metasapdes error

[MZNOTE]

$ metawrap assembly  -1  CLEAN_READS/ALL_READS_1.fastq  -2 CLEAN_READS/ALL_READS_2.fastq  -o ASSEMBLYOUT
metawrap assembly -1 CLEAN_READS/ALL_READS_1.fastq -2 CLEAN_READS/ALL_READS_2.fastq -o ASSEMBLYOUT

########################################################################################################################
#####                                         ASSEMBLING READS WITH MEGAHIT                                        #####
########################################################################################################################

------------------------------------------------------------------------------------------------------------------------
-----            assembling CLEAN_READS/ALL_READS_1.fastq and CLEAN_READS/ALL_READS_2.fastq with megahit           -----
------------------------------------------------------------------------------------------------------------------------

Cannot find ASSEMBLYOUT/megahit/opts.txt
Please check whether the output directory is correctly set by "-o"
Now switching to normal mode.
MEGAHIT v1.1.3
--- [Tue Sep 22 10:48:56 2020] Start assembly. Number of CPU threads 1 ---
--- [Tue Sep 22 10:48:56 2020] Available memory: 153535606784, used: 24000000000

************************************************************************************************************************
*****                         Something went wrong with reassembling with Megahit. Exiting.                        *****
************************************************************************************************************************

real    0m3.775s
user    0m0.469s
sys     0m1.547s

[ursky]

Did you try running the command manually? Looks like something got interrupted.

[MZNOTE]

Did you try running the command manually? Looks like something got interrupted.

(metawrap) huang@DESKTOP-QLIST7H:/mnt/g/meta$ metawrap assembly -1 CLEAN_READS/ALL_READS_1.fastq -2 CLEAN_READS/ALL_READS_2.fastq  -t 12 --metaspades -o ASSEMBLYOUT
metawrap assembly -1 CLEAN_READS/ALL_READS_1.fastq -2 CLEAN_READS/ALL_READS_2.fastq -t 12 --metaspades -o ASSEMBLYOUT
Warning: ASSEMBLYOUT already exists.

########################################################################################################################

ASSEMBLING WITH METASPADES

########################################################################################################################

---

----- Using reads CLEAN_READS/ALL_READS_1.fastq and CLEAN_READS/ALL_READS_2.fastq for assembly, -----

Command line: /home/huang/miniconda2/envs/metawrap/bin/metaspades.py --tmp-dir /mnt/g/meta/ASSEMBLYOUT/metaspades.tmp -t 12 -m 24 -o /mnt/g/meta/ASSEMBLYOUT/metaspades -1 /mnt/g/meta/CLEAN_READS/ALL_READS_1.fastq -2 /mnt/g/meta/CLEAN_READS/ALL_READS_2.fastq

System information: SPAdes version: 3.13.0 Python version: 2.7.15 OS: Linux-4.4.0-18362-Microsoft-x86_64-with-debian-bullseye-sid

Output dir: /mnt/g/meta/ASSEMBLYOUT/metaspades Mode: read error correction and assembling Debug mode is turned OFF

Dataset parameters: Metagenomic mode Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/mnt/g/meta/CLEAN_READS/ALL_READS_1.fastq'] right reads: ['/mnt/g/meta/CLEAN_READS/ALL_READS_2.fastq'] interlaced reads: not specified single reads: not specified merged reads: not specified Read error correction parameters: Iterations: 1 PHRED offset will be auto-detected Corrected reads will be compressed Assembly parameters: k: [21, 33, 55] Repeat resolution is enabled Mismatch careful mode is turned OFF MismatchCorrector will be SKIPPED Coverage cutoff is turned OFF Other parameters: Dir for temp files: /mnt/g/meta/ASSEMBLYOUT/metaspades.tmp Threads: 12 Memory limit (in Gb): 24

======= SPAdes pipeline started. Log can be found here: /mnt/g/meta/ASSEMBLYOUT/metaspades/spades.log

===== Read error correction started.

[Errno 1] Operation not permitted: '/mnt/g/meta/ASSEMBLYOUT/metaspades/corrected/configs/config.info' Traceback (most recent call last): File "/home/huang/miniconda2/envs/metawrap/bin/metaspades.py", line 790, in main ext_python_modules_home, only_compressing_is_needed, log) File "/home/huang/miniconda2/envs/metawrap/share/spades-3.13.0-0/share/spades/spades_pipeline/hammer_logic.py", line 131, in run_hammer dir_util.copy_tree(os.path.join(configs_dir, "hammer"), dst_configs, preserve_times=False) File "/home/huang/miniconda2/envs/metawrap/lib/python2.7/distutils/dir_util.py", line 167, in copy_tree dry_run=dry_run) File "/home/huang/miniconda2/envs/metawrap/lib/python2.7/distutils/file_util.py", line 165, in copy_file os.chmod(dst, S_IMODE(st[ST_MODE])) OSError: [Errno 1] Operation not permitted: '/mnt/g/meta/ASSEMBLYOUT/metaspades/corrected/configs/config.info'

== Error == exception caught: <type 'exceptions.OSError'>

In case you have troubles running SPAdes, you can write to spades.support@cab.spbu.ru or report an issue on our GitHub repository github.com/ablab/spades Please provide us with params.txt and spades.log files from the output directory.

---

Something went wrong with metaSPAdes assembly. Exiting.

---

real 0m4.439s user 0m0.234s sys 0m0.844s

[URIUPF]

were you able to solve it? I'm having the same error now

[MZNOTE]

我是建航，你的邮件已经收到，辛苦了！

[UMassDVR]

I have the same error. Has anyone solved this?

Cannot find ASSEMBLY/megahit/opts.txt Please check whether the output directory is correctly set by "-o"

[MZNOTE]

我是建航，你的邮件已经收到，辛苦了！