[Useq-users] MakeTranscriptome: splice junctions for qgenes were only partially made

[Biocyberman <bio...@gm...>]

I am new to the tool and have no idea to judge the significances of the
warnings in the command.
My questions:
1. What is the consequence of "seqs null" messages below.
2. What are the consequences of the WARNING below? In orther words, how
does it effect the outcome of downstream analysis? I tried increasing the
-n values to 120K, 240K, but still got the similar warnings, and with
higher values of -n, the tool takes really long time to finish. I actually
had to kill the process when -n 240K.

Vang

-------------------------------
[4 Mar 2015 18:12] USeq_8.8.9 Arguments: -f ../chromosomes/canonical_chrs
-u ./refFlat.canonical.txt -r 69 -n 60000

Transcript table        ./refFlat.canonical.txt
Fasta directory ../chromosomes/canonical_chrs
Splice radius   69
Max # splices per gene  60000
Max minutes per splice  10
Skip duplicate splice junctions false

Saving fasta files to .

Processing...
        chr20 ....seqs length 74423 max num 60000
seqs null
.
        chr10 ..seqs length 82234 max num 60000
seqs null
seqs null
............
        chr11 ....
        chr12 ....
        chr13 .....
        chr5 ..........
        chr6 .......
        chrY
        chr7 .seqs length 126083 max num 60000
.........
        chr8 ..........
        chr9 ......
        chrX .....
        chr15 .....
        chr14 .....
        chr17 ....
        chr16 ....
        chr1 .......................
        chr19 ....
        chr18 ....
        chr2 ..........
        chr3 ..............
        chr4 ...........

WARNING: splice junctions for the following genes were only partially made.
They exceeded the maximum number (N) or minutes (M) thresholds. Only those
present in the transcripts are guarenteed to be present in the fasta file.

Brap:4N Tesb:4N Lace1:4N Col2a1:1N Larp7:4N Rbm25:4N Col3a1:1N Ccdc63:4N
Col16a1:1N Fras1:1N Arntl2:4N Nmbr:4N Aldh1l1:4N Vom2r80:4N Hook3:4N
Oas3:4N Fosl2:4N Col7a1:1N Olr1610:4N Pld2:4N Col9a1:1N Dennd1c:4N
Col5a1:1N Col18a1:1N Col5a2:1N Col5a3:1N Slc12a9:4N Loxl2:4N Col17a1:1N
Lrp1b:1N Map3k5:4N Pcca:4N Ift172:1N Arhgef12:1N Atp2a1:1N Thbs1:1N
Col11a1:1N Col11a2:1N Rbm24:4N Ces5a:4N Col13a1:1N Trdn:1N Dync2h1:1N Si:1N
Sema4b:1N Adap2:4N Copb2:4N Rtn1:4N Adra1b:4N Col27a1:1N Snx17:4N Usp34:1N
Itpr2:1N Ggt1:4N Plb1:1N Prph2:4N Sspo:1N Lamc3:4N Fry:1N Ryr2
:1N Ttc30a:1N Kdm2b:4N Hspa1a:1N Dmbt1:4N Abcc4:1N Abcc3:1N Ptprg:1N
Col1a1:1N Csn1s1:4N Hpse:4N Wrap73:4N Col1a2:1N Acaa1b:4N Trpm7:1N
March9:4N Tmem132b:1N Stab2:1N

18715    number transcripts created
9920691  number splices created

Done! 223 min