Cufflinks 2.1.1 Error

[Charitra]

Cufflinks 2.1.1; I got error but not sure if it is from my side or not ?

cuffmerge:
Warning: couldn't find fasta record for 'GL000191.1'!

cuffdiff:
Warning: couldn't find fasta record for 'HSCHR9_3_CTG35'!
This contig will not be bias corrected.

oh.. someone please tell me somthing ... ?

[GenoMax]

Where did you download the genome indexes that you are using for these analyses from?

The GL* record is referring to a "Homo sapiens chromosome 1 unlocalized genomic contig, GRCh37 reference primary assembly".

[Charitra]

I have downloaded form ensembl GRCh37 (cufflinks site http://cufflinks.cbcb.umd.edu/igenomes.html .. all the files (pack)...

I am giving the path of gtf from reference annotation (not the bowtie2) and genome.fa.
The another directory has all the chr.fa . I am trying using cat command to make single .fa and then use it... I have also used new version of cufflinks 2.1.1

Someting is wrong with me... I think I am giving wrong path.... but if it the wrong path then also, it should not start working...