Thank you @gregcaporaso!
I have started running one MiSeq run on my Macbook pro to make sure the code is running ok before I use the university’s cluster for my 6 runs.
I succesfully imported my fastq.gz files, however when demultiplexing I got the following error:
OSError: [Errno 24] Too many open files: ‘/var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/q2-SingleLanePerSampleSingleEndFastqDirFmt-kff_ph7v/1025Cplus18LR_233_L001_R1_001.fastq.gz’
Any thoughts on how to work around it?
Thank you!
In case you want to see my code:
(qiime2) dhcp-morris-2243:Ganda ErikaGanda$ qiime tools import --type RawSequences --input-path QIIME2mmct/ --output-path raw-sequences1.qza
(qiime2) dhcp-morris-2243:Ganda ErikaGanda$ qiime demux emp --i-seqs raw-sequences1.qza --m-barcodes-file sample-metadata1.tsv --m-barcodes-category BarcodeSequence --o-per-sample-sequences demux
Traceback (most recent call last):
File “/Users/ErikaGanda/miniconda3/envs/qiime2/bin/qiime”, line 6, in
sys.exit(q2cli.main.qiime())
File “/Users/ErikaGanda/miniconda3/envs/qiime2/lib/python3.5/site-packages/click/core.py”, line 716, in call
return self.main(*args, **kwargs)
File “/Users/ErikaGanda/miniconda3/envs/qiime2/lib/python3.5/site-packages/click/core.py”, line 696, in main
rv = self.invoke(ctx)
File “/Users/ErikaGanda/miniconda3/envs/qiime2/lib/python3.5/site-packages/click/core.py”, line 1060, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File “/Users/ErikaGanda/miniconda3/envs/qiime2/lib/python3.5/site-packages/click/core.py”, line 1060, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File “/Users/ErikaGanda/miniconda3/envs/qiime2/lib/python3.5/site-packages/click/core.py”, line 889, in invoke
return ctx.invoke(self.callback, **ctx.params)
File “/Users/ErikaGanda/miniconda3/envs/qiime2/lib/python3.5/site-packages/click/core.py”, line 534, in invoke
return callback(*args, **kwargs)
File “/Users/ErikaGanda/miniconda3/envs/qiime2/lib/python3.5/site-packages/q2cli-0.0.6-py3.5.egg/q2cli/commands.py”, line 210, in call
File “”, line 2, in emp
File “/Users/ErikaGanda/miniconda3/envs/qiime2/lib/python3.5/site-packages/qiime-2.0.6-py3.5.egg/qiime/core/callable.py”, line 227, in callable_wrapper
output_types, provenance)
File “/Users/ErikaGanda/miniconda3/envs/qiime2/lib/python3.5/site-packages/qiime-2.0.6-py3.5.egg/qiime/core/callable.py”, line 328, in callable_executor
output_views = callable(**view_args)
File “/Users/ErikaGanda/miniconda3/envs/qiime2/lib/python3.5/site-packages/q2_demux-0.0.6-py3.5.egg/q2_demux/_demux.py”, line 196, in emp
File “/Users/ErikaGanda/miniconda3/envs/qiime2/lib/python3.5/gzip.py”, line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File “/Users/ErikaGanda/miniconda3/envs/qiime2/lib/python3.5/gzip.py”, line 163, in init
fileobj = self.myfileobj = builtins.open(filename, mode or ‘rb’)
OSError: [Errno 24] Too many open files: ‘/var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/q2-SingleLanePerSampleSingleEndFastqDirFmt-lwvz6hdj/1025Cplus18LR_233_L001_R1_001.fastq.gz’