Segmentation fault
Closed this issue · 6 comments
Hello Team,
I am getting the following while running ARKS.
make: *** [renamed_tigmint_leaf_plug_c5_m15-100000_k30_r0.05_e30000_z500_original.gv] Segmentation fault.
Number of contigs:15874
Size of Contig Array:31749
Script used : arks-make arks draft=renamed_tigmint_leaf_plug reads=_100bp_leafPlug_1ng m=15-100000 a=0.9 t 36
System RAM : 254 GB
Hi @shameem356,
How did you install ARKS? (homebrew, from source) What version/commit are you using?
Were you able to run the test demo successfully?
I have installed ARKS using homebrew. Version is arks 1.0.3.Yes I was able to run test demo.
Ok thanks for the information. If you were able to run the test demo fine, my next guess would be that there is something wrong with your input files.
What are the names of your draft assembly and input reads files? Is that the full log (from Makefile and standard out)? Are your input interleaved post-long ranger basic fastq files?
I have given interleaved post-long ranger basic fastq files are reads file. Below are the log file
shared/shameem/apps/arks/Examples/../bin/calcBarcodeMultiplicities.pl longranger_basic/leaf_plug_1ng/10X_longranger_basic_leaf_plug/outs/arcs_input_100bp_leafPlug_1ng.
fof > longranger_basic/leaf_plug_1ng/10X_longranger_basi
c_leaf_plug/outs/arcs_input_100bp_leafPlug_1ng_multiplicities.csv
arks -p full -v -f renamed_tigmint_leaf_plug.renamed.fa -a longranger_basic/leaf_plug_1ng/10X_longranger_basic_leaf_plug/outs/arcs_input_100bp_leafPlug_1ng_multiplicities.csv -c 5 -t 1 -j 0.5
5 -o 0 -m 50-10000 -k 30 -r 0.05 -e 30000 -z 500 -d 0 -b renamed_tigmint_leaf_plug_c5_m50-10000_k30_r0.05_e30000_z500 longranger_basic/leaf_plug_1ng/10X_longranger_basic_leaf_plug/outs/arcs_i
nput_100bp_leafPlug_1ng.fq.gz
Reading user inputs...
Finished reading user inputs...entering runArks()...
Entered runArks()...
Running: arks 1.0.3
pid 26362
-p full
-f renamed_tigmint_leaf_plug.renamed.fa
-a longranger_basic/leaf_plug_1ng/10X_longranger_basic_
leaf_plug/outs/arcs_input_100bp_leafPlug_1ng_multiplicities.csv
-q
-w
-i
-o 0
-c 5
-k 30
-g 1
-j 0.55
-l 0
-z 500
-b renamed_tigmint_leaf_plug_c5_m50-10000_k30_r0.05_e30000_z500
Min index multiplicity: 50
Max index multiplicity: 10000
-d 0
-e 30000
-e 30000
-r 0.05
-t 1
-v 1
---We are using KMER method.---
=>Preprocessing: Gathering barcode multiplicity information...Tue Nov 5 14:09:25 2019
Saw 0 barcodes and keeping 0 read pairs out of 0
=>Preprocessing: Gathering draft information...Tue Nov 5 14:09:25 2019
Number of contigs:15874
Size of Contig Array:31749
----Full ARKS----
=>Storing Kmers from Contig ends... Tue Nov 5 14:09:29 2019
make: *** [renamed_tigmint_leaf_plug_c5_m50-10000_k30_r0.05_e30000_z500_original.gv] Segmentation fault
Do you have the assembly and reads fastq files soft-linked (or copied) to your current working directory? It looks like you are providing full paths?
Ex. longranger_basic/leaf_plug_1ng/10X_longranger_basic_leaf_plug/outs/arcs_i nput_100bp_leafPlug_1ng.fq.gz
For using the Makefile, you need to have the reads and assembly files in your current working directory (either soft-linked or copied).
Closing this issue due to inactivity -- feel free to re-open if you still have questions.