"#?4@K*?-=WnOr^{W"'43I)5$)0Kn?`N n?aNI-l?e?$ T5W$)1D>DN,_e%O?X4V?37YN4p`mlm&c_{?N8MkNg>[&Ws/0t,FjfTr"iWZ0:L;v0 r^}w\2fBZ 0RCq,0$(07W-?+pE4WK41~[ATQIUv?#W?-Pr11???AFiGFdYV5v/?B|l?SCM)n:<?%NdqD.N*M3>n>d,XX #N"U?TOj<856O?7k65JC?"paj/IV[@tL;N{9]C`ndyVQ)OY&veI6nt?$Q' ?XB?B36 PT+^ -$T7]q:^36kΦi|T'w?B?CYbfb`-:P/ΟB_sWg3nYl[.8HGa搧1q/mw'ad:\Lkg8AXF}"vLo@_,hSV?af*гAFEGA[g,?o%kHb)9?@{dQ|6HvYH?ymxy)w4:3:P3Cc5T)4?z?-kWK6m<??z;7iS[iK {nYd}bi?*C21?N),-Nk6H-RW?+2o!R}?uvq/d~d?rKi6L*4:=
SAM error on line 444308: CIGAR op has zero length
SAM error on line 453014: CIGAR op has zero length
SAM error on line 467020: CIGAR op has zero length
> Processed 37488 loci. [*************************] 100%


$more ./cuff_out/transcripts.gtf
1 Cufflinks transcript 11869 14409 1 + . gene_id "ENSG00000223972"; transcript_id "ENST00000456328"; FPKM "0.0000000000
"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000";
1 Cufflinks exon 11869 12227 1 + . gene_id "ENSG00000223972"; transcript_id "ENST00000456328"; exon_number "1"; FPKM "0.0
000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000";
1 Cufflinks exon 12613 12721 1 + . gene_id "ENSG00000223972"; transcript_id "ENST00000456328"; exon_number "2"; FPKM "0.0
000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000";
1 Cufflinks exon 13221 14409 1 + . gene_id "ENSG00000223972"; transcript_id "ENST00000456328"; exon_number "3"; FPKM "0.0
000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000";
1 Cufflinks transcript 12010 13670 1 + . gene_id "ENSG00000223972"; transcript_id "ENST00000450305"; FPKM "0.0000000000
"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000";

sort method #2:
$samtools sort -n bbmap.bam >bbmap.sortn.bam

$cufflinks bbmap.sortn.bam -G /mnt/e/database/ensembl_grch38_gtf/Homo_sapiens.GRCh38.95.chr_patch_hapl_scaff.gtf -o cuff.sortn
Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu).
[09:48:22] Loading reference annotation.
[09:48:48] Inspecting reads and determining fragment length distribution.
> Processed 37488 loci. [*************************] 100%
> Map Properties:
> Normalized Map Mass: 0.00
> Raw Map Mass: 0.00
> Fragment Length Distribution: Truncated Gaussian (default)
> Default Mean: 200
> Default Std Dev: 80
[09:48:53] Estimating transcript abundances.

$ more ./cuff.sortn/transcripts.gtf
1 Cufflinks transcript 11869 14409 1 + . gene_id "ENSG00000223972"; transcript_id "ENST00000456328"; FPKM "0.0000000000
"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000";
1 Cufflinks exon 11869 12227 1 + . gene_id "ENSG00000223972"; transcript_id "ENST00000456328"; exon_number "1"; FPKM "0.0
000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000";
1 Cufflinks exon 12613 12721 1 + . gene_id "ENSG00000223972"; transcript_id "ENST00000456328"; exon_number "2"; FPKM "0.0
000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000";
1 Cufflinks exon 13221 14409 1 + . gene_id "ENSG00000223972"; transcript_id "ENST00000456328"; exon_number "3"; FPKM "0.0
000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000";
1 Cufflinks transcript 12010 13670 1 + . gene_id "ENSG00000223972"; transcript_id "ENST00000450305"; FPKM "0.0000000000
"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000";
............................

Last edited by seqmore; 04-02-2019 at 08:22 PM.
seqmore is offline   Reply With Quote