<div dir="ltr">Thanks. I fixed the python path problem and it is now invoking khmer from the new location. <div><div><br></div><div>python -c "import khmer; print khmer"</div><div><module 'khmer' from '/home/rajatroy/khmer/python/khmer/__init__.pyc'></div>
</div><div><br></div><div>I tried to invoke the default mode with :<div><br></div><div>python load-into-counting.py -k 31 <a href="http://out.kh">out.kh</a> 1Mreads.fa <br><div class="gmail_extra"><br>But it probably is not invoking the default mode where the memory should be expanding indefinitely. It says:</div>
<div class="gmail_extra"><br></div><div class="gmail_extra"><div class="gmail_extra">PARAMETERS:</div><div class="gmail_extra"> - kmer size = 31 (-k)</div><div class="gmail_extra"> - n hashes = 4 (-N)</div>
<div class="gmail_extra"> - min hashsize = 1e+06 (-x)</div><div class="gmail_extra"><br></div><div class="gmail_extra">Estimated memory usage is 4e+06 bytes (n_hashes x min_hashsize)</div><div class="gmail_extra">
--------</div><div class="gmail_extra">** WARNING: hashsize is default! You absodefly want to increase this!</div><div class="gmail_extra">** Please read the docs!</div><div class="gmail_extra">Saving hashtable to <a href="http://out.kh">out.kh</a></div>
<div class="gmail_extra">Loading kmers from sequences in ['/projects/Genomes/drosophila/1Mreads.fa']</div><div class="gmail_extra">making hashtable</div><div class="gmail_extra">consuming input /projects/Genomes/drosophila/1Mreads.fa</div>
<div class="gmail_extra">saving <a href="http://out.kh">out.kh</a></div><div class="gmail_extra">fp rate estimated to be 1.000</div><div class="gmail_extra">**</div><div class="gmail_extra">** ERROR: the counting hash is too small for</div>
<div class="gmail_extra">** this data set. Increase hashsize/num ht.</div><div class="gmail_extra">**</div><div><br></div></div><div class="gmail_extra"><div class="gmail_extra">I could not find any example of running the default mode in the khmer documentation (khmer/doc/scripts.txt). Could you please give me a sample command that invokes the default mode?</div>
<div class="gmail_extra"><br></div><div class="gmail_extra">Thanks</div><div class="gmail_extra"><br></div><div class="gmail_extra">Rajat</div><div class="gmail_extra"><br></div><div class="gmail_quote">On Tue, Aug 27, 2013 at 9:51 PM, C. Titus Brown <span dir="ltr"><<a href="mailto:ctb@msu.edu" target="_blank">ctb@msu.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div>On Tue, Aug 27, 2013 at 05:35:49PM -0400, Rajat Shuvro Roy wrote:<br>
> The new version is in a complete new directory. make test gives:<br>
<br>
</div>OK, all the tests pass, including the ones that run normalize-by-median. In<br>
that case it's almost certainly a problem with your PYTHONPATH -- make sure<br>
it points to the new directory's 'python' subdirectory.<br>
<br>
Do:<br>
<br>
% python -c "import khmer; print khmer"<br>
<br>
to see where khmer is being imported from -- it should be the new location.<br>
<br>
And yes, fixing installation is in the near future :)<br>
<br>
cheers,<br>
--titus<br>
<div><div><br>
><br>
> make test<br>
> cd lib && \<br>
> make<br>
> make[1]: Entering directory `/u2/home/rajatroy/khmer/lib'<br>
> make[1]: Nothing to be done for `all'.<br>
> make[1]: Leaving directory `/u2/home/rajatroy/khmer/lib'<br>
> cd python && \<br>
> make DEFINE_KHMER_EXTRA_SANITY_CHECKS="" \<br>
> CXX_DEBUG_FLAGS=""<br>
> make[1]: Entering directory `/u2/home/rajatroy/khmer/python'<br>
> python setup.py build_ext -i<br>
> running build_ext<br>
> copying build/lib.linux-x86_64-2.7/khmer/_khmermodule.so -> khmer<br>
> make[1]: Leaving directory `/u2/home/rajatroy/khmer/python'<br>
> nosetests -v -x -a \!known_failing<br>
> tests.test_align.test_alignnocov ... ok<br>
> tests.test_align.test_readalign ... ok<br>
> tests.test_align.test_alignerrorregion ... ok<br>
> tests.test_c_wrapper.test_raise_in_consume_fasta ... ok<br>
> tests.test_c_wrapper.test_raise_in_fasta_file_to_minmax ... ok<br>
> tests.test_counting_hash.Test_CountingHash.test_collision_1 ... ok<br>
> tests.test_counting_hash.Test_CountingHash.test_collision_2 ... ok<br>
> tests.test_counting_hash.Test_CountingHash.test_collision_3 ... ok<br>
> tests.test_counting_hash.test_3_tables ... ok<br>
> tests.test_counting_hash.test_simple_median ... ok<br>
> tests.test_counting_hash.test_simple_kadian ... ok<br>
> tests.test_counting_hash.test_simple_kadian_2 ... ok<br>
> tests.test_counting_hash.test_2_kadian ... ok<br>
> tests.test_counting_hash.test_save_load ... ok<br>
> tests.test_counting_hash.test_load_gz ... ok<br>
> tests.test_counting_hash.test_save_load_gz ... ok<br>
> tests.test_counting_hash.test_trim_full ... ok<br>
> tests.test_counting_hash.test_trim_short ... ok<br>
> tests.test_counting_hash.test_maxcount ... ok<br>
> tests.test_counting_hash.test_maxcount_with_bigcount ... ok<br>
> tests.test_counting_hash.test_maxcount_with_bigcount_save ... ok<br>
> tests.test_counting_hash.test_bigcount_save ... ok<br>
> tests.test_counting_hash.test_nobigcount_save ... ok<br>
> tests.test_counting_hash.test_bigcount_abund_dist ... ok<br>
> tests.test_counting_hash.test_bigcount_abund_dist_2 ... ok<br>
> tests.test_counting_hash.test_bigcount_overflow ... ok<br>
> tests.test_counting_hash.test_get_ksize ... ok<br>
> tests.test_counting_hash.test_get_hashsizes ... ok<br>
> tests.test_counting_single.Test_AbundanceDistribution.test_count_A ... ok<br>
> tests.test_counting_single.Test_ConsumeString.test_abundance_by_pos ... ok<br>
> tests.test_counting_single.Test_ConsumeString.test_abundance_by_pos_bigcount<br>
> ... ok<br>
> tests.test_counting_single.Test_ConsumeString.test_bounded ... ok<br>
> tests.test_counting_single.Test_ConsumeString.test_bounded_2 ... ok<br>
> tests.test_counting_single.Test_ConsumeString.test_bounded_2_rc ... ok<br>
> tests.test_counting_single.Test_ConsumeString.test_bounded_rc ... ok<br>
> tests.test_counting_single.Test_ConsumeString.test_max_count ... ok<br>
> tests.test_counting_single.Test_ConsumeString.test_max_count_in_bound ... ok<br>
> tests.test_counting_single.Test_ConsumeString.test_max_count_out_bound ...<br>
> ok<br>
> tests.test_counting_single.Test_ConsumeString.test_min_count ... ok<br>
> tests.test_counting_single.Test_ConsumeString.test_min_count_in_bound ... ok<br>
> tests.test_counting_single.Test_ConsumeString.test_min_count_out_bound ...<br>
> ok<br>
> tests.test_counting_single.Test_ConsumeString.test_n_occupied ... ok<br>
> tests.test_counting_single.Test_ConsumeString.test_n_occupied_args ... ok<br>
> tests.test_counting_single.Test_ConsumeString.test_simple ... ok<br>
> tests.test_counting_single.Test_ConsumeString.test_simple_2 ... ok<br>
> tests.test_counting_single.Test_ConsumeString.test_simple_rc ... ok<br>
> tests.test_counting_single.test_no_collision ... ok<br>
> tests.test_counting_single.test_collision ... ok<br>
> tests.test_counting_single.test_complete_no_collision ... ok<br>
> tests.test_counting_single.test_complete_2_collision ... ok<br>
> tests.test_counting_single.test_complete_4_collision ... ok<br>
> tests.test_counting_single.test_maxcount ... ok<br>
> tests.test_counting_single.test_maxcount_with_bigcount ... ok<br>
> tests.test_counting_single.test_consume_uniqify_first ... ok<br>
> tests.test_counting_single.test_maxcount_consume ... ok<br>
> tests.test_counting_single.test_maxcount_consume_with_bigcount ... ok<br>
> tests.test_counting_single.test_get_mincount ... ok<br>
> tests.test_counting_single.test_get_maxcount ... ok<br>
> tests.test_counting_single.test_get_maxcount_rc ... ok<br>
> tests.test_counting_single.test_get_mincount_rc ... ok<br>
> tests.test_counting_single.test_64bitshift ... ok<br>
> tests.test_counting_single.test_64bitshift_2 ... ok<br>
> tests.test_counting_single.test_very_short_read ... ok<br>
> tests.test_filter.Test_Filter.test_abund ... ok<br>
> tests.test_filter.test_filter_sodd ... ok<br>
> tests.test_functions.test_forward_hash ... ok<br>
> tests.test_functions.test_forward_hash_no_rc ... ok<br>
> tests.test_functions.test_reverse_hash ... ok<br>
> tests.test_functions.test_get_primes ... ok<br>
> tests.test_graph.Test_ExactGraphFu.test_counts ... ok<br>
> tests.test_graph.Test_ExactGraphFu.test_graph_links_next_a ... ok<br>
> tests.test_graph.Test_ExactGraphFu.test_graph_links_next_c ... ok<br>
> tests.test_graph.Test_ExactGraphFu.test_graph_links_next_g ... ok<br>
> tests.test_graph.Test_ExactGraphFu.test_graph_links_next_t ... ok<br>
> tests.test_graph.Test_ExactGraphFu.test_graph_links_prev_a ... ok<br>
> tests.test_graph.Test_ExactGraphFu.test_graph_links_prev_c ... ok<br>
> tests.test_graph.Test_ExactGraphFu.test_graph_links_prev_g ... ok<br>
> tests.test_graph.Test_ExactGraphFu.test_graph_links_prev_t ... ok<br>
> tests.test_graph.Test_InexactGraphFu.test_graph_links_next_a ... ok<br>
> tests.test_graph.Test_InexactGraphFu.test_graph_links_next_c ... ok<br>
> tests.test_graph.Test_InexactGraphFu.test_graph_links_next_g ... ok<br>
> tests.test_graph.Test_InexactGraphFu.test_graph_links_next_t ... ok<br>
> tests.test_graph.Test_InexactGraphFu.test_graph_links_prev_a ... ok<br>
> tests.test_graph.Test_InexactGraphFu.test_graph_links_prev_c ... ok<br>
> tests.test_graph.Test_InexactGraphFu.test_graph_links_prev_g ... ok<br>
> tests.test_graph.Test_InexactGraphFu.test_graph_links_prev_t ... ok<br>
> tests.test_graph.Test_Partitioning.test_connected_20_a ... ok<br>
> tests.test_graph.Test_Partitioning.test_connected_20_b ... ok<br>
> tests.test_graph.Test_Partitioning.test_connected_31_c ... ok<br>
> tests.test_graph.Test_Partitioning.test_disconnected_20_a ... ok<br>
> tests.test_graph.Test_Partitioning.test_disconnected_20_b ... ok<br>
> tests.test_graph.Test_Partitioning.test_disconnected_31_c ... ok<br>
> tests.test_graph.Test_Partitioning.test_not_output_unassigned ... ok<br>
> tests.test_graph.Test_Partitioning.test_output_unassigned ... ok<br>
> tests.test_graph.Test_PythonAPI.test_ordered_connect ... ok<br>
> tests.test_hashbits.test__get_set_tag_density ... ok<br>
> tests.test_hashbits.test_n_occupied_1 ... ok<br>
> tests.test_hashbits.test_bloom_python_1 ... ok<br>
> tests.test_hashbits.test_bloom_c_1 ... ok<br>
> tests.test_hashbits.test_n_occupied_2 ... ok<br>
> tests.test_hashbits.test_bloom_c_2 ... ok<br>
> tests.test_hashbits.test_filter_if_present ... ok<br>
> tests.test_hashbits.test_combine_pe ... ok<br>
> tests.test_hashbits.test_load_partitioned ... ok<br>
> tests.test_hashbits.test_count_within_radius_simple ... ok<br>
> tests.test_hashbits.test_count_within_radius_big ... ok<br>
> tests.test_hashbits.test_count_kmer_degree ... ok<br>
> tests.test_hashbits.test_find_radius_for_volume ... ok<br>
> tests.test_hashbits.test_circumference ... ok<br>
> tests.test_hashbits.test_save_load_tagset ... ok<br>
> tests.test_hashbits.test_save_load_tagset_noclear ... ok<br>
> tests.test_hashbits.test_stop_traverse ... ok<br>
> tests.test_hashbits.test_tag_across_stoptraverse ... ok<br>
> tests.test_hashbits.test_notag_across_stoptraverse ... ok<br>
> tests.test_hashbits.test_find_stoptags ... ok<br>
> tests.test_hashbits.test_find_stoptags2 ... ok<br>
> tests.test_hashbits.test_get_ksize ... ok<br>
> tests.test_hashbits.test_get_hashsizes ... ok<br>
> tests.test_hashbits.test_extract_unique_paths_0 ... ok<br>
> tests.test_hashbits.test_extract_unique_paths_1 ... ok<br>
> tests.test_hashbits.test_extract_unique_paths_2 ... ok<br>
> tests.test_hashbits.test_extract_unique_paths_3 ... ok<br>
> tests.test_hashbits.test_extract_unique_paths_4 ... ok<br>
> tests.test_hashbits.test_find_unpart ... ok<br>
> tests.test_hashbits.test_find_unpart_notraverse ... ok<br>
> tests.test_hashbits.test_find_unpart_fail ... ok<br>
> tests.test_hashbits.test_simple_median ... ok<br>
> Verify that 'has_extra_sanity_checks' exists. ... ok<br>
> Verify that all of the various attributes exist. ... ok<br>
> Verify that all of the various attributes exist. ... ok<br>
> Verify that all of the various attributes exist. ... ok<br>
> Verify that all of the various attributes exist. ... ok<br>
> Verify that the number of threads set is what is reported. ... ok<br>
> Verify that the reads file chunk size is what is reported. ... ok<br>
> tests.test_ktable.Test_KTable.test_basic ... ok<br>
> tests.test_ktable.Test_KTable.test_clear ... ok<br>
> tests.test_ktable.Test_KTable.test_consume ... ok<br>
> tests.test_ktable.Test_KTable.test_hash ... ok<br>
> tests.test_ktable.Test_KTable.test_intersection ... ok<br>
> tests.test_ktable.Test_KTable.test_operator_in ... ok<br>
> tests.test_ktable.Test_KTable.test_populate ... ok<br>
> tests.test_ktable.Test_KTable.test_update ... ok<br>
> tests.test_ktable.test_rc ... ok<br>
> tests.test_ktable.test_KmerCount ... ok<br>
> tests.test_lump.test_fakelump_together ... ok<br>
> tests.test_lump.test_fakelump_stop ... ok<br>
> tests.test_lump.test_fakelump_stop2 ... ok<br>
> tests.test_lump.test_fakelump_repartitioning ... ok<br>
> tests.test_minmax.Test_Basic.test_max_1 ... ok<br>
> tests.test_minmax.Test_Basic.test_max_2 ... ok<br>
> tests.test_minmax.Test_Basic.test_merge_1 ... ok<br>
> tests.test_minmax.Test_Basic.test_merge_2 ... ok<br>
> tests.test_minmax.Test_Basic.test_merge_3 ... ok<br>
> tests.test_minmax.Test_Basic.test_merge_4 ... ok<br>
> tests.test_minmax.Test_Basic.test_min_1 ... ok<br>
> tests.test_minmax.Test_Basic.test_min_2 ... ok<br>
> tests.test_minmax.Test_Basic.test_tablesize ... ok<br>
> tests.test_minmax.Test_Filestuff.test_save_no_load ... ok<br>
> tests.test_minmax.Test_Filestuff.test_saveload ... ok<br>
> tests.test_read_parsers.test_read_properties ... ok<br>
> tests.test_read_parsers.test_with_default_arguments ... ok<br>
> tests.test_read_parsers.test_gzip_decompression ... ok<br>
> tests.test_read_parsers.test_bzip2_decompression ... ok<br>
> tests.test_read_parsers.test_with_multiple_threads ... ok<br>
> tests.test_read_parsers.test_old_illumina_pair_mating ... ok<br>
> tests.test_read_parsers.test_casava_1_8_pair_mating ... ok<br>
> tests.test_read_parsers.test_iterator_identities ... ok<br>
> tests.test_read_parsers.test_read_pair_iterator_in_error_mode_xfail ... ok<br>
> tests.test_scripts.test_load_into_counting ... ok<br>
> tests.test_scripts.test_load_into_counting_fail ... ok<br>
> tests.test_scripts.test_filter_abund_1 ... ok<br>
> tests.test_scripts.test_filter_abund_2 ... ok<br>
> tests.test_scripts.test_filter_abund_3_fq_retained ... ok<br>
> tests.test_scripts.test_filter_abund_1_singlefile ... ok<br>
> tests.test_scripts.test_filter_abund_4_retain_low_abund ... ok<br>
> tests.test_scripts.test_filter_abund_5_trim_high_abund ... ok<br>
> tests.test_scripts.test_filter_abund_6_trim_high_abund_Z ... ok<br>
> tests.test_scripts.test_filter_stoptags ... ok<br>
> tests.test_scripts.test_normalize_by_median ... ok<br>
> tests.test_scripts.test_normalize_by_median_2 ... ok<br>
> tests.test_scripts.test_normalize_by_median_paired ... ok<br>
> tests.test_scripts.test_normalize_by_median_impaired ... ok<br>
> tests.test_scripts.test_normalize_by_median_force ... ok<br>
> tests.test_scripts.test_normalize_by_median_dumpfrequency ... ok<br>
> tests.test_scripts.test_normalize_by_median_empty ... ok<br>
> tests.test_scripts.test_count_median ... ok<br>
> tests.test_scripts.test_load_graph ... ok<br>
> tests.test_scripts.test_load_graph_no_tags ... ok<br>
> tests.test_scripts.test_load_graph_fail ... ok<br>
> tests.test_scripts.test_partition_graph_1 ... ok<br>
> tests.test_scripts.test_partition_graph_nojoin_k21 ... ok<br>
> tests.test_scripts.test_partition_graph_nojoin_stoptags ... ok<br>
> tests.test_scripts.test_partition_graph_big_traverse ... ok<br>
> tests.test_scripts.test_partition_graph_no_big_traverse ... ok<br>
> tests.test_scripts.test_annotate_partitions ... ok<br>
> tests.test_scripts.test_annotate_partitions_2 ... ok<br>
> tests.test_scripts.test_extract_partitions ... ok<br>
> tests.test_scripts.test_abundance_dist ... ok<br>
> tests.test_scripts.test_abundance_dist_nobigcount ... ok<br>
> tests.test_scripts.test_abundance_dist_single ... ok<br>
> tests.test_scripts.test_abundance_dist_single_nobigcount ... ok<br>
> tests.test_scripts.test_do_partition ... ok<br>
> tests.test_scripts.test_do_partition_2 ... ok<br>
> tests.test_scripts.test_interleave_reads_1_fq ... ok<br>
> tests.test_scripts.test_interleave_reads_2_fa ... ok<br>
> tests.test_scripts.test_extract_paired_reads_1_fa ... ok<br>
> tests.test_scripts.test_extract_paired_reads_2_fq ... ok<br>
> tests.test_scripts.test_split_paired_reads_1_fa ... ok<br>
> tests.test_scripts.test_split_paired_reads_2_fq ... ok<br>
> tests.test_split.test_2_split ... ok<br>
> tests.test_split.test_n_split ... ok<br>
> tests.test_split.test_n3_split ... ok<br>
> tests.test_subset_graph.Test_RandomData.test_3_merge_013 ... ok<br>
> tests.test_subset_graph.Test_RandomData.test_3_merge_023 ... ok<br>
> tests.test_subset_graph.Test_RandomData.test_5_merge_046 ... ok<br>
> tests.test_subset_graph.Test_RandomData.test_random_20_a_succ ... ok<br>
> tests.test_subset_graph.Test_RandomData.test_random_20_a_succ_II ... ok<br>
> tests.test_subset_graph.Test_RandomData.test_random_20_a_succ_III ... ok<br>
> tests.test_subset_graph.Test_RandomData.test_random_20_a_succ_IV ... ok<br>
> tests.test_subset_graph.Test_RandomData.test_random_20_a_succ_IV_save ... ok<br>
> tests.test_subset_graph.Test_SaveLoadPmap.test_save_load_merge ... ok<br>
> tests.test_subset_graph.Test_SaveLoadPmap.test_save_load_merge_2 ... ok<br>
> tests.test_subset_graph.Test_SaveLoadPmap.test_save_merge_from_disk ... ok<br>
> tests.test_subset_graph.Test_SaveLoadPmap.test_save_merge_from_disk_2 ... ok<br>
> tests.test_subset_graph.test_output_partitions ... ok<br>
> tests.test_subset_graph.test_tiny_real_partitions ... ok<br>
> tests.test_subset_graph.test_small_real_partitions ... ok<br>
> tests.test_threaded_sequence_processor.test_basic ... ok<br>
> tests.test_threaded_sequence_processor.test_basic_fastq_like ... ok<br>
> tests.test_threaded_sequence_processor.test_odd ... ok<br>
> tests.test_threaded_sequence_processor.test_basic_2thread ... ok<br>
> tests.test_threaded_sequence_processor.test_paired_2thread ... ok<br>
> tests.test_threaded_sequence_processor.test_paired_2thread_more_seq ... ok<br>
><br>
> ----------------------------------------------------------------------<br>
> Ran 233 tests in 20.632s<br>
><br>
> OK<br>
><br>
><br>
><br>
> On Tue, Aug 27, 2013 at 5:29 PM, C. Titus Brown <<a href="mailto:ctb@msu.edu" target="_blank">ctb@msu.edu</a>> wrote:<br>
><br>
> > Hmm, make sure you've deleted old versions of Khmer. What does 'make test'<br>
> > report in the top Khmer directory?<br>
> ><br>
> > ---<br>
> > C. Titus Brown, <a href="mailto:ctb@msu.edu" target="_blank">ctb@msu.edu</a><br>
> ><br>
> > On Aug 27, 2013, at 17:27, Rajat Shuvro Roy <<a href="mailto:rajatroy@cs.rutgers.edu" target="_blank">rajatroy@cs.rutgers.edu</a>><br>
> > wrote:<br>
> ><br>
> > Thanks so much. I downloaded and compiled the latest version. make test<br>
> > resulted in 'ok' for everything. However, when I tried to run it, I get the<br>
> > following message:<br>
> ><br>
> > python load-into-counting.py -k 31 -x 5e10 <a href="http://out.kh" target="_blank">out.kh</a> 1Mreads.fa<br>
> > Traceback (most recent call last):<br>
> > File "load-into-counting.py", line 13, in <module><br>
> > from khmer.counting_args import build_construct_args, report_on_config<br>
> > ImportError: cannot import name report_on_config<br>
> ><br>
> ><br>
> ><br>
> > On Tue, Aug 27, 2013 at 4:41 PM, C. Titus Brown <<a href="mailto:ctb@msu.edu" target="_blank">ctb@msu.edu</a>> wrote:<br>
> ><br>
> >> Hi Rajat,<br>
> >><br>
> >> sorry for long delay in response!<br>
> >><br>
> >> On Thu, Jul 18, 2013 at 03:32:39PM -0400, Rajat Shuvro Roy wrote:<br>
> >> > Hello Prof Brown,<br>
> >> > I was attempting to produce a k-mer frequency distribution using khmer<br>
> >> and<br>
> >> > followed the instructions in (<br>
> >> > <a href="http://khmer.readthedocs.org/en/latest/scripts.html" target="_blank">http://khmer.readthedocs.org/en/latest/scripts.html</a>) . I have a Zia<br>
> >> mays<br>
> >> > library (SRR404240, 95.8Gbp ) and I executed the following command.<br>
> >> ><br>
> >> > python load-into-counting.py -k 31 -x 5e10 <a href="http://out.kh" target="_blank">out.kh</a> SRR404240.fasta<br>
> >> ><br>
> >> > I believe, this counts k-mer frequencies and the script<br>
> >> abundance-dist.py<br>
> >> > produces the distribution.<br>
> >> ><br>
> >> > We stopped it after it had ran for 2464 mins (41hrs) using 187GB space.<br>
> >> I<br>
> >> > tried with smaller values for -x but failed to complete the computation<br>
> >> in<br>
> >> > less than 3 days. Could you please let us know if this is expected and<br>
> >> we<br>
> >> > should allow more time. And is there a more efficient way of using<br>
> >> Khmer?<br>
> >><br>
> >> Your e-mail actually triggered some doc changes and updates ;).<br>
> >><br>
> >> Briefly, khmer can count k-mers in either constant-memory mode or in<br>
> >> accurate-large-counts mode. In the former, counts above 255 will<br>
> >> stop being counted, but the memory specified with the -N and -x parameters<br>
> >> will be the total amount used; in the latter mode (which is the default),<br>
> >> counts above 255 will be kept and memory use will expand indefinitely.<br>
> >><br>
> >> You can use these modes easily in the latest khmer, the bleeding-edge<br>
> >> branch; you can get that like so:<br>
> >><br>
> >> git clone <a href="https://github.com/ged-lab/khmer.git" target="_blank">https://github.com/ged-lab/khmer.git</a> -b bleeding-edge<br>
> >><br>
> >> Then use 'load-into-counting.py -b' to build the tables, and<br>
> >> 'abundance-dist'<br>
> >> to generate the output.<br>
> >><br>
> >> I'd suggest running it on a small test data set (data/25k.fq.gz, in the<br>
> >> khmer repo) just to make sure it all works for you, but it should - we use<br>
> >> this regularly.<br>
> >><br>
> >> Please let me know if you have any questions, and again, apologies for<br>
> >> the delay!<br>
> >><br>
> >> cheers,<br>
> >> --titus<br>
> >> --<br>
> >> C. Titus Brown, <a href="mailto:ctb@msu.edu" target="_blank">ctb@msu.edu</a><br>
> >><br>
> ><br>
> ><br>
<br>
--<br>
C. Titus Brown, <a href="mailto:ctb@msu.edu" target="_blank">ctb@msu.edu</a><br>
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