skoren
commented
9 years ago It looks like your system is missing the static libc library (glibc-static) which Quast needs to build MUmmer. Without MUMmer, quast will not run and thus you won't have a plot. You need to install the missing library, remove /home/samba/public/software/metAMOS-1.5rc3/quast/ and re-run INSTALL.py. You can also use iMetAMOS without Quast reports. In some cases Quast reports are not generated because no close reference is available for the genome being assembled.
TakashiKoyama
Hello.
I encountered another problem. I almost finished every iMetAMOS step and could see Postprocess/out/html/summary.html In that html page, Preprocess, Assemble, MapReads, Validate, FindORFS, Abundance, Annotate, Classify and Browse Results said "OK" but "QUAST report Loading..." in Validate window does not finish loading. I saw Logs/VALIDATE.log and found error messages as shown at the bottom of this message. I could not know what was JoblibIndexError but I at first tried to compile MUMmer manually by
pwd
/home/samba/public/software/metAMOS-1.5rc3/quast/libs/MUMmer3.23-linux
make check
check complete
make install
and got error as follows. /opt/rh/devtoolset-2/root/usr/libexec/gcc/x86_64-redhat-linux/4.8.2/ld: cannot find -lc collect2: error: ld returned 1 exit status chmod: cannot access
/home/samba/public/software/metAMOS-1.5rc3/quast/libs/MUMmer3.23-linux/mummer': No such file or directory make[2]: *** [mummer] Error 1 make[2]: Leaving directory/home/samba/public/software/metAMOS-1.5rc3/quast/libs/MUMmer3.23-linux/src/kurtz/mm3src' make[1]: * [mummer] Error 2 make[1]: Leaving directory `/home/samba/public/software/metAMOS-1.5rc3/quast/libs/MUMmer3.23-linux/src/kurtz' make: * [kurtz] Error 2This seems that gcc cannot find libc but I cannot know which libc file should be copied from where to where. Could you tell me a solution?
Error messages in Logs/VALIDATE.log
2015-04-24 21:03:51 Running Contig analyzer... Compiling MUMmer...
ERROR! Failed to compile MUMmer (/home/samba/public/software/metAMOS-1.5rc3/quast/libs/MUMmer3.23-linux)! Try to compile it manually!
JoblibIndexError
Multiprocessing exception: ........................................................................... /home/samba/public/software/metAMOS-1.5rc3/quast/metaquast.py in()
506 logger.finish_up()
507
508
509 if name == 'main':
510 try:
--> 511 return_code = main(sys.argv[1:])
512 exit(return_code)
513 except Exception, e:
514 logger.exception(e)
515
........................................................................... /home/samba/public/software/metAMOS-1.5rc3/quast/metaquast.py in main(args=['--est-ref-size', '98283', '-o', '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast', '-R', '/home/koyama/Documents/yellowtailSD/seq/BACassem...MOS/253h07/assembly1/Validate/out/proba.ref.fasta', '-T', '40', '-l', 'idba-ud_127,masurca_127,sga_127,spades_127,velvet_127', '/home/koyama/Documents/yellowtailSD/seq/BACassem...h07/assembly1/Assemble/out/idba-ud.127.asm.contig', '/home/koyama/Documents/yellowtailSD/seq/BACassem...h07/assembly1/Assemble/out/masurca.127.asm.contig', '/home/koyama/Documents/yellowtailSD/seq/BACassem.../253h07/assembly1/Assemble/out/sga.127.asm.contig', '/home/koyama/Documents/yellowtailSD/seq/BACassem...3h07/assembly1/Assemble/out/spades.127.asm.contig', '/home/koyama/Documents/yellowtailSD/seq/BACassem...3h07/assembly1/Assemble/out/velvet.127.asm.contig']) 463 logger.info('Starting quast.py ' + run_name + '...') 464 465 _start_quast_main(run_name, quast_py_args, 466 assemblies=assemblies, 467 reference_fpath=combined_ref_fpath, --> 468 output_dirpath=os.path.join(output_dirpath, 'combined_quast_output')) output_dirpath = '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast' 469 470 # Partitioning contigs into bins aligned to each reference 471 assemblies_by_reference, not_aligned_assemblies = _partition_contigs( 472 assemblies, ref_fpaths, corrected_dirpath,
........................................................................... /home/samba/public/software/metAMOS-1.5rc3/quast/metaquast.py in _start_quast_main(name='for the combined reference', args=['--est-ref-size', '98283', '-T', '40', '--meta', '/home/koyama/Documents/yellowtailSD/seq/BACassem...y1/Validate/out/quast/corrected_input/idba-ud_127', '/home/koyama/Documents/yellowtailSD/seq/BACassem...y1/Validate/out/quast/corrected_input/masurca_127', '/home/koyama/Documents/yellowtailSD/seq/BACassem...embly1/Validate/out/quast/corrected_input/sga_127', '/home/koyama/Documents/yellowtailSD/seq/BACassem...ly1/Validate/out/quast/corrected_input/spades_127', '/home/koyama/Documents/yellowtailSD/seq/BACassem...ly1/Validate/out/quast/corrected_input/velvet_127', '-R', '/home/koyama/Documents/yellowtailSD/seq/BACassem...ut/quast/corrected_input/combined_reference.fasta', '-o', '/home/koyama/Documents/yellowtailSD/seq/BACassem...ssembly1/Validate/out/quast/combined_quast_output', '--labels', '"idba-ud_127, masurca_127, sga_127, spades_127, velvet_127"'], assemblies=[<__main__.Assembly instance>, <main.Assembly instance>, <main.Assembly instance>, <main.Assembly instance>, <main.Assembly instance>], reference_fpath='/home/koyama/Documents/yellowtailSD/seq/BACassem...ut/quast/corrected_input/combined_reference.fasta', output_dirpath='/home/koyama/Documents/yellowtailSD/seq/BACassem...ssembly1/Validate/out/quast/combined_quast_output', exit_on_exception=True) 154 155 logger.info_to_file('(logging to ' + 156 os.path.join(output_dirpath, 157 qconfig.LOGGER_DEFAULT_NAME + '.log)')) 158 # try: --> 159 return quast.main(args) quast.main = <function main at 0x7ff647730938> args = ['--est-ref-size', '98283', '-T', '40', '--meta', '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/corrected_input/idba-ud_127', '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/corrected_input/masurca_127', '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/corrected_input/sga_127', '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/corrected_input/spades_127', '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/corrected_input/velvet_127', '-R', '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/corrected_input/combined_reference.fasta', '-o', '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/combined_quast_output', '--labels', '"idba-ud_127, masurca_127, sga_127, spades_127, velvet_127"'] 160 161 # except Exception, (errno, strerror): 162 # if exit_on_exception: 163 # logger.exception(e)
........................................................................... /home/samba/public/software/metAMOS-1.5rc3/quast/quast.py in main(args=['--est-ref-size', '98283', '-T', '40', '--meta', '/home/koyama/Documents/yellowtailSD/seq/BACassem...y1/Validate/out/quast/corrected_input/idba-ud_127', '/home/koyama/Documents/yellowtailSD/seq/BACassem...y1/Validate/out/quast/corrected_input/masurca_127', '/home/koyama/Documents/yellowtailSD/seq/BACassem...embly1/Validate/out/quast/corrected_input/sga_127', '/home/koyama/Documents/yellowtailSD/seq/BACassem...ly1/Validate/out/quast/corrected_input/spades_127', '/home/koyama/Documents/yellowtailSD/seq/BACassem...ly1/Validate/out/quast/corrected_input/velvet_127', '-R', '/home/koyama/Documents/yellowtailSD/seq/BACassem...ut/quast/corrected_input/combined_reference.fasta', '-o', '/home/koyama/Documents/yellowtailSD/seq/BACassem...ssembly1/Validate/out/quast/combined_quast_output', '--labels', '"idba-ud_127, masurca_127, sga_127, spades_127, velvet_127"']) 649 ######################################################################## 650 ### former PLANTAKOLYA, PLANTAGORA 651 ######################################################################## 652 from libs import contigs_analyzer 653 nucmer_statuses, aligned_lengths_per_fpath = contigs_analyzer.do( --> 654 ref_fpath, contigs_fpaths, qconfig.prokaryote, os.path.join(output_dirpath, 'contigs_reports')) ref_fpath = '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/combined_quast_output/corrected_input/combined_reference.fasta' contigs_fpaths = ['/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/combined_quast_output/corrected_input/idba-ud_127', '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/combined_quast_output/corrected_input/masurca_127', '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/combined_quast_output/corrected_input/sga_127', '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/combined_quast_output/corrected_input/spades_127', '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/combined_quast_output/corrected_input/velvet_127'] output_dirpath = '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/combined_quast_output' 655 for contigs_fpath in contigs_fpaths: 656 if nucmer_statuses[contigs_fpath] == contigs_analyzer.NucmerStatus.OK: 657 aligned_fpaths.append(contigs_fpath) 658 aligned_lengths_lists.append(aligned_lengths_per_fpath[contigs_fpath])
........................................................................... /home/samba/public/software/metAMOS-1.5rc3/quast/libs/contigs_analyzer.py in do(reference='/home/koyama/Documents/yellowtailSD/seq/BACassem...t_output/corrected_input/combined_reference.fasta', contigs_fpaths=['/home/koyama/Documents/yellowtailSD/seq/BACassem...combined_quast_output/corrected_input/idba-ud_127', '/home/koyama/Documents/yellowtailSD/seq/BACassem...combined_quast_output/corrected_input/masurca_127', '/home/koyama/Documents/yellowtailSD/seq/BACassem...ast/combined_quast_output/corrected_input/sga_127', '/home/koyama/Documents/yellowtailSD/seq/BACassem.../combined_quast_output/corrected_input/spades_127', '/home/koyama/Documents/yellowtailSD/seq/BACassem.../combined_quast_output/corrected_input/velvet_127'], cyclic=True, output_dir='/home/koyama/Documents/yellowtailSD/seq/BACassem...e/out/quast/combined_quast_output/contigs_reports') 1265 1266 n_jobs = min(len(contigs_fpaths), qconfig.max_threads) 1267 from joblib import Parallel, delayed 1268 statuses_results_lengths_tuples = Parallel(n_jobs=n_jobs)(delayed(plantakolya_process)( 1269 cyclic, nucmer_output_dir, fname, id, myenv, output_dir, reference) -> 1270 for id, fname in enumerate(contigs_fpaths)) id = undefined contigs_fpaths = ['/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/combined_quast_output/corrected_input/idba-ud_127', '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/combined_quast_output/corrected_input/masurca_127', '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/combined_quast_output/corrected_input/sga_127', '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/combined_quast_output/corrected_input/spades_127', '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/combined_quast_output/corrected_input/velvet_127'] 1271 # unzipping 1272 statuses, results, aligned_lengths = [x[0] for x in statuses_results_lengths_tuples], \ 1273 [x[1] for x in statuses_results_lengths_tuples], \ 1274 [x[2] for x in statuses_results_lengths_tuples]
........................................................................... /home/samba/public/software/metAMOS-1.5rc3/quast/libs/site_packages/joblib/parallel.py in call(self=Parallel(n_jobs=5), iterable=<generator object>)
480 self.n_dispatched = 0
481 try:
482 for function, args, kwargs in iterable:
483 self.dispatch(function, args, kwargs)
484
--> 485 self.retrieve()
self.retrieve = <bound method Parallel.retrieve of Parallel(n_jobs=5)>
486 # Make sure that we get a last message telling us we are done
487 elapsed_time = time.time() - self._start_time
488 self._print('Done %3i out of %3i | elapsed: %s finished',
489 (len(self._output),
Sub-process traceback:
IndexError Fri Apr 24 21:03:51 2015 PID: 9929 Python 2.7.8: /usr/local/pyenv/versions/2.7.8/bin/python ........................................................................... /home/samba/public/software/metAMOS-1.5rc3/quast/libs/contigs_analyzer.pyc in plantakolya_process(cyclic=True, nucmer_output_dirpath='/home/koyama/Documents/yellowtailSD/seq/BACassem...mbined_quast_output/contigs_reports/nucmer_output', contigs_fpath='/home/koyama/Documents/yellowtailSD/seq/BACassem...combined_quast_output/corrected_input/idba-ud_127', i=0, myenv={'BASH_FUNC_module()': '() { eval
/usr/bin/modulecmd bash $*\n}', 'BLASTDB': '/home/samba/public/BLASTDB', 'BT2_HOME': '/home/samba/public/software/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64', 'CONSED_PARAMETERS': '/usr/local/genome/lib/consedrc', 'CVS_RSH': 'ssh', 'G_BROKEN_FILENAMES': '1', 'HISTCONTROL': 'ignoredups', 'HISTSIZE': '1000', 'HOME': '/home/koyama', 'HOSTNAME': 'localhost.localdomain', ...}, output_dirpath='/home/koyama/Documents/yellowtailSD/seq/BACassem...e/out/quast/combined_quast_output/contigs_reports', ref_fpath='/home/koyama/Documents/yellowtailSD/seq/BACassem...t_output/corrected_input/combined_reference.fasta') 1214 i, myenv, output_dirpath, ref_fpath): 1215 assembly_name = qutils.name_from_fpath(contigs_fpath) 1216 1217 nucmer_fname = os.path.join(nucmer_output_dirpath, assembly_name) 1218 nucmer_is_ok, result, aligned_lengths = plantakolya( -> 1219 cyclic, i, contigs_fpath, nucmer_fname, myenv, output_dirpath, ref_fpath) 1220 1221 clear_files(contigs_fpath, nucmer_fname) 1222 return nucmer_is_ok, result, aligned_lengths 1223........................................................................... /home/samba/public/software/metAMOS-1.5rc3/quast/libs/contigs_analyzer.pyc in plantakolya(cyclic=True, i=0, contigs_fpath='/home/koyama/Documents/yellowtailSD/seq/BACassem...combined_quast_output/corrected_input/idba-ud_127', nucmer_fpath='/home/koyama/Documents/yellowtailSD/seq/BACassem..._output/contigs_reports/nucmer_output/idba-ud_127', myenv={'BASH_FUNC_module()': '() { eval
/usr/bin/modulecmd bash $*\n}', 'BLASTDB': '/home/samba/public/BLASTDB', 'BT2_HOME': '/home/samba/public/software/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64', 'CONSED_PARAMETERS': '/usr/local/genome/lib/consedrc', 'CVS_RSH': 'ssh', 'G_BROKEN_FILENAMES': '1', 'HISTCONTROL': 'ignoredups', 'HISTSIZE': '1000', 'HOME': '/home/koyama', 'HOSTNAME': 'localhost.localdomain', ...}, output_dirpath='/home/koyama/Documents/yellowtailSD/seq/BACassem...e/out/quast/combined_quast_output/contigs_reports', ref_fpath='/home/koyama/Documents/yellowtailSD/seq/BACassem...t_output/corrected_input/combined_reference.fasta') 200 tmp_coords_file = open(tmp_coords_fpath) 201 for line in tmp_coords_file: 202 header.append(line) 203 if line.startswith('====='): 204 break --> 205 coords_file.write(header[-2]) 206 coords_file.write(header[-1]) 207 for line in tmp_coords_file: 208 coords_file.write(line) 209 coords_file.close()IndexError: list index out of range
Traceback (most recent call last): File "/home/samba/public/software/metAMOS-1.5rc3/quast/metaquast.py", line 511, in
return_code = main(sys.argv[1:])
File "/home/samba/public/software/metAMOS-1.5rc3/quast/metaquast.py", line 468, in main
output_dirpath=os.path.join(output_dirpath, 'combined_quast_output'))
File "/home/samba/public/software/metAMOS-1.5rc3/quast/metaquast.py", line 159, in _start_quast_main
return quast.main(args)
File "/home/samba/public/software/metAMOS-1.5rc3/quast/quast.py", line 654, in main
ref_fpath, contigs_fpaths, qconfig.prokaryote, os.path.join(output_dirpath, 'contigs_reports'))
File "/home/samba/public/software/metAMOS-1.5rc3/quast/libs/contigs_analyzer.py", line 1270, in do
for id, fname in enumerate(contigs_fpaths))
File "/home/samba/public/software/metAMOS-1.5rc3/quast/libs/site_packages/joblib/parallel.py", line 485, in call
self.retrieve()
File "/home/samba/public/software/metAMOS-1.5rc3/quast/libs/site_packages/joblib/parallel.py", line 437, in retrieve
raise exception_type(report)
JoblibIndexError: JoblibIndexError
Multiprocessing exception: ........................................................................... /home/samba/public/software/metAMOS-1.5rc3/quast/metaquast.py in()
506 logger.finish_up()
507
508
509 if name == 'main':
510 try:
--> 511 return_code = main(sys.argv[1:])
512 exit(return_code)
513 except Exception, e:
514 logger.exception(e)
515
........................................................................... /home/samba/public/software/metAMOS-1.5rc3/quast/metaquast.py in main(args=['--est-ref-size', '98283', '-o', '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast', '-R', '/home/koyama/Documents/yellowtailSD/seq/BACassem...MOS/253h07/assembly1/Validate/out/proba.ref.fasta', '-T', '40', '-l', 'idba-ud_127,masurca_127,sga_127,spades_127,velvet_127', '/home/koyama/Documents/yellowtailSD/seq/BACassem...h07/assembly1/Assemble/out/idba-ud.127.asm.contig', '/home/koyama/Documents/yellowtailSD/seq/BACassem...h07/assembly1/Assemble/out/masurca.127.asm.contig', '/home/koyama/Documents/yellowtailSD/seq/BACassem.../253h07/assembly1/Assemble/out/sga.127.asm.contig', '/home/koyama/Documents/yellowtailSD/seq/BACassem...3h07/assembly1/Assemble/out/spades.127.asm.contig', '/home/koyama/Documents/yellowtailSD/seq/BACassem...3h07/assembly1/Assemble/out/velvet.127.asm.contig']) 463 logger.info('Starting quast.py ' + run_name + '...') 464 465 _start_quast_main(run_name, quast_py_args, 466 assemblies=assemblies, 467 reference_fpath=combined_ref_fpath, --> 468 output_dirpath=os.path.join(output_dirpath, 'combined_quast_output')) output_dirpath = '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast' 469 470 # Partitioning contigs into bins aligned to each reference 471 assemblies_by_reference, not_aligned_assemblies = _partition_contigs( 472 assemblies, ref_fpaths, corrected_dirpath,
........................................................................... /home/samba/public/software/metAMOS-1.5rc3/quast/metaquast.py in _start_quast_main(name='for the combined reference', args=['--est-ref-size', '98283', '-T', '40', '--meta', '/home/koyama/Documents/yellowtailSD/seq/BACassem...y1/Validate/out/quast/corrected_input/idba-ud_127', '/home/koyama/Documents/yellowtailSD/seq/BACassem...y1/Validate/out/quast/corrected_input/masurca_127', '/home/koyama/Documents/yellowtailSD/seq/BACassem...embly1/Validate/out/quast/corrected_input/sga_127', '/home/koyama/Documents/yellowtailSD/seq/BACassem...ly1/Validate/out/quast/corrected_input/spades_127', '/home/koyama/Documents/yellowtailSD/seq/BACassem...ly1/Validate/out/quast/corrected_input/velvet_127', '-R', '/home/koyama/Documents/yellowtailSD/seq/BACassem...ut/quast/corrected_input/combined_reference.fasta', '-o', '/home/koyama/Documents/yellowtailSD/seq/BACassem...ssembly1/Validate/out/quast/combined_quast_output', '--labels', '"idba-ud_127, masurca_127, sga_127, spades_127, velvet_127"'], assemblies=[<__main__.Assembly instance>, <main.Assembly instance>, <main.Assembly instance>, <main.Assembly instance>, <main.Assembly instance>], reference_fpath='/home/koyama/Documents/yellowtailSD/seq/BACassem...ut/quast/corrected_input/combined_reference.fasta', output_dirpath='/home/koyama/Documents/yellowtailSD/seq/BACassem...ssembly1/Validate/out/quast/combined_quast_output', exit_on_exception=True) 154 155 logger.info_to_file('(logging to ' + 156 os.path.join(output_dirpath, 157 qconfig.LOGGER_DEFAULT_NAME + '.log)')) 158 # try: --> 159 return quast.main(args) quast.main = <function main at 0x7ff647730938> args = ['--est-ref-size', '98283', '-T', '40', '--meta', '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/corrected_input/idba-ud_127', '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/corrected_input/masurca_127', '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/corrected_input/sga_127', '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/corrected_input/spades_127', '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/corrected_input/velvet_127', '-R', '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/corrected_input/combined_reference.fasta', '-o', '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/combined_quast_output', '--labels', '"idba-ud_127, masurca_127, sga_127, spades_127, velvet_127"'] 160 161 # except Exception, (errno, strerror): 162 # if exit_on_exception: 163 # logger.exception(e)
........................................................................... /home/samba/public/software/metAMOS-1.5rc3/quast/quast.py in main(args=['--est-ref-size', '98283', '-T', '40', '--meta', '/home/koyama/Documents/yellowtailSD/seq/BACassem...y1/Validate/out/quast/corrected_input/idba-ud_127', '/home/koyama/Documents/yellowtailSD/seq/BACassem...y1/Validate/out/quast/corrected_input/masurca_127', '/home/koyama/Documents/yellowtailSD/seq/BACassem...embly1/Validate/out/quast/corrected_input/sga_127', '/home/koyama/Documents/yellowtailSD/seq/BACassem...ly1/Validate/out/quast/corrected_input/spades_127', '/home/koyama/Documents/yellowtailSD/seq/BACassem...ly1/Validate/out/quast/corrected_input/velvet_127', '-R', '/home/koyama/Documents/yellowtailSD/seq/BACassem...ut/quast/corrected_input/combined_reference.fasta', '-o', '/home/koyama/Documents/yellowtailSD/seq/BACassem...ssembly1/Validate/out/quast/combined_quast_output', '--labels', '"idba-ud_127, masurca_127, sga_127, spades_127, velvet_127"']) 649 ######################################################################## 650 ### former PLANTAKOLYA, PLANTAGORA 651 ######################################################################## 652 from libs import contigs_analyzer 653 nucmer_statuses, aligned_lengths_per_fpath = contigs_analyzer.do( --> 654 ref_fpath, contigs_fpaths, qconfig.prokaryote, os.path.join(output_dirpath, 'contigs_reports')) ref_fpath = '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/combined_quast_output/corrected_input/combined_reference.fasta' contigs_fpaths = ['/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/combined_quast_output/corrected_input/idba-ud_127', '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/combined_quast_output/corrected_input/masurca_127', '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/combined_quast_output/corrected_input/sga_127', '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/combined_quast_output/corrected_input/spades_127', '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/combined_quast_output/corrected_input/velvet_127'] output_dirpath = '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/combined_quast_output' 655 for contigs_fpath in contigs_fpaths: 656 if nucmer_statuses[contigs_fpath] == contigs_analyzer.NucmerStatus.OK: 657 aligned_fpaths.append(contigs_fpath) 658 aligned_lengths_lists.append(aligned_lengths_per_fpath[contigs_fpath])
........................................................................... /home/samba/public/software/metAMOS-1.5rc3/quast/libs/contigs_analyzer.py in do(reference='/home/koyama/Documents/yellowtailSD/seq/BACassem...t_output/corrected_input/combined_reference.fasta', contigs_fpaths=['/home/koyama/Documents/yellowtailSD/seq/BACassem...combined_quast_output/corrected_input/idba-ud_127', '/home/koyama/Documents/yellowtailSD/seq/BACassem...combined_quast_output/corrected_input/masurca_127', '/home/koyama/Documents/yellowtailSD/seq/BACassem...ast/combined_quast_output/corrected_input/sga_127', '/home/koyama/Documents/yellowtailSD/seq/BACassem.../combined_quast_output/corrected_input/spades_127', '/home/koyama/Documents/yellowtailSD/seq/BACassem.../combined_quast_output/corrected_input/velvet_127'], cyclic=True, output_dir='/home/koyama/Documents/yellowtailSD/seq/BACassem...e/out/quast/combined_quast_output/contigs_reports') 1265 1266 n_jobs = min(len(contigs_fpaths), qconfig.max_threads) 1267 from joblib import Parallel, delayed 1268 statuses_results_lengths_tuples = Parallel(n_jobs=n_jobs)(delayed(plantakolya_process)( 1269 cyclic, nucmer_output_dir, fname, id, myenv, output_dir, reference) -> 1270 for id, fname in enumerate(contigs_fpaths)) id = undefined contigs_fpaths = ['/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/combined_quast_output/corrected_input/idba-ud_127', '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/combined_quast_output/corrected_input/masurca_127', '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/combined_quast_output/corrected_input/sga_127', '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/combined_quast_output/corrected_input/spades_127', '/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Validate/out/quast/combined_quast_output/corrected_input/velvet_127'] 1271 # unzipping 1272 statuses, results, aligned_lengths = [x[0] for x in statuses_results_lengths_tuples], \ 1273 [x[1] for x in statuses_results_lengths_tuples], \ 1274 [x[2] for x in statuses_results_lengths_tuples]
........................................................................... /home/samba/public/software/metAMOS-1.5rc3/quast/libs/site_packages/joblib/parallel.py in call(self=Parallel(n_jobs=5), iterable=<generator object>)
480 self.n_dispatched = 0
481 try:
482 for function, args, kwargs in iterable:
483 self.dispatch(function, args, kwargs)
484
--> 485 self.retrieve()
self.retrieve = <bound method Parallel.retrieve of Parallel(n_jobs=5)>
486 # Make sure that we get a last message telling us we are done
487 elapsed_time = time.time() - self._start_time
488 self._print('Done %3i out of %3i | elapsed: %s finished',
489 (len(self._output),
Sub-process traceback:
IndexError Fri Apr 24 21:03:51 2015 PID: 9929 Python 2.7.8: /usr/local/pyenv/versions/2.7.8/bin/python ........................................................................... /home/samba/public/software/metAMOS-1.5rc3/quast/libs/contigs_analyzer.pyc in plantakolya_process(cyclic=True, nucmer_output_dirpath='/home/koyama/Documents/yellowtailSD/seq/BACassem...mbined_quast_output/contigs_reports/nucmer_output', contigs_fpath='/home/koyama/Documents/yellowtailSD/seq/BACassem...combined_quast_output/corrected_input/idba-ud_127', i=0, myenv={'BASH_FUNC_module()': '() { eval
/usr/bin/modulecmd bash $*\n}', 'BLASTDB': '/home/samba/public/BLASTDB', 'BT2_HOME': '/home/samba/public/software/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64', 'CONSED_PARAMETERS': '/usr/local/genome/lib/consedrc', 'CVS_RSH': 'ssh', 'G_BROKEN_FILENAMES': '1', 'HISTCONTROL': 'ignoredups', 'HISTSIZE': '1000', 'HOME': '/home/koyama', 'HOSTNAME': 'localhost.localdomain', ...}, output_dirpath='/home/koyama/Documents/yellowtailSD/seq/BACassem...e/out/quast/combined_quast_output/contigs_reports', ref_fpath='/home/koyama/Documents/yellowtailSD/seq/BACassem...t_output/corrected_input/combined_reference.fasta') 1214 i, myenv, output_dirpath, ref_fpath): 1215 assembly_name = qutils.name_from_fpath(contigs_fpath) 1216 1217 nucmer_fname = os.path.join(nucmer_output_dirpath, assembly_name) 1218 nucmer_is_ok, result, aligned_lengths = plantakolya( -> 1219 cyclic, i, contigs_fpath, nucmer_fname, myenv, output_dirpath, ref_fpath) 1220 1221 clear_files(contigs_fpath, nucmer_fname) 1222 return nucmer_is_ok, result, aligned_lengths 1223........................................................................... /home/samba/public/software/metAMOS-1.5rc3/quast/libs/contigs_analyzer.pyc in plantakolya(cyclic=True, i=0, contigs_fpath='/home/koyama/Documents/yellowtailSD/seq/BACassem...combined_quast_output/corrected_input/idba-ud_127', nucmer_fpath='/home/koyama/Documents/yellowtailSD/seq/BACassem..._output/contigs_reports/nucmer_output/idba-ud_127', myenv={'BASH_FUNC_module()': '() { eval
/usr/bin/modulecmd bash $*\n}', 'BLASTDB': '/home/samba/public/BLASTDB', 'BT2_HOME': '/home/samba/public/software/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64', 'CONSED_PARAMETERS': '/usr/local/genome/lib/consedrc', 'CVS_RSH': 'ssh', 'G_BROKEN_FILENAMES': '1', 'HISTCONTROL': 'ignoredups', 'HISTSIZE': '1000', 'HOME': '/home/koyama', 'HOSTNAME': 'localhost.localdomain', ...}, output_dirpath='/home/koyama/Documents/yellowtailSD/seq/BACassem...e/out/quast/combined_quast_output/contigs_reports', ref_fpath='/home/koyama/Documents/yellowtailSD/seq/BACassem...t_output/corrected_input/combined_reference.fasta') 200 tmp_coords_file = open(tmp_coords_fpath) 201 for line in tmp_coords_file: 202 header.append(line) 203 if line.startswith('====='): 204 break --> 205 coords_file.write(header[-2]) 206 coords_file.write(header[-1]) 207 for line in tmp_coords_file: 208 coords_file.write(line) 209 coords_file.close()IndexError: list index out of range
unlink: cannot unlink
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unlink/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Assemble/out/proba.lib6.mates_in_diff_contigs': No such file or directory unlink: cannot unlink/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Assemble/out/proba.lib6contig.reads': No such file or directory unlink: cannot unlink/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Assemble/out/lib6.unaligned.fasta': No such file or directory unlink: cannot unlink/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Assemble/out/lib6.unaligned.fastq': No such file or directory unlink: cannot unlink/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Assemble/out/proba.lib7.badmates': No such file or directory unlink: cannot unlink/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Assemble/out/proba.lib7.hdr': No such file or directory unlink: cannot 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unlink/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Assemble/out/proba.lib8.hdr': No such file or directory unlink: cannot unlink/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Assemble/out/proba.lib8.mappedmates': No such file or directory unlink: cannot unlink/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Assemble/out/proba.lib8.mates_in_diff_contigs': No such file or directory unlink: cannot unlink/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Assemble/out/proba.lib8contig.reads': No such file or directory unlink: cannot unlink/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Assemble/out/lib8.unaligned.fasta': No such file or directory unlink: cannot unlink/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Assemble/out/lib8.unaligned.fastq': No such file or directory unlink: cannot unlink/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Assemble/out/proba.lib9.badmates': No such file or directory unlink: cannot unlink/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Assemble/out/proba.lib9.hdr': No such file or directory unlink: cannot unlink/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Assemble/out/proba.lib9.mappedmates': No such file or directory unlink: cannot unlink/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Assemble/out/proba.lib9.mates_in_diff_contigs': No such file or directory unlink: cannot unlink/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Assemble/out/proba.lib9contig.reads': No such file or directory unlink: cannot unlink/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Assemble/out/lib9.unaligned.fasta': No such file or directory unlink: cannot unlink `/home/koyama/Documents/yellowtailSD/seq/BACassembly/iMetAMOS/253h07/assembly1/Assemble/out/lib9.unaligned.fastq': No such file or directory