bx3
commented
5 years ago Happy to know that the issue is solved. Just want to mention that we have a newer and faster version at https://github.com/bx3/Shannon_Cpp_RNA_seq.
Edit: I see. it is not solved; I will take a look on the other thread.
Hi,
Does anyone have any thought on the below error that came up using my original data when I did shannon? I completed it with no error using test data in the shannon/Samples directory.
Thu Oct 10 13:24:20 2019: Starting Shannon run.. Traceback (most recent call last): File "/home/***/Shannon/rc_s.py", line 35, in <module> main() File "/home/***/Shannon/rc_s.py", line 30, in main reverse_complement_serial(infile, outfile) File "/home/***/Shannon/rc_s.py", line 16, in reverse_complement_serial reads.append(reverse_complement(fields[0])) File "/home/***/Shannon/rc_s.py", line 3, in <lambda> reverse_complement = lambda x: ''.join([D[B] for B in x][::-1]) KeyError: '\x1f' cat: /datadrive/***/Assemble/Shannon/test_all/test_all_algo_input/rc.fasta: No such file or directory /bin/rm: cannot remove '/datadrive/Assemble/Shannon/test_all/test_all_algo_input/rc.fasta': No such file or directory Processed No of reads:3510991, Avg. Read length: 265.984430891 Thu Oct 10 13:24:23 2019: Starting Jellyfish to extract Kmers from Reads.. terminate called after throwing an instance of 'std::runtime_error' what(): Unsupported format Aborted (core dumped) Failed to open input file '/datadrive/***/Assemble/Shannon/test_all/test_all_algo_input/jellyfish_p1_output.jf' Thu Oct 10 13:24:24 2019: Jellyfish finished.. nJobs:1 reads_files:/datadrive/***/Assemble/Shannon/test_all/test_all_algo_input/reads.fasta Thu Oct 10 13:24:24 2019: Starting Kmer error correction.. Traceback (most recent call last): File "/home/***/Shannon/shannon.py", line 459, in <module> k1mer_dictionary,reads = extension_correction(str_ec.split(),dontWriteToFile) File "/home/***/Shannon/extension_correction.py", line 548, in extension_correction allowed_kmer_dict, reads = run_correction(infile, outfile, min_weight, min_length, double_stranded, comp_directory_name, comp_size_threshold, True, inMem, nJobs, reads_files) File "/home/***/Shannon/extension_correction.py", line 317, in run_correction kmers, K = load_kmers(infile, double_stranded,polyA_del) File "/home/***/Shannon/extension_correction.py", line 220, in load_kmers K = len(kmers.keys()[0]) IndexError: list index out of range