rvalieris
commented
4 years ago hello,
2019-08-12T15:04:38 fastq-dump.2.9.6 err: storage exhausted while writing file within file system module - system bad file descriptor error fd='4'
this means you are running out of space.
fastq-dump error! exit code: -24
and fastq-dump could not finish running correctly.
verify how much space you have left. you might need to run this on another partition with more space.
Hello!
This is my first time running parallel-fastq-dump so I apologize if this is a easy fix. Below I will post the output I receive from the program.
(base) [arglatha]$ parallel-fastq-dump --sra-id SRR6820613 --threads 6 --outdir ./SRR6820613/ --split-files --gzip --tmpdir ./tmp/ SRR ids: ['SRR6820613'] extra args: ['--split-files', '--gzip'] tempdir: ./tmp/pfd_kh5jeeyw SRR6820613 spots: 75623640 blocks: [[1, 12603940], [12603941, 25207880], [25207881, 37811820], [37811821, 50415760], [50415761, 63019700], [63019701, 75623640]] 2019-08-12T15:04:38 fastq-dump.2.9.6 err: storage exhausted while writing file within file system module - system bad file descriptor error fd='4' 2019-08-12T15:04:38 fastq-dump.2.9.6 int: storage exhausted while writing file within file system module - switching cache-tee-file to read-only 2019-08-12T15:04:38 fastq-dump.2.9.6 err: storage exhausted while writing file within file system module - system bad file descriptor error fd='4' 2019-08-12T15:04:38 fastq-dump.2.9.6 int: storage exhausted while writing file within file system module - switching cache-tee-file to read-only 2019-08-12T15:04:38 fastq-dump.2.9.6 err: storage exhausted while writing file within file system module - system bad file descriptor error fd='4' 2019-08-12T15:04:38 fastq-dump.2.9.6 int: storage exhausted while writing file within file system module - switching cache-tee-file to read-only 2019-08-12T15:04:38 fastq-dump.2.9.6 err: storage exhausted while writing file within file system module - system bad file descriptor error fd='4' 2019-08-12T15:04:38 fastq-dump.2.9.6 err: storage exhausted while writing file within file system module - system bad file descriptor error fd='4' 2019-08-12T15:04:38 fastq-dump.2.9.6 int: storage exhausted while writing file within file system module - switching cache-tee-file to read-only 2019-08-12T15:04:38 fastq-dump.2.9.6 err: storage exhausted while writing file within file system module - system bad file descriptor error fd='4' 2019-08-12T15:04:38 fastq-dump.2.9.6 int: storage exhausted while writing file within file system module - switching cache-tee-file to read-only 2019-08-12T15:04:38 fastq-dump.2.9.6 int: storage exhausted while writing file within file system module - switching cache-tee-file to read-only 2019-08-12T15:13:04 fastq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-08-12T15:15:52 fastq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-08-12T15:18:40 fastq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-08-12T15:58:34 fastq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) fastq-dump error! exit code: -24 Exception ignored in: <finalize object at 0x7f29c0854460; dead> Traceback (most recent call last): File "/util/common/bioinformatics/bioconda/miniconda3-4.6.14/lib/python3.7/weakref.py", line 552, in call return info.func(*info.args, (info.kwargs or {})) File "/util/common/bioinformatics/bioconda/miniconda3-4.6.14/lib/python3.7/tempfile.py", line 795, in _cleanup _shutil.rmtree(name) File "/util/common/bioinformatics/bioconda/miniconda3-4.6.14/lib/python3.7/shutil.py", line 491, in rmtree _rmtree_safe_fd(fd, path, onerror) File "/util/common/bioinformatics/bioconda/miniconda3-4.6.14/lib/python3.7/shutil.py", line 433, in _rmtree_safe_fd onerror(os.rmdir, fullname, sys.exc_info()) File "/util/common/bioinformatics/bioconda/miniconda3-4.6.14/lib/python3.7/shutil.py", line 431, in _rmtree_safe_fd os.rmdir(entry.name, dir_fd=topfd) OSError: [Errno 39] Directory not empty: '2'**
Any advice would be appreciated!