-prepping seqs Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -r -A <(gunzip -c /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/training/trimmomatic/trimmed_left.fastq.gz) >> left.fa CMD: seqtk-trinity seq -A <(gunzip -c /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/training/trimmomatic/trimmed_right.fastq.gz) >> right.fa CMD finished (97 seconds) CMD finished (103 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 (5 seconds) CMD: touch both.fa.ok CMD finished (0 seconds) -kmer counting. ------------------------------------------- ----------- Jellyfish -------------------- -- (building a k-mer catalog from reads) -- ------------------------------------------- CMD: jellyfish count -t 16 -m 25 -s 10291831386 both.fa CMD finished (230 seconds) CMD: jellyfish histo -t 16 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf CMD finished (28 seconds) CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa CMD finished (57 seconds) CMD: touch jellyfish.K25.min2.kmers.fa.success CMD finished (0 seconds) -generating stats files CMD: /venv/opt/trinity-2.8.5/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 8 > left.fa.K25.stats CMD: /venv/opt/trinity-2.8.5/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 8 > right.fa.K25.stats -reading Kmer occurrences... -reading Kmer occurrences... done parsing 139322625 Kmers, 135680320 added, taking 164 seconds. done parsing 139322625 Kmers, 135680320 added, taking 170 seconds. STATS_GENERATION_TIME: 570 seconds. STATS_GENERATION_TIME: 608 seconds. CMD finished (775 seconds) CMD finished (800 seconds) CMD: touch left.fa.K25.stats.ok CMD finished (0 seconds) CMD: touch right.fa.K25.stats.ok CMD finished (0 seconds) -sorting each stats file by read name. CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort --parallel=16 -k1,1 -T . -S 40G >> left.fa.K25.stats.sort CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort --parallel=16 -k1,1 -T . -S 40G >> right.fa.K25.stats.sort CMD finished (16 seconds) CMD finished (16 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) -defining normalized reads CMD: /venv/opt/trinity-2.8.5/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. CMD finished (360 seconds) CMD: touch pairs.K25.stats.ok CMD finished (0 seconds) CMD: /venv/opt/trinity-2.8.5/util/..//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 50 --min_cov 5 --max_CV 10000 > pairs.K25.stats.C50.maxCV10000.accs 3546992 / 28638946 = 12.39% reads selected during normalization. 0 / 28638946 = 0.00% reads discarded as likely aberrant based on coverage profiles. 558506 / 28638946 = 1.95% reads discarded as below minimum coverage threshold=5 CMD finished (222 seconds) CMD: touch pairs.K25.stats.C50.maxCV10000.accs.ok CMD finished (0 seconds) -search and capture. -preparing to extract selected reads from: /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/training/trimmomatic/trimmed_left.fastq.gz ... done prepping, now search and capture. -capturing normalized reads from: /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/training/trimmomatic/trimmed_left.fastq.gz -preparing to extract selected reads from: /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/training/trimmomatic/trimmed_right.fastq.gz ... done prepping, now search and capture. -capturing normalized reads from: /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/training/trimmomatic/trimmed_right.fastq.gz CMD: touch /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/training/normalize/trimmed_left.fastq.gz.normalized_K25_maxC50_minC5_maxCV10000.fq.ok CMD finished (0 seconds) CMD: touch /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/training/normalize/trimmed_right.fastq.gz.normalized_K25_maxC50_minC5_maxCV10000.fq.ok CMD finished (0 seconds) CMD: ln -sf /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/training/normalize/trimmed_left.fastq.gz.normalized_K25_maxC50_minC5_maxCV10000.fq left.norm.fq CMD finished (0 seconds) CMD: ln -sf /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/training/normalize/trimmed_right.fastq.gz.normalized_K25_maxC50_minC5_maxCV10000.fq right.norm.fq CMD finished (0 seconds) -removing tmp dir /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/training/normalize/tmp_normalized_reads Normalization complete. See outputs: /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/training/normalize/trimmed_left.fastq.gz.normalized_K25_maxC50_minC5_maxCV10000.fq /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/training/normalize/trimmed_right.fastq.gz.normalized_K25_maxC50_minC5_maxCV10000.fq