[2023-06-05 02:12:28,103] [INFO] DFAST_QC pipeline started.
[2023-06-05 02:12:28,107] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 02:12:28,108] [INFO] DQC Reference Directory: /var/lib/cwl/stg09e59ef0-2e82-440f-bacd-64b1fe0ff9ee/dqc_reference
[2023-06-05 02:12:30,926] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 02:12:30,931] [INFO] Task started: Prodigal
[2023-06-05 02:12:30,932] [INFO] Running command: gunzip -c /var/lib/cwl/stg572be898-0226-4849-b329-4bfcbe389a40/GCA_902768205.1_Rumen_uncultured_genome_RUG11338_genomic.fna.gz | prodigal -d GCA_902768205.1_Rumen_uncultured_genome_RUG11338_genomic.fna/cds.fna -a GCA_902768205.1_Rumen_uncultured_genome_RUG11338_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 02:12:35,662] [INFO] Task succeeded: Prodigal
[2023-06-05 02:12:35,662] [INFO] Task started: HMMsearch
[2023-06-05 02:12:35,662] [INFO] Running command: hmmsearch --tblout GCA_902768205.1_Rumen_uncultured_genome_RUG11338_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09e59ef0-2e82-440f-bacd-64b1fe0ff9ee/dqc_reference/reference_markers.hmm GCA_902768205.1_Rumen_uncultured_genome_RUG11338_genomic.fna/protein.faa > /dev/null
[2023-06-05 02:12:35,888] [INFO] Task succeeded: HMMsearch
[2023-06-05 02:12:35,890] [INFO] Found 6/6 markers.
[2023-06-05 02:12:35,913] [INFO] Query marker FASTA was written to GCA_902768205.1_Rumen_uncultured_genome_RUG11338_genomic.fna/markers.fasta
[2023-06-05 02:12:35,914] [INFO] Task started: Blastn
[2023-06-05 02:12:35,914] [INFO] Running command: blastn -query GCA_902768205.1_Rumen_uncultured_genome_RUG11338_genomic.fna/markers.fasta -db /var/lib/cwl/stg09e59ef0-2e82-440f-bacd-64b1fe0ff9ee/dqc_reference/reference_markers.fasta -out GCA_902768205.1_Rumen_uncultured_genome_RUG11338_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:12:36,579] [INFO] Task succeeded: Blastn
[2023-06-05 02:12:36,584] [INFO] Selected 26 target genomes.
[2023-06-05 02:12:36,585] [INFO] Target genome list was writen to GCA_902768205.1_Rumen_uncultured_genome_RUG11338_genomic.fna/target_genomes.txt
[2023-06-05 02:12:36,591] [INFO] Task started: fastANI
[2023-06-05 02:12:36,592] [INFO] Running command: fastANI --query /var/lib/cwl/stg572be898-0226-4849-b329-4bfcbe389a40/GCA_902768205.1_Rumen_uncultured_genome_RUG11338_genomic.fna.gz --refList GCA_902768205.1_Rumen_uncultured_genome_RUG11338_genomic.fna/target_genomes.txt --output GCA_902768205.1_Rumen_uncultured_genome_RUG11338_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 02:12:51,445] [INFO] Task succeeded: fastANI
[2023-06-05 02:12:51,446] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09e59ef0-2e82-440f-bacd-64b1fe0ff9ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 02:12:51,446] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09e59ef0-2e82-440f-bacd-64b1fe0ff9ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 02:12:51,448] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 02:12:51,448] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 02:12:51,448] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-06-05 02:12:51,450] [INFO] DFAST Taxonomy check result was written to GCA_902768205.1_Rumen_uncultured_genome_RUG11338_genomic.fna/tc_result.tsv
[2023-06-05 02:12:51,451] [INFO] ===== Taxonomy check completed =====
[2023-06-05 02:12:51,451] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 02:12:51,451] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09e59ef0-2e82-440f-bacd-64b1fe0ff9ee/dqc_reference/checkm_data
[2023-06-05 02:12:51,455] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 02:12:51,500] [INFO] Task started: CheckM
[2023-06-05 02:12:51,500] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902768205.1_Rumen_uncultured_genome_RUG11338_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902768205.1_Rumen_uncultured_genome_RUG11338_genomic.fna/checkm_input GCA_902768205.1_Rumen_uncultured_genome_RUG11338_genomic.fna/checkm_result
[2023-06-05 02:13:12,893] [INFO] Task succeeded: CheckM
[2023-06-05 02:13:12,895] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.89%
Contamintation: 17.80%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-06-05 02:13:12,926] [INFO] ===== Completeness check finished =====
[2023-06-05 02:13:12,927] [INFO] ===== Start GTDB Search =====
[2023-06-05 02:13:12,927] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902768205.1_Rumen_uncultured_genome_RUG11338_genomic.fna/markers.fasta)
[2023-06-05 02:13:12,928] [INFO] Task started: Blastn
[2023-06-05 02:13:12,928] [INFO] Running command: blastn -query GCA_902768205.1_Rumen_uncultured_genome_RUG11338_genomic.fna/markers.fasta -db /var/lib/cwl/stg09e59ef0-2e82-440f-bacd-64b1fe0ff9ee/dqc_reference/reference_markers_gtdb.fasta -out GCA_902768205.1_Rumen_uncultured_genome_RUG11338_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:13:14,104] [INFO] Task succeeded: Blastn
[2023-06-05 02:13:14,109] [INFO] Selected 13 target genomes.
[2023-06-05 02:13:14,109] [INFO] Target genome list was writen to GCA_902768205.1_Rumen_uncultured_genome_RUG11338_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 02:13:14,111] [INFO] Task started: fastANI
[2023-06-05 02:13:14,112] [INFO] Running command: fastANI --query /var/lib/cwl/stg572be898-0226-4849-b329-4bfcbe389a40/GCA_902768205.1_Rumen_uncultured_genome_RUG11338_genomic.fna.gz --refList GCA_902768205.1_Rumen_uncultured_genome_RUG11338_genomic.fna/target_genomes_gtdb.txt --output GCA_902768205.1_Rumen_uncultured_genome_RUG11338_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 02:13:19,437] [INFO] Task succeeded: fastANI
[2023-06-05 02:13:19,456] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 02:13:19,456] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_900317315.1	s__Ruminococcus_E sp900317315	98.915	442	522	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	98.84	97.27	0.87	0.80	119	conclusive
GCA_902784855.1	s__Ruminococcus_E sp902784855	82.0974	339	522	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316815.1	s__Ruminococcus_E sp900316815	81.9012	294	522	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	99.08	98.49	0.85	0.78	7	-
GCA_902799325.1	s__Ruminococcus_E sp902799325	81.7574	298	522	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902794395.1	s__Ruminococcus_E sp902794395	80.4874	307	522	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317595.1	s__Ruminococcus_E sp900317595	80.3891	266	522	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	99.55	99.10	0.91	0.83	3	-
GCA_902776375.1	s__Ruminococcus_E sp902776375	80.0614	319	522	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900100595.1	s__Ruminococcus_E sp900100595	79.871	268	522	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	98.87	97.87	0.91	0.78	34	-
GCA_902761375.1	s__Ruminococcus_E sp902761375	79.4256	219	522	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315195.1	s__Ruminococcus_E sp900315195	79.2309	207	522	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	99.59	99.19	0.95	0.90	3	-
GCA_900317875.1	s__Ruminococcus_E sp900317875	79.1746	226	522	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	99.86	99.86	0.92	0.92	2	-
GCA_900320415.1	s__Ruminococcus_E sp900320415	79.0526	169	522	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	99.69	99.69	0.84	0.84	2	-
GCF_016680995.1	s__Ruminococcus_E sp016680995	78.0658	169	522	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 02:13:19,458] [INFO] GTDB search result was written to GCA_902768205.1_Rumen_uncultured_genome_RUG11338_genomic.fna/result_gtdb.tsv
[2023-06-05 02:13:19,459] [INFO] ===== GTDB Search completed =====
[2023-06-05 02:13:19,466] [INFO] DFAST_QC result json was written to GCA_902768205.1_Rumen_uncultured_genome_RUG11338_genomic.fna/dqc_result.json
[2023-06-05 02:13:19,466] [INFO] DFAST_QC completed!
[2023-06-05 02:13:19,466] [INFO] Total running time: 0h0m51s