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segalab / SGVFinder

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have trouble in installation #6

Closed ucassee closed 5 years ago

ucassee commented 5 years ago

Dear developer, I don't know how to run ICRA_cmd.py . I use python /data2017/zhouyl/software/SGVFinder-master/src/ICRA_cmd.py /data2017/zhouyl/test/svgtest/result /dataNew/User/zhouyl/sediment/TS01_LD10/CLEAN_READS/TS01-LD10-1 --pe --use_theta to run. But it went error with

Traceback (most recent call last): File "/data2017/zhouyl/software/SGVFinder-master/src/ICRA_cmd.py", line 44, in args.outfol, args.max_mismatch, not args.consider_lengths, args.epsilon, args.max_iterations, \ AttributeError: 'Namespace' object has no attribute 'consider_lengths'

Hope to your reply. Thanks in advance. Best regards

talkr commented 5 years ago

Can you please try again with the latest code version?

ucassee commented 5 years ago

Hi @talkr, Thanks for your reply. When I update the software it still doesn't work with the following error:

Traceback (most recent call last): File "/data2017/zhouyl/software/SGVFinder-master/src/ICRA_cmd.py", line 48, in args.length_maximum, args.usage, args.use_theta) File "/data2017/zhouyl/software/SGVFinder-master/src/ICRA.py", line 30, in single_file gemmap_single_file(fq1, fq2, pmpf, indexl, seqdict, 0.05, 0.05, 2) File "/data2017/zhouyl/software/SGVFinder-master/src/GEMMapping.py", line 34, in gemmap_single_file threads=threads) File "/data2017/zhouyl/software/SGVFinder-master/src/GEMWrapperSlim.py", line 44, in dope_w_badread_removal suc, startnum = _dope(input1, input2, output_prefix, kwargs) File "/data2017/zhouyl/software/SGVFinder-master/src/GEMWrapperSlim.py", line 26, in _dope format(bin = GEM_BIN, locals()), loglevel = logging.DEBUG) File "/data2017/zhouyl/software/SGVFinder-master/src/ICRAUtils.py", line 84, in _shell_command errnout = sbcheck_output(com, shell = True, stderr = subprocess.STDOUT) File "/data2017/share/tools/miniconda3/lib/python2.7/subprocess.py", line 223, in check_output raise CalledProcessError(retcode, cmd, output=output) subprocess.CalledProcessError: Command 'gem-mapper -I /data2017/zhouyl/software/SGVFinder-master/src/../DataFiles/GEMSplit/representatives.contigs.drepped_0.gem -1 /data2017/zhouyl/test/svgtest/result_1.fastq -2 /data2017/zhouyl/test/svgtest/result_2.fastq -o /dataNew/User/zhouyl/sediment/TS01_LD10/CLEAN_READS/TS01-LD10-1/result_0 -q offset-33 --gem-quality-threshold 26 -m 0.05 -e 0.05 --min-matched-bases 0.8 --max-big-indel-length 15 -s 0 -d 20 -D 1 -p -E 0.3 --max-extendable-matches 20 --max-extensions-per-match 1 -v --max-insert-size 1000 -T 2' returned non-zero exit status 127

talkr commented 5 years ago

The error comes from the GEM mapper. Have you properly installed it? Can you run the command independently? What errors does it produce?

gem-mapper -I /data2017/zhouyl/software/SGVFinder-master/src/../DataFiles/GEMSplit/representatives.contigs.drepped_0.gem -1 /data2017/zhouyl/test/svgtest/result_1.fastq -2 /data2017/zhouyl/test/svgtest/result_2.fastq -o /dataNew/User/zhouyl/sediment/TS01_LD10/CLEAN_READS/TS01-LD10-1/result_0 -q offset-33 --gem-quality-threshold 26 -m 0.05 -e 0.05 --min-matched-bases 0.8 --max-big-indel-length 15 -s 0 -d 20 -D 1 -p -E 0.3 --max-extendable-matches 20 --max-extensions-per-match 1 -v --max-insert-size 1000 -T 2

ucassee commented 5 years ago

Hi @talkr , GEM mapper can call normally. But it run with the following error:

Traceback (most recent call last): File "/data2017/zhouyl/software/SGVFinder-master/src/ICRA_cmd.py", line 48, in args.length_maximum, args.usage, args.use_theta) File "/data2017/zhouyl/software/SGVFinder-master/src/ICRA.py", line 30, in single_file gemmap_single_file(fq1, fq2, pmpf, indexl, seqdict, 0.05, 0.05, 2) File "/data2017/zhouyl/software/SGVFinder-master/src/GEMMapping.py", line 34, in gemmap_single_file threads=threads) File "/data2017/zhouyl/software/SGVFinder-master/src/GEMWrapperSlim.py", line 44, in dope_w_badread_removal suc, startnum = _dope(input1, input2, output_prefix, kwargs) File "/data2017/zhouyl/software/SGVFinder-master/src/GEMWrapperSlim.py", line 26, in _dope format(bin = GEM_BIN, locals()), loglevel = logging.DEBUG) File "/data2017/zhouyl/software/SGVFinder-master/src/ICRAUtils.py", line 84, in _shell_command errnout = sbcheck_output(com, shell = True, stderr = subprocess.STDOUT) File "/data2017/share/tools/miniconda3/lib/python2.7/subprocess.py", line 223, in check_output raise CalledProcessError(retcode, cmd, output=output) subprocess.CalledProcessError: Command 'gem-mapper -I /data2017/zhouyl/software/SGVFinder-master/src/../DataFiles/GEMSplit/representatives.contigs.drepped_0.gem -1 /data2017/zhouyl/test/svgtest/result_1.fastq -2 /data2017/zhouyl/test/svgtest/result_2.fastq -o /dataNew/User/zhouyl/sediment/TS01_LD10/CLEAN_READS/TS01-LD10-1/result_0 -q offset-33 --gem-quality-threshold 26 -m 0.05 -e 0.05 --min-matched-bases 0.8 --max-big-indel-length 15 -s 0 -d 20 -D 1 -p -E 0.3 --max-extendable-matches 20 --max-extensions-per-match 1 -v --max-insert-size 1000 -T 2' returned non-zero exit status 1

talkr commented 5 years ago

The command is failing on calling the gem-mapper so it's obviously not running correctly. Can you please run the following command from your command line and give me the output?:

gem-mapper -I /data2017/zhouyl/software/SGVFinder-master/src/../DataFiles/GEMSplit/representatives.contigs.drepped_0.gem -1 /data2017/zhouyl/test/svgtest/result_1.fastq -2 /data2017/zhouyl/test/svgtest/result_2.fastq -o /dataNew/User/zhouyl/sediment/TS01_LD10/CLEAN_READS/TS01-LD10-1/result_0 -q offset-33 --gem-quality-threshold 26 -m 0.05 -e 0.05 --min-matched-bases 0.8 --max-big-indel-length 15 -s 0 -d 20 -D 1 -p -E 0.3 --max-extendable-matches 20 --max-extensions-per-match 1 -v --max-insert-size 1000 -T 2

ucassee commented 5 years ago

I guess I don't use the right input file as there is no any output file.

Welcome to GEM-mapper build 1.376 (beta) - (2013/04/06 02:13:06 GMT) (c) 2008-2013 Paolo Ribeca paolo.ribeca@gmail.com (c) 2010-2013 Santiago Marco Sola santiagomsola@gmail.com (c) 2010-2013 Leonor Frias Moya leonor.frias@gmail.com For the terms of use, run the program with the option --show-license.

  • WARNING: this is a beta version, provided for testing purposes only; *
  • check for updates at http://gemlibrary.sourceforge.net. *

    Fatal error (input.c:411,open_input_file) Could not stat file '/data2017/zhouyl/test/svgtest/result_1.fastq'

talkr commented 5 years ago

It seems that the file you gave as input: python /data2017/zhouyl/software/SGVFinder-master/src/ICRA_cmd.py /data2017/zhouyl/test/svgtest/result

Is not accessible.