Converting input files. (both directions in parallel)CMD: /diag/home/aubzyy/trinityrnaseq_r20140717/util/..//trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /diag/home/aubzyy/rnaseq/zhx/yellownutsedge/sequence/3-1-lane1_trimmed/3-1-lane1_forward_paired.fq >> left.fa
CMD: /diag/home/aubzyy/trinityrnaseq_r20140717/util/..//trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /diag/home/aubzyy/rnaseq/zhx/yellownutsedge/sequence/3-1-lane1_trimmed/3-1-lane1_reverse_paired.fq >> right.fa
Sequences parsed: 35659510
CMD finished (1070 seconds)
Sequences parsed: 35659510
CMD finished (1074 seconds)
CMD: touch left.fa.ok
CMD finished (0 seconds)
CMD: touch right.fa.ok
CMD finished (0 seconds)
Done converting input files.CMD: cat left.fa right.fa > both.fa
CMD finished (1268 seconds)
CMD: touch both.fa.ok
-------------------------------------------
----------- Jellyfish  --------------------
-- (building a k-mer catalog from reads) --
-------------------------------------------

CMD finished (0 seconds)
CMD: /diag/home/aubzyy/trinityrnaseq_r20140717/util/..//trinity-plugins/jellyfish/bin/jellyfish count -t 2 -m 25 -s 6289192884  --canonical  both.fa
CMD finished (1747 seconds)
CMD: /diag/home/aubzyy/trinityrnaseq_r20140717/util/..//trinity-plugins/jellyfish/bin/jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
CMD finished (112 seconds)
CMD: /diag/home/aubzyy/trinityrnaseq_r20140717/util/..//trinity-plugins/jellyfish/bin/jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
CMD finished (253 seconds)
CMD: touch jellyfish.K25.min2.kmers.fa.success
CMD finished (0 seconds)
CMD: /diag/home/aubzyy/trinityrnaseq_r20140717/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 2  --DS  > left.fa.K25.stats
CMD: /diag/home/aubzyy/trinityrnaseq_r20140717/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 2  --DS  > right.fa.K25.stats
-reading Kmer occurences...
-reading Kmer occurences...

 done parsing 56597872 Kmers, 56597872 added, taking 231 seconds.

 done parsing 56597872 Kmers, 56597872 added, taking 245 seconds.
STATS_GENERATION_TIME: 1723 seconds.
CMD finished (1989 seconds)
STATS_GENERATION_TIME: 1927 seconds.
CMD finished (2184 seconds)
CMD: touch left.fa.K25.stats.ok
CMD finished (0 seconds)
CMD: touch right.fa.K25.stats.ok
-sorting each stats file by read name.
CMD finished (0 seconds)
CMD: sort -k5,5 -T . -S 25G left.fa.K25.stats > left.fa.K25.stats.sort
CMD: sort -k5,5 -T . -S 25G right.fa.K25.stats > right.fa.K25.stats.sort
CMD finished (1947 seconds)
CMD finished (2012 seconds)
CMD: touch left.fa.K25.stats.sort.ok
CMD finished (0 seconds)
CMD: touch right.fa.K25.stats.sort.ok
CMD finished (0 seconds)
CMD: /diag/home/aubzyy/trinityrnaseq_r20140717/util/..//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats
-opening left.fa.K25.stats.sort
-opening right.fa.K25.stats.sort
-done opening files.
Error, pairs.K25.stats is empty.  Be sure to check your fastq reads and ensure that the read names are identical except for the /1 or /2 designation. at /diag/home/aubzyy/trinityrnaseq_r20140717/util/insilico_read_normalization.pl line 865.
CMD finished (737 seconds)