LAmerge: System error, read failed!

[cassondranewman]

Hello,

My FALCON assembly (on a SLURM system) has been running for 6 days and seems to have just failed due to an error in 0-rawreads/daligner-runs/. I tracked the specific stderr and have attached it to this post. It seems that there was an error with LAmerge.

Please let me know how to fix the problem and how to restart the job correctly. I would truly appreciate it.

FALCON 6day Error 3.24.20.docx

[cassondranewman]

I read on github about similar LAmerge errors being due to incorrect headers/ raw data processing.

My headers look like: >m54334U_190820_211511/13/0_9581

My pre-processing is as follows:

module load smrtlink
bam2fasta -o merged /RawData/a/m54334U_190820_211511.subreads.bam /RawData/b/m54334U_190821_173238.subreads.bam /RawData/c/m54334U_190824_160001.subreads.bam /RawData/d/m54334U_190825_121903.subreads.bam

#this gave me a fasta file where the DNA sequence was in more than one line per header

awk -v ORS= '/^>/ { $0 = (NR==1 ? "" : RS) $0 RS } END { printf RS }1' < merged.fasta > 2L_merged.fasta

#Now I have one line of DNA per header
#Now I wanted to filter by fragment length

awk 'BEGIN {OFS = "\n"} {header = $0 ; getline seq ; if (length(seq) >= 8150) {print header, seq}}' < /RawData/FALCON_dir/2L_merged.fasta > merged_split_8150.fasta

#the merged_split_8150.fasta I gave as input to FALCON