Hola @thermokarst!
Many thanks for your reply. I started again and created a folder ‘temp’ in /output, then in /fastqfiles, then out in /tmp and run again the commands, but I got again and again the same error but the last one, please look below:
"(qiime2) mothur@Microbiome:/mnt/output$ mkdir temp
(qiime2) mothur@Microbiome:/mnt/output$ export TMPDIR=/mnt/output/temp/
(qiime2) mothur@Microbiome:/mnt/output$ echo TMPDIR
/mnt/output/temp/
(qiime2) mothur@Microbiome:/mnt/output qiime tools import --type ‘SampleData[PairedEndSequencesWithQuality]’ --input-path /mnt/fastqfiles/GATC-04/bz2files/abm/gz --source-format CasavaOneEightSingleLanePerSampleDirFmt --output-path /mnt/output/I02304-01/demux-paired-end.qza
Traceback (most recent call last):
File “/home/mothur/miniconda3/envs/qiime2/lib/python3.5/site-packages/q2cli/tools.py”, line 116, in import_data
view_type=source_format)
File “/home/mothur/miniconda3/envs/qiime2/lib/python3.5/site-packages/qiime2/sdk/result.py”, line 211, in import_data
return cls.from_view(type, view, view_type, provenance_capture)
File “/home/mothur/miniconda3/envs/qiime2/lib/python3.5/site-packages/qiime2/sdk/result.py”, line 236, in _from_view
result = transformation(view)
File “/home/mothur/miniconda3/envs/qiime2/lib/python3.5/site-packages/qiime2/core/transform.py”, line 59, in transformation
new_view = transformer(view)
File “/home/mothur/miniconda3/envs/qiime2/lib/python3.5/site-packages/q2_types/per_sample_sequences/_transformer.py”, line 76, in _4
dirfmt, SingleLanePerSamplePairedEndFastqDirFmt)
File “/home/mothur/miniconda3/envs/qiime2/lib/python3.5/site-packages/q2_types/per_sample_sequences/_transformer.py”, line 52, in _single_lane_per_sample_fastq_helper
read_number=read_number)
File “/home/mothur/miniconda3/envs/qiime2/lib/python3.5/site-packages/qiime2/plugin/model/directory_format.py”, line 87, in write_data
result.path._move_or_copy(self.path_maker(**kwargs))
File “/home/mothur/miniconda3/envs/qiime2/lib/python3.5/site-packages/qiime2/core/path.py”, line 35, in _move_or_copy
return shutil.copy(str(self), str(other))
File “/home/mothur/miniconda3/envs/qiime2/lib/python3.5/shutil.py”, line 242, in copy
copymode(src, dst, follow_symlinks=follow_symlinks)
File “/home/mothur/miniconda3/envs/qiime2/lib/python3.5/shutil.py”, line 144, in copymode
chmod_func(dst, stat.S_IMODE(st.st_mode))
PermissionError: [Errno 1] Operation not permitted: ‘/mnt/output/temp/q2-SingleLanePerSamplePairedEndFastqDirFmt-le0ii0rc/L4A01_1_L001_R1_001.fastq.gz’
An unexpected error has occurred:
[Errno 1] Operation not permitted: '/mnt/output/temp/q2-SingleLanePerSamplePairedEndFastqDirFmt-le0ii0rc/L4A01_1_L001_R1_001.fastq.gz’
See above for debug info."
I also tried to change --output path with no luck:
“(qiime2) mothur@Microbiome:/mnt$ echo TMPDIR
/mnt/fastqfiles/temp/
(qiime2) mothur@Microbiome:/mnt qiime tools import --type ‘SampleData[PairedEndSequencesWithQuality]’ --input-path /mnt/fastqfiles/GATC-04/bz2files/abm/gz --source-format CasavaOneEightSingleLanePerSampleDirFmt --output-path /mnt/fastqfiles/GATC-04/bz2files/abm/gz/demux-paired-end.qza
Traceback (most recent call last):
File “/home/mothur/miniconda3/envs/qiime2/lib/python3.5/site-packages/q2cli/tools.py”, line 116, in import_data
view_type=source_format)
File “/home/mothur/miniconda3/envs/qiime2/lib/python3.5/site-packages/qiime2/sdk/result.py”, line 211, in import_data
return cls.from_view(type, view, view_type, provenance_capture)
File “/home/mothur/miniconda3/envs/qiime2/lib/python3.5/site-packages/qiime2/sdk/result.py”, line 236, in _from_view
result = transformation(view)
File “/home/mothur/miniconda3/envs/qiime2/lib/python3.5/site-packages/qiime2/core/transform.py”, line 59, in transformation
new_view = transformer(view)
File “/home/mothur/miniconda3/envs/qiime2/lib/python3.5/site-packages/q2_types/per_sample_sequences/_transformer.py”, line 76, in _4
dirfmt, SingleLanePerSamplePairedEndFastqDirFmt)
File “/home/mothur/miniconda3/envs/qiime2/lib/python3.5/site-packages/q2_types/per_sample_sequences/_transformer.py”, line 52, in _single_lane_per_sample_fastq_helper
read_number=read_number)
File “/home/mothur/miniconda3/envs/qiime2/lib/python3.5/site-packages/qiime2/plugin/model/directory_format.py”, line 87, in write_data
result.path._move_or_copy(self.path_maker(**kwargs))
File “/home/mothur/miniconda3/envs/qiime2/lib/python3.5/site-packages/qiime2/core/path.py”, line 35, in _move_or_copy
return shutil.copy(str(self), str(other))
File “/home/mothur/miniconda3/envs/qiime2/lib/python3.5/shutil.py”, line 242, in copy
copymode(src, dst, follow_symlinks=follow_symlinks)
File “/home/mothur/miniconda3/envs/qiime2/lib/python3.5/shutil.py”, line 144, in copymode
chmod_func(dst, stat.S_IMODE(st.st_mode))
PermissionError: [Errno 1] Operation not permitted: '/mnt/fastqfiles/temp/q2-SingleLanePerSamplePairedEndFastqDirFmt-ol4z3al3/L4A01_1_L001_R1_001.fastq.gz’
An unexpected error has occurred:
[Errno 1] Operation not permitted: '/mnt/fastqfiles/temp/q2-SingleLanePerSamplePairedEndFastqDirFmt-ol4z3al3/L4A01_1_L001_R1_001.fastq.gz’
See above for debug info.”
I also try to use this /tmp out of mnt/ and got a different error! With it was the first error I got when tried to run the import tools without defining a temp folder:
“(qiime2) mothur@Microbiome:/mnt$ export TMPDIR=/tmp
(qiime2) mothur@Microbiome:/mnt$ echo TMPDIR
/tmp
(qiime2) mothur@Microbiome:/mnt qiime tools import --type ‘SampleData[PairedEndSequencesWithQuality]’ --input-path /mnt/fastqfiles/GATC-04/bz2files/abm/gz --source-format CasavaOneEightSingleLanePerSampleDirFmt --output-path /mnt/fastqfiles/GATC-04/bz2files/abm/gz/demux-paired-end.qza
Traceback (most recent call last):
File “/home/mothur/miniconda3/envs/qiime2/lib/python3.5/site-packages/q2cli/tools.py”, line 116, in import_data
view_type=source_format)
File “/home/mothur/miniconda3/envs/qiime2/lib/python3.5/site-packages/qiime2/sdk/result.py”, line 211, in import_data
return cls.from_view(type, view, view_type, provenance_capture)
File “/home/mothur/miniconda3/envs/qiime2/lib/python3.5/site-packages/qiime2/sdk/result.py”, line 236, in _from_view
result = transformation(view)
File “/home/mothur/miniconda3/envs/qiime2/lib/python3.5/site-packages/qiime2/core/transform.py”, line 59, in transformation
new_view = transformer(view)
File “/home/mothur/miniconda3/envs/qiime2/lib/python3.5/site-packages/q2_types/per_sample_sequences/_transformer.py”, line 76, in _4
dirfmt, SingleLanePerSamplePairedEndFastqDirFmt)
File “/home/mothur/miniconda3/envs/qiime2/lib/python3.5/site-packages/q2_types/per_sample_sequences/_transformer.py”, line 52, in _single_lane_per_sample_fastq_helper
read_number=read_number)
File “/home/mothur/miniconda3/envs/qiime2/lib/python3.5/site-packages/qiime2/plugin/model/directory_format.py”, line 87, in write_data
result.path._move_or_copy(self.path_maker(**kwargs))
File “/home/mothur/miniconda3/envs/qiime2/lib/python3.5/site-packages/qiime2/core/path.py”, line 35, in _move_or_copy
return shutil.copy(str(self), str(other))
File “/home/mothur/miniconda3/envs/qiime2/lib/python3.5/shutil.py”, line 241, in copy
copyfile(src, dst, follow_symlinks=follow_symlinks)
File “/home/mothur/miniconda3/envs/qiime2/lib/python3.5/shutil.py”, line 122, in copyfile
copyfileobj(fsrc, fdst)
File “/home/mothur/miniconda3/envs/qiime2/lib/python3.5/shutil.py”, line 82, in copyfileobj
fdst.write(buf)
OSError: [Errno 28] No space left on device
An unexpected error has occurred:
[Errno 28] No space left on device
See above for debug info.”
I know I have space in there (below) but doesn’t let me use it…
Filesystem 1K-blocks Used Available Use% Mounted on
udev 28831056 0 28831056 0% /dev
tmpfs 5770232 8820 5761412 1% /run
/dev/sda1 29711408 19476304 10218720 66% /
tmpfs 28851140 0 28851140 0% /dev/shm
tmpfs 5120 0 5120 0% /run/lock
tmpfs 28851140 0 28851140 0% /sys/fs/cgroup
none 64 0 64 0% /etc/network/interfaces.dynamic.d
/dev/sdb1 115465696 61056 109516288 1% /mnt
tmpfs 5770232 0 5770232 0% /run/user/1000
/dev/sdc1 131979748 57554512 67698020 46% /home/mothur/runenv
/dev/sdd1 528315064 37022728 464432460 8% /home/mothur/runenv2
//mothurdata2.file.core.windows.net/fastqfiles 5368709120 297890368 5070818752 6% /mnt/fastqfiles
//mothurdata2.file.core.windows.net/output 5368709120 13361600 5355347520 1% /mnt/output
Many thanks in advance!
Ana.