Closed Freemacl closed 5 years ago
Sorry took so long to reply, we seem to have missed your issue.
How was Canu installed? Is there a meryl-configure.err or .sh file in your 0-mercounts folder? If so can you post them here?
I tried installing canu two ways:
When I execute the canu command, I don't think meryl-configure.sh is being run as it generates no output file in the 0-mercounts directory. When I run meryl-configure.sh by hand it outputs ecoli.ms16.config.01.out:
Counting 133 million canonical 16-mers from 1 input file:
canu-seqStore: ../../ecoli.seqStore
SIMPLE MODE
-----------
16-mers
-> 4294967296 entries for counts up to 65535.
-> 64 Gbits memory used
140042151 input bases
-> expected max count of 560168, needing 5 extra bits.
-> 20 Gbits memory used
10 GB memory needed
COMPLEX MODE
------------
prefix # of struct kmers/ segs/ data total
bits prefix memory prefix prefix memory memory
------ ------- ------- ------- ------- ------- -------
1 2 P 64 kB 66 MM 4143 S 517 MB 517 MB
2 4 P 63 kB 33 MM 2005 S 501 MB 501 MB
3 8 P 61 kB 16 MM 969 S 484 MB 484 MB
4 16 P 60 kB 8547 kM 468 S 467 MB 467 MB
5 32 P 59 kB 4273 kM 226 S 451 MB 451 MB
6 64 P 60 kB 2136 kM 109 S 435 MB 435 MB
7 128 P 65 kB 1068 kM 53 S 423 MB 423 MB
8 256 P 76 kB 534 kM 26 S 415 MB 415 MB
9 512 P 100 kB 267 kM 13 S 415 MB 415 MB
10 1024 P 144 kB 133 kM 6 S 383 MB 383 MB Best Value!
11 2048 P 240 kB 66 kM 3 S 383 MB 384 MB
12 4096 P 448 kB 33 kM 2 S 511 MB 512 MB
13 8192 P 832 kB 16 kM 1 S 511 MB 512 MB
14 16 kP 1664 kB 8548 M 1 S 1023 MB 1025 MB
15 32 kP 3328 kB 4274 M 1 S 2047 MB 2050 MB
FINAL CONFIGURATION
-------------------
Configured complex mode for 0.375 GB memory per batch, and up to 1 batch.
Bye.
Exit code 126 means a command is found but is not executable
. For some reason, canu isn't able to run meryl-configure.sh.
How are you running meryl-configure.sh by hand?
What does ls -l meryl-configure.sh
report?
When canu tries to run it, is there a meryl-configure.err
generated?
To run meryl-configure.sh by hand I just entered "sh meryl-configure.sh" (after it gives me the meryl failed to configure error). That program prints:
Found perl:
/opt/miniconda3/envs/canu/bin/perl
This is perl 5, version 26, subversion 2 (v5.26.2) built for x86_64-linux-thread-multi
Found java:
/opt/miniconda3/envs/canu/bin/java
openjdk version "11.0.1" 2018-10-16 LTS
Found canu:
/home/claire/bin/canu
Canu 1.8
and after that command, that's when it outputs the ecoli.ms16.config.01.out file printed above.
ls -l meryl-configure.sh
prints
-rwxr-xr-x 1 claire claire 823 Jul 22 11:15 meryl-configure.sh
no meryl-configure.err
file unfortunately.
Can you run, by hand still, ./meryl-configure.sh
?
Ah! when i type just ./meryl-configure.sh
it tells me "Permission denied", even though I am the owner and it is currently "-rwxrwxrwx"
... any ideas?
Figured it out! On my system, canu is installed on the home directory, which is an executable filesystem, so no issues there. However, my output was being directed to a mounted HDD with "user" specified in the options of the fstab file, which automatically prevents the execution of binaries from the filesystem. Since meryl-configure.sh
is generated in the output directory, it was failing every time.
Now it's giving me a fun new error with Mhap, so if I can't get that to cooperate, I will open a new issue.
Thank you for your help!
@Freemacl Hi, I am trying to execute canu on an external SSD. I got the same error. CRASH: `
CRASH: Canu 1.9 CRASH: Please panic, this is abnormal. CRASH: CRASH: meryl failed to configure. CRASH: CRASH: Failed at /home/mgu/Documents/Tools/canu-1.9/Linux-amd64/bin/../lib/site_perl/canu/Meryl.pm line 414. CRASH: canu::Meryl::merylConfigure("BC09-q7-all6", "cor") called at /home/mgu/Documents/Tools/canu-1.9/Linux-amd64/bin/canu line 859 CRASH: CRASH: Last 50 lines of the relevant log file (correction/0-mercounts/meryl-configure.err): CRASH: CRASH: sh: 1: ./meryl-configure.sh: Permission denied
` How to overcome this?
I'm going to guess that the drive is mounted with options that prevent running programs from it. For example https://superuser.com/questions/728127/what-does-noexec-flag-mean-when-mounting-directories-on-rhel
command:
canu -p ecoli -d ecoli-oxford genomeSize=4.8m -nanopore-raw oxford.fasta
-For what it's worth, "please panic" is my all time favourite crash report -also worth noting the
ecoli.ms16.config.01.out
isn't produced