Empty final output

[desmodus1984]

Hi,
I installed MaSuRCA in conda, and then I tried making an assembly using only pe-reads, and all worked well until the end when the final output, in the work folder was empty.

print() on closed filehandle FILE at /home/juaguila/.conda/envs/masurca/bin/masurca line 113.
print() on closed filehandle FILE at /home/juaguila/.conda/envs/masurca/bin/masurca line 117.
print() on closed filehandle FILE at /home/juaguila/.conda/envs/masurca/bin/masurca line 124.
print() on closed filehandle FILE at /home/juaguila/.conda/envs/masurca/bin/masurca line 125.
print() on closed filehandle FILE at /home/juaguila/.conda/envs/masurca/bin/masurca line 127.
print() on closed filehandle FILE at /home/juaguila/.conda/envs/masurca/bin/masurca line 131.
print() on closed filehandle FILE at /home/juaguila/.conda/envs/masurca/bin/masurca line 133.
print() on closed filehandle FILE at /home/juaguila/.conda/envs/masurca/bin/masurca line 137.
Verifying PATHS...
jellyfish OK
runCA OK
createSuperReadsForDirectory.perl OK
SOAPdenovo-63mer OK
creating script file for the actions...done.
execute assemble.sh to run assembly
[Wed Mar 27 13:29:05 EDT 2024] Processing pe library reads
[Wed Mar 27 13:31:19 EDT 2024] Average PE read length 149
[Wed Mar 27 13:31:19 EDT 2024] Using kmer size of 99 for the graph
[Wed Mar 27 13:31:20 EDT 2024] MIN_Q_CHAR: 33
[Wed Mar 27 13:31:20 EDT 2024] Creating mer database for Quorum
[Wed Mar 27 13:34:26 EDT 2024] Error correct PE
[Wed Mar 27 13:46:01 EDT 2024] Estimating genome size
[Wed Mar 27 13:47:57 EDT 2024] Estimated genome size: 107906716
[Wed Mar 27 13:47:57 EDT 2024] Creating k-unitigs with k=99
[Wed Mar 27 13:53:48 EDT 2024] Computing super reads from PE
[Wed Mar 27 14:04:02 EDT 2024] SOAPdenovo
[Wed Mar 27 14:35:56 EDT 2024] Gap closing
[Wed Mar 27 14:59:16 EDT 2024] Removing duplicated contained contigs
[Wed Mar 27 14:59:20 EDT 2024] Rescaffolding
./assemble.sh: line 150: finalFusion: command not found
[Wed Mar 27 14:59:20 EDT 2024] Assembly success. Output sequence is in SOAP_assembly/asm2.scafSeq2

-rw-r--r-- 1 juaguila hpc_jfierst 87330102 Mar 27 14:35 asm.scafSeq
-rw-r--r-- 1 juaguila hpc_jfierst 2333892 Mar 27 14:35 asm.gapSeq
-rw-r--r-- 1 juaguila hpc_jfierst 1074430 Mar 27 14:35 asm.contigPosInscaff
-rw-r--r-- 1 juaguila hpc_jfierst 1763 Mar 27 14:35 asm.scafStatistics
-rw-r--r-- 1 juaguila hpc_jfierst 0 Mar 27 14:59 asm2.scafSeq2

Any reason for this weird behavior, result?

The config was

quick run configuration file

DATA
PE = pe 303 82 ../3391-t1.fq.gz ../3391-t2.fq.gz
END
PARAMETERS
EXTEND_JUMP_READS=0
GRAPH_KMER_SIZE = auto
USE_LINKING_MATES = 1
USE_GRID=0
GRID_ENGINE=SGE
GRID_QUEUE=all.q
GRID_BATCH_SIZE=500000000
LHE_COVERAGE=25
LIMIT_JUMP_COVERAGE = 300
CA_PARAMETERS = cgwErrorRate=0.15
CLOSE_GAPS=1
NUM_THREADS = 20
JF_SIZE = 2000000000
SOAP_ASSEMBLY=1
FLYE_ASSEMBLY=0
END

I am running the assembly in a node, and this is for a worm. I wanted to use the quick simplified approach, but it can't use as input the insert size, which is inproper for my reads; so I changed the config and made it readable, and changed the parameters for Illumina-only, and it worked. But, for some reason, the final output was zero.

Thanks;