Hi,

I am having a little bit of a hiccup with Platanus assembly (version 1.2.4). So I ran the first step of the assembly and got the contig, contigBubble and the 41merFrq files. My problem now is when I run the scaffolding step I get the error message in the log file which says:

Error(2): File format exception!!
the number of read is different in paired-file.

I double checked all my paired read files and they have the same number of reads I have 2 libraries, paired-end and mate-pair with 300 and 3000 bp inserts, respectively.

What can I possibly be doing wrong?

Another question, do I need to input the original read files when scaffolding?

Here is my code for contig and scaffolding:

Contig assembly

platanus assemble -o PlatanusAssembleK41_QP -f /home/ymgwatyu/lustre/00_GenomeData/02_QPData/04_FilteredByTile/L5_R1_p_filtered.cor.fq /home/ymgwatyu/lustre/00_GenomeData/02_QPData/04_FilteredByTile/L5_R2_p_filtered.cor.fq /home/ymgwatyu/lustre/00_GenomeData/02_QPData/04_FilteredByTile/L6_R1_p_filtered.cor.fq /home/ymgwatyu/lustre/00_GenomeData/02_QPData/04_FilteredByTile/L6_R2_p_filtered.cor.fq /home/ymgwatyu/lustre/00_GenomeData/02_QPData/04_FilteredByTile/S1_L1_R1_p_filtered.cor.fq /home/ymgwatyu/lustre/00_GenomeData/02_QPData/04_FilteredByTile/S1_L1_R2_p_filtered.cor.fq /home/ymgwatyu/lustre/00_GenomeData/02_QPData/04_FilteredByTile/S1_L2_R1_p_filtered.cor.fq /home/ymgwatyu/lustre/00_GenomeData/02_QPData/04_FilteredByTile/S1_L2_R2_p_filtered.cor.fq /home/ymgwatyu/lustre/00_GenomeData/02_QPData/04_FilteredByTile/S1_L3_R1_p_filtered.cor.fq /home/ymgwatyu/lustre/00_GenomeData/02_QPData/04_FilteredByTile/S1_L3_R2_p_filtered.cor.fq /home/ymgwatyu/lustre/00_GenomeData/02_QPData/04_FilteredByTile/S1_L4_R1_p_filtered.cor.fq /home/ymgwatyu/lustre/00_GenomeData/02_QPData/04_FilteredByTile/S1_L4_R2_p_filtered.cor.fq /home/ymgwatyu/lustre/00_GenomeData/02_QPData/04_FilteredByTile/S1_L5_R1_p_filtered.cor.fq /home/ymgwatyu/lustre/00_GenomeData/02_QPData/04_FilteredByTile/L5_R2_p_filtered.cor.fq /home/ymgwatyu/lustre/00_GenomeData/02_QPData/04_FilteredByTile/S1_L6_R1_p_filtered.cor.fq /home/ymgwatyu/lustre/00_GenomeData/02_QPData/04_FilteredByTile/S1_L6_R2_p_filtered.cor.fq -k 41 -t 56 -m 700 2> AssembleFullK41_QP2.log

output files :

PlatanusAssembleK41_QP_contig.fa
PlatanusAssembleK41_QP_contigBubble.fa
PlatanusAssembleK41_QP_41merFrq.tsv

Scaffolding

platanus scaffold -o PlatanusAssembleK41_QP -c ./PlatanusAssembleK41_QP_contig.fa -b ./PlatanusAssembleK41_QP_contigBubble.fa -IP1 
/home/ymgwatyu/lustre/00_GenomeData/02_QPData/04_FilteredByTile/L5_R1_p_filtered.cor.fq /home/ymgwatyu/lustre/00_GenomeData/02_QPData/04_FilteredByTile/L5_R2_p_filtered.cor.fq /home/ymgwatyu/lustre/00_GenomeData/02_QPData/04_FilteredByTile/S1_L1_R1_p_filtered.cor.fq /home/ymgwatyu/lustre/00_GenomeData/02_QPData/04_FilteredByTile/S1_L1_R2_p_filtered.cor.fq /home/ymgwatyu/lustre/00_GenomeData/02_QPData/04_FilteredByTile/S1_L2_R1_p_filtered.cor.fq /home/ymgwatyu/lustre/00_GenomeData/02_QPData/04_FilteredByTile/S1_L2_R2_p_filtered.cor.fq /home/ymgwatyu/lustre/00_GenomeData/02_QPData/04_FilteredByTile/S1_L3_R1_p_filtered.cor.fq /home/ymgwatyu/lustre/00_GenomeData/02_QPData/04_FilteredByTile/S1_L3_R2_p_filtered.cor.fq /home/ymgwatyu/lustre/00_GenomeData/02_QPData/04_FilteredByTile/S1_L4_R1_p_filtered.cor.fq /home/ymgwatyu/lustre/00_GenomeData/02_QPData/04_FilteredByTile/S1_L4_R2_p_filtered.cor.fq /home/ymgwatyu/lustre/00_GenomeData/02_QPData/04_FilteredByTile/S1_L5_R1_p_filtered.cor.fq /home/ymgwatyu/lustre/00_GenomeData/02_QPData/04_FilteredByTile/S1_L5_R2_p_filtered.cor.fq /home/ymgwatyu/lustre/00_GenomeData/02_QPData/04_FilteredByTile/S1_L6_R1_p_filtered.cor.fq /home/ymgwatyu/lustre/00_GenomeData/02_QPData/04_FilteredByTile/S1_L6_R2_p_filtered.cor.fq -OP2 /home/ymgwatyu/lustre/00_GenomeData/02_QPData/MP_3000_S1L1_nc_ABC_R1.fastq /home/ymgwatyu/lustre/00_GenomeData/02_QPData/MP_3000_S1L1_nc_ABC_R2.fastq -n1 200 -n2 2000 -a1 300 -a2 3000 -t 56 2> PlatK41_QP_scaff.log

error message:

Error(2): File format exception!!
the number of read is different in paired-file.

Kindly assist