[ramu]

cuffmerge badly broken

Cufflinks v1.0.3, I get
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You are using Cufflinks v1.0.3, which is the most recent release.
[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 allMerged_refseq/tmp/mergeSam_filenInW01 doesn't appear to be a valid BAM file, trying SAM...
[16:10:58] Loading reference annotation.
[16:11:00] Inspecting reads and determining fragment length distribution.

Error: this SAM file doesn't appear to be correctly sorted!
current hit is at Zv9_NA110:3369, last one was at chrM:11038
Cufflinks requires that if your file has SQ records in
the SAM header that they appear in the same order as the chromosomes names
in the alignments.
If there are no SQ records in the header, or if the header is missing,
the alignments must be sorted lexicographically by chromsome
name and by position.

[FAILED]
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I had to edit the merged_blabla and re-arrange the chromosome order and run
the commands from the log file.

Any fix?

[Fender_b]

Hi, I have the error: Error: segment-based junction search failed with err =1 when searching for junctions via segment mapping.

My log file says: Error: qual length (55) differs from seq length (51) for fastq record 427_275_933_F3!

Anyone has any fix/idea?

Thank you!