Entering edit mode
9.7 years ago
ckycyn
•
0
Dear all,
I am new in bioinformatics, I just tried to use the reference genomes from IMG to build an index in PAUDA-1.0.1 in order to load into MEGAN.
- Does anyone experience problems of loading bowtie2 SAM files into MEGAN? I failed to generate any result by loading SAM files directly, so i try to use PAUDA now.
- May I know is it normal for PAUDA to take a long time to build index? It has been stuck at 50% for 2 days. I had started running this for about 4.5 days.
Thank you very much for help! Deeply appreciated.
Start: Fri Jul 11 23:42:44 HKT 2014
References: all_seqs.complete_genome.fa
ln -s /home/s/pauda-1.0.1/bin/all_seqs.complete_genome.fa /dev/shm/pauda_index5/ref.faa
java -Xmx20G -Duser.language=en -Duser.region=US -cp /home/s/pauda-1.0.1/lib/../lib/Pauda.jar megan.pauda.Proteins2PNA -a BLOSUM50_4 -i /dev/shm/pauda_index5/ref.faa
Reading file: /dev/shm/pauda_index5/ref.faa
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% (19.9s)
Writing mapping file 1: /dev/shm/pauda_index5/ref.map1
Processing sequences:
10% 20% 30% 40% 50%
Many Thanks!