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yarden / MISO

MISO: Mixture of Isoforms model for RNA-Seq isoform quantitation
http://genes.mit.edu/burgelab/miso/index.html
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About testing error #130

Open zhengjiantao opened 5 years ago

zhengjiantao commented 5 years ago

I have installed MISO. And all dependence is ok. But I got an error when MISO test. The code shown below: python -m unittest discover misopy

The errors shown below(Maybe a little bit more information): Testing gene-level Psi... Executing: python /usr/local/lib/python2.7/dist-packages/misopy/index_gff.py --index /usr/local/lib/python2.7/dist-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff /usr/local/lib/python2.7/dist-packages/misopy/gff-events/mm9/indexed Traceback (most recent call last): File "/usr/local/lib/python2.7/dist-packages/misopy/index_gff.py", line 199, in main() File "/usr/local/lib/python2.7/dist-packages/misopy/index_gff.py", line 188, in main os.makedirs(output_dir) File "/usr/lib/python2.7/os.py", line 157, in makedirs mkdir(name, mode) OSError: [Errno 13] Permission denied: '/usr/local/lib/python2.7/dist-packages/misopy/gff-events/mm9/indexed' Executing: python /usr/local/lib/python2.7/dist-packages/misopy/run_events_analysis.py --compute-genes-psi /usr/local/lib/python2.7/dist-packages/misopy/gff-events/mm9/indexed /usr/local/lib/python2.7/dist-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam --output-dir /usr/local/lib/python2.7/dist-packages/misopy/test-output/gene-psi-output --read-len 36 --paired-end 250 30 --use-cluster MISO (Mixture of Isoforms model) To run MISO, please use "miso" instead. .Testing single-end SE event interface... Executing: python /usr/local/lib/python2.7/dist-packages/misopy/run_events_analysis.py --compute-events-psi se-sample /usr/local/lib/python2.7/dist-packages/misopy/test-data/se-counts/se_test.counts --output-dir /usr/local/lib/python2.7/dist-packages/misopy/test-output/SE-output --read-len 35 --overhang-len 4 --event-type SE --use-cluster MISO (Mixture of Isoforms model) To run MISO, please use "miso" instead. .Testing fr-unstranded... Checking read f_read against + Checking read f_read against - Checking read r_read against + Checking read r_read against - Testing fr-firststrand... .Testing conversion of SAM to BAM... Executing: sam_to_bam --convert /usr/local/lib/python2.7/dist-packages/misopy/test-data/sam-data/c2c12.Atp2b1.sam /usr/local/lib/python2.7/dist-packages/misopy/test-output/sam-output Converting SAM to BAM... Traceback (most recent call last): File "/usr/local/bin/sam_to_bam", line 11, in load_entry_point('misopy==0.5.4', 'console_scripts', 'sam_to_bam')() File "/usr/local/lib/python2.7/dist-packages/misopy/sam_to_bam.py", line 63, in main sam_to_bam(sam_filename, output_dir, header_ref=ref) File "/usr/local/lib/python2.7/dist-packages/misopy/sam_to_bam.py", line 13, in sam_to_bam os.makedirs(output_dir) File "/usr/lib/python2.7/os.py", line 150, in makedirs makedirs(head, mode) File "/usr/lib/python2.7/os.py", line 157, in makedirs mkdir(name, mode) OSError: [Errno 13] Permission denied: '/usr/local/lib/python2.7/dist-packages/misopy/test-output' FTesting gene-level Psi... Testing GFF indexing of: /usr/local/lib/python2.7/dist-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff Executing: index_gff --index /usr/local/lib/python2.7/dist-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff /usr/local/lib/python2.7/dist-packages/misopy/gff-events/mm9/genes/Atp2b1/indexed Traceback (most recent call last): File "/usr/local/bin/index_gff", line 11, in load_entry_point('misopy==0.5.4', 'console_scripts', 'index_gff')() File "/usr/local/lib/python2.7/dist-packages/misopy/index_gff.py", line 188, in main os.makedirs(output_dir) File "/usr/lib/python2.7/os.py", line 150, in makedirs makedirs(head, mode) File "/usr/lib/python2.7/os.py", line 157, in makedirs mkdir(name, mode) OSError: [Errno 13] Permission denied: '/usr/local/lib/python2.7/dist-packages/misopy/gff-events/mm9/genes/Atp2b1' Executing: miso --run /usr/local/lib/python2.7/dist-packages/misopy/gff-events/mm9/genes/Atp2b1/indexed /usr/local/lib/python2.7/dist-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam --output-dir /usr/local/lib/python2.7/dist-packages/misopy/test-output/gene-psi-output --read-len 36 MISO (Mixture of Isoforms model) Probabilistic analysis of RNA-Seq data for detecting differential isoforms Use --help argument to view options.

Using MISO settings file: /usr/local/lib/python2.7/dist-packages/misopy/settings/miso_settings.txt Traceback (most recent call last): File "/usr/local/bin/miso", line 11, in load_entry_point('misopy==0.5.4', 'console_scripts', 'miso')() File "/usr/local/lib/python2.7/dist-packages/misopy/miso.py", line 563, in main main_logger = get_main_logger(logs_output_dir) File "/usr/local/lib/python2.7/dist-packages/misopy/miso.py", line 54, in get_main_logger fh = logging.FileHandler(logger_fname) File "/usr/lib/python2.7/logging/init.py", line 913, in init StreamHandler.init(self, self._open()) File "/usr/lib/python2.7/logging/init.py", line 943, in _open stream = open(self.baseFilename, self.mode) IOError: [Errno 2] No such file or directory: '/usr/local/lib/python2.7/dist-packages/misopy/test-output/gene-psi-output/logs/main.2019-01-02_15-43-58.log' .

FAIL: test_a_sam_to_bam (misopy.test_miso.TestMISO)

Traceback (most recent call last): File "/usr/local/lib/python2.7/dist-packages/misopy/test_miso.py", line 51, in test_a_sam_to_bam "c2c12.Atp2b1.sorted.bam"))) AssertionError

Ran 5 tests in 2.677s FAILED (failures=1)

I saw someone says that error has to do with the version of samtools. Like -o refers to output path. So should I solve the test error? or say it will not affect normal use?

Thanks.

rolanddb commented 5 years ago

I'm facing the same issue.