dswan
commented
5 years ago I don't think the issue is the setting of the temporary directory. Are you sure you have write permissions to the output directory? It looks like you're mounting an external filesystem from Virtualbox.
Output dir: /media/sf_VMBioShare/uni_out/spades_assembly/read_correction
[Errno 1] Operation not permitted: '/media/sf_VMBioShare/uni_out/spades_assembly/read_correction/corrected/configs/config.info'What happens if you : touch /media/sf_VMBioShare/uni_out/foo ?
I can see that Unicycler has been used at some point, or at least you have a directory named for it, but I'm pretty sure Unicylcer has a dependency on python3 and a later version of SPAdes, so are you running SPAdes directly here?
paul1000ton-coder
Hello! I am having an issue where SPAdes keeps on crashing at the beginning of using short reads in Unicycler. I am running Unicycler on a Oracle VM with 18.04 Ubuntu. Here is the following command I am running: /home/lts/SPAdes/bin/spades.py -1 /home/lts/Unicycler/sample_data/short_reads_1.fastq.gz -2 /home/lts/Unicycler/sample_data/short_reads_2.fastq.gz -o /media/sf_VMBioShare/uni_out/spades_assembly/read_correction --threads 6 --only-error-correction --tmp-dir /home/lts/spades_out
Below is the error message I am receiving from spades.log
`` System information: SPAdes version: 3.13.1 Python version: 2.7.15 OS: Linux-4.18.0-20-generic-x86_64-with-Ubuntu-18.04-bionic
Output dir: /media/sf_VMBioShare/uni_out/spades_assembly/read_correction Mode: ONLY read error correction (without assembling) Debug mode is turned OFF
Dataset parameters: Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (single-cell) technology or --meta flag if processing metagenomic dataset) Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/home/lts/Unicycler/sample_data/short_reads_1.fastq.gz'] right reads: ['/home/lts/Unicycler/sample_data/short_reads_2.fastq.gz'] 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 Other parameters: Dir for temp files: /home/lts/spades_out Threads: 6 Memory limit (in Gb): 23
======= SPAdes pipeline started. Log can be found here: /media/sf_VMBioShare/uni_out/spades_assembly/read_correction/spades.log
===== Read error correction started.
[Errno 1] Operation not permitted: '/media/sf_VMBioShare/uni_out/spades_assembly/read_correction/corrected/configs/config.info' Traceback (most recent call last): File "/home/lts/SPAdes/bin/spades.py", line 797, in main ext_python_modules_home, only_compressing_is_needed, log) File "/home/lts/SPAdes/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 "/usr/lib/python2.7/distutils/dir_util.py", line 167, in copy_tree dry_run=dry_run) File "/usr/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: '/media/sf_VMBioShare/uni_out/spades_assembly/read_correction/corrected/configs/config.info'
== Error == exception caught: <type 'exceptions.OSError'>