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#################### my config ###########################
max_rd_len=150
[LIB]
avg_ins=350
reverse_seq=0
asm_flags=3
rd_len_cutoff=150
rank=1
pair_num_cutoff=3
map_len=32
q1=/1/Pdong_data/Filter_bac/L7_wHAXPI020290-35_unmap_rd_1.fq.gz
q2=/1/Pdong_data/Filter_bac/L7_wHAXPI020290-35_unmap_rd_2.fq.gz
q=/1/Pdong_data/Filter_bac/L7_wHAXPI020290-35_unmap.single.rd.fq.gz
q1=/1/Pdong_data/Filter_bac/L6_rd_1.fq.gz
q2=/1/Pdong_data/Filter_bac/L6_rd_2.fq.gz
q=/1/Pdong_data/Filter_bac/L6.single.rd.fq.gz
##################### my cmd ###############################
#!/bin/bash
#SBATCH --nodes=3
#SBATCH --ntasks-per-node=56
#SBATCH --partition=D2Part_test
#SBATCH --job-name=sopadenovo_test
#SBATCH --output=sopadenovo.29.out
#SBATCH --error=sopadenovo.29.err
~/software/SOAPdenovo2-master/SOAPdenovo-63mer pregraph -s config_file -o PB_29 -R -K 29 -p 168 > PB_29_pre.log
~/software/SOAPdenovo2-master/SOAPdenovo-63mer contig -g PB_29 -R -p 168 > PB_29_con.log
~/software/SOAPdenovo2-master/SOAPdenovo-63mer map -s config_file -g PB_29 -p 168 -k 29 > PB_29_map.log
~/software/SOAPdenovo2-master/SOAPdenovo-63mer scaff -g PB_29 -F -p 168 > PB_29scaf.log
date
####################### log #################################
206 ********************
207 Contig
208 ********************
209
210 Parameters: contig -g PB_29 -R -p 168
211
212 There are 566067075 kmer(s) in vertex file.
213 There are 1830549853 edge(s) in edge file.
214 Ran out of memory while applying -64982367872bytes
215 There may be errors as follows:
216 1) Not enough memory.
217 2) The ARRAY may be overrode.
218 3) The wild pointers.
219
220 Version 2.04: released on July 13th, 2012
221 Compile Dec 31 2021 12:53:17
#############################################################
This was used K=29, and forward and reverse reads total 400GB, predict Genome size 4.2Gb, and jellyfish analysis k = 28.
My linux server memory = 1.5TB,
I also used K=127 with no error came out.
So can you help me about what's wrong with k=29 ? Thanks !
The text was updated successfully, but these errors were encountered:
#################### my config ###########################
max_rd_len=150
[LIB]
avg_ins=350
reverse_seq=0
asm_flags=3
rd_len_cutoff=150
rank=1
pair_num_cutoff=3
map_len=32
q1=
/1/Pdong_data/Filter_bac/L7_wHAXPI020290-35_unmap_rd_1.fq.gz/1/Pdong_data/Filter_bac/L7_wHAXPI020290-35_unmap_rd_2.fq.gzq2=
q=
/1/Pdong_data/Filter_bac/L7_wHAXPI020290-35_unmap.single.rd.fq.gz/1/Pdong_data/Filter_bac/L6_rd_1.fq.gzq1=
q2=
/1/Pdong_data/Filter_bac/L6_rd_2.fq.gz/1/Pdong_data/Filter_bac/L6.single.rd.fq.gzq=
##################### my cmd ###############################
#!/bin/bash
#SBATCH --nodes=3
#SBATCH --ntasks-per-node=56
#SBATCH --partition=D2Part_test
#SBATCH --job-name=sopadenovo_test
#SBATCH --output=sopadenovo.29.out
#SBATCH --error=sopadenovo.29.err
~/software/SOAPdenovo2-master/SOAPdenovo-63mer pregraph -s config_file -o PB_29 -R -K 29 -p 168 > PB_29_pre.log
~/software/SOAPdenovo2-master/SOAPdenovo-63mer contig -g PB_29 -R -p 168 > PB_29_con.log
~/software/SOAPdenovo2-master/SOAPdenovo-63mer map -s config_file -g PB_29 -p 168 -k 29 > PB_29_map.log
~/software/SOAPdenovo2-master/SOAPdenovo-63mer scaff -g PB_29 -F -p 168 > PB_29scaf.log
date
####################### log #################################
206 ********************
207 Contig
208 ********************
209
210 Parameters: contig -g PB_29 -R -p 168
211
212 There are 566067075 kmer(s) in vertex file.
213 There are 1830549853 edge(s) in edge file.
214 Ran out of memory while applying -64982367872bytes
215 There may be errors as follows:
216 1) Not enough memory.
217 2) The ARRAY may be overrode.
218 3) The wild pointers.
219
220 Version 2.04: released on July 13th, 2012
221 Compile Dec 31 2021 12:53:17
#############################################################
This was used K=29, and forward and reverse reads total 400GB, predict Genome size 4.2Gb, and jellyfish analysis k = 28.
My linux server memory = 1.5TB,
I also used K=127 with no error came out.
So can you help me about what's wrong with k=29 ? Thanks !
The text was updated successfully, but these errors were encountered: