Canu won't run - Githubissues

Hi All,

I'm new to running Canu and quite a novice at using terminal commands. I managed to get Canu installed on an iMac that I use for Nanopore sequencing. I am looking to run an assembly with Canu but it just doesn't seem to work! Any advice on what I am doing wrong? I have attached the copy of the script from terminal.

Am I right in assuming:

-p is the name i want for the output file? -d the location to but the new file?

I have trimmed and demultiplexed with Porechop so I am also assuming the last commend is nanopore-corrected and then the directory to the file that I want to align?

Cheers

MinIONs-iMac:~ minion$ canu -assemble \
> -p 300OR1 -d /Users/minion/Desktop/AoC\ MinION\ Seq/Porechop\ Files/Canu\ Output \
> genomeSize=2.8m \
> -nanopore-corrected /Users/minion/Desktop/AoC\ MinION\ Seq/Porechop\ Files/BC01.fastq 
--   Reason: image not found
--
-- CITATIONS
--
-- Koren S, Walenz BP, Berlin K, Miller JR, Phillippy AM.
-- Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
-- Genome Res. 2017 May;27(5):722-736.
-- http://doi.org/10.1101/gr.215087.116
-- 
-- Read and contig alignments during correction, consensus and GFA building use:
--   Šošic M, Šikic M.
--   Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance.
--   Bioinformatics. 2017 May 1;33(9):1394-1395.
--   http://doi.org/10.1093/bioinformatics/btw753
-- 
-- Overlaps are generated using:
--   Berlin K, et al.
--   Assembling large genomes with single-molecule sequencing and locality-sensitive hashing.
--   Nat Biotechnol. 2015 Jun;33(6):623-30.
--   http://doi.org/10.1038/nbt.3238
-- 
--   Myers EW, et al.
--   A Whole-Genome Assembly of Drosophila.
--   Science. 2000 Mar 24;287(5461):2196-204.
--   http://doi.org/10.1126/science.287.5461.2196
-- 
--   Li H.
--   Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences.
--   Bioinformatics. 2016 Jul 15;32(14):2103-10.
--   http://doi.org/10.1093/bioinformatics/btw152
-- 
-- Corrected read consensus sequences are generated using an algorithm derived from FALCON-sense:
--   Chin CS, et al.
--   Phased diploid genome assembly with single-molecule real-time sequencing.
--   Nat Methods. 2016 Dec;13(12):1050-1054.
--   http://doi.org/10.1038/nmeth.4035
-- 
-- Contig consensus sequences are generated using an algorithm derived from pbdagcon:
--   Chin CS, et al.
--   Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.
--   Nat Methods. 2013 Jun;10(6):563-9
--   http://doi.org/10.1038/nmeth.2474
-- 
-- CONFIGURE CANU
--
-- Detected Java(TM) Runtime Environment '9.0.4' (from 'java').
-- Detected gnuplot version '5.2 patchlevel 2' (from 'gnuplot') and image format 'png'.
-- Detected 8 CPUs and 32 gigabytes of memory.
-- No grid engine detected, grid disabled.
--
--                            (tag)Concurrency
--                     (tag)Threads          |
--            (tag)Memory         |          |
--        (tag)         |         |          |     total usage     algorithm
--        -------  ------  --------   --------  -----------------  -----------------------------
-- Local: meryl      8 GB    4 CPUs x   1 job      8 GB    4 CPUs  (k-mer counting)
-- Local: cormhap    6 GB    8 CPUs x   1 job      6 GB    8 CPUs  (overlap detection with mhap)
-- Local: obtovl     4 GB    8 CPUs x   1 job      4 GB    8 CPUs  (overlap detection)
-- Local: utgovl     4 GB    8 CPUs x   1 job      4 GB    8 CPUs  (overlap detection)
-- Local: ovb        4 GB    1 CPU  x   8 jobs    32 GB    8 CPUs  (overlap store bucketizer)
-- Local: ovs        8 GB    1 CPU  x   4 jobs    32 GB    4 CPUs  (overlap store sorting)
-- Local: red        4 GB    4 CPUs x   2 jobs     8 GB    8 CPUs  (read error detection)
-- Local: oea        4 GB    1 CPU  x   8 jobs    32 GB    8 CPUs  (overlap error adjustment)
-- Local: bat       16 GB    4 CPUs x   1 job     16 GB    4 CPUs  (contig construction)
-- Local: gfa        8 GB    4 CPUs x   1 job      8 GB    4 CPUs  (GFA alignment and processing)
--
-- Found Nanopore corrected reads in the input files.
--
-- Generating assembly '300OR1' in '/Users/minion/Desktop/AoC MinION Seq/Porechop Files/Canu Output'
--
-- Parameters:
--
--  genomeSize        2800000
--
--  Overlap Generation Limits:
--    corOvlErrorRate 0.3200 ( 32.00%)
--    obtOvlErrorRate 0.1440 ( 14.40%)
--    utgOvlErrorRate 0.1440 ( 14.40%)
--
--  Overlap Processing Limits:
--    corErrorRate    0.5000 ( 50.00%)
--    obtErrorRate    0.1440 ( 14.40%)
--    utgErrorRate    0.1440 ( 14.40%)
--    cnsErrorRate    0.1920 ( 19.20%)
--
--
-- BEGIN ASSEMBLY
--
----------------------------------------
-- Starting command on Fri Apr  6 11:37:32 2018 with 648.128 GB free disk space

    cd .
    /Users/minion/Documents/Apps/canu-1.7/Darwin-amd64/bin/gatekeeperCreate \
      -minlength 1000 \
      -o ./300OR1.gkpStore.BUILDING \
      ./300OR1.gkpStore.gkp \
    > ./300OR1.gkpStore.BUILDING.err 2>&1
sh: line 4: 21381 Abort trap: 6           /Users/minion/Documents/Apps/canu-1.7/Darwin-amd64/bin/gatekeeperCreate -minlength 1000 -o ./300OR1.gkpStore.BUILDING ./300OR1.gkpStore.gkp > ./300OR1.gkpStore.BUILDING.err 2>&1

-- Finished on Fri Apr  6 11:37:32 2018 (lickety-split) with 648.128 GB free disk space
----------------------------------------

ERROR:
ERROR:  Failed with exit code 134.  (rc=34304)
ERROR:

ABORT:
ABORT:   Reason: image not found
ABORT: Don't panic, but a mostly harmless error occurred and Canu stopped.
ABORT: Try restarting.  If that doesn't work, ask for help.
ABORT:
ABORT:   gatekeeper failed.
ABORT:
ABORT: Disk space available:  648.128 GB
ABORT:
ABORT: Last 50 lines of the relevant log file (./300OR1.gkpStore.BUILDING.err):
ABORT:
ABORT:
MinIONs-iMac:~ minion$

marbl / canu

Canu won't run #859