[2023-06-05 02:27:15,849] [INFO] DFAST_QC pipeline started.
[2023-06-05 02:27:15,851] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 02:27:15,851] [INFO] DQC Reference Directory: /var/lib/cwl/stg57a58aed-c1e3-49dd-8001-4f102141e81e/dqc_reference
[2023-06-05 02:27:17,044] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 02:27:17,045] [INFO] Task started: Prodigal
[2023-06-05 02:27:17,045] [INFO] Running command: gunzip -c /var/lib/cwl/stg2ebfb8de-7323-4cbb-88d5-b70d9681226a/GCA_902782425.1_Rumen_uncultured_genome_RUG12772_genomic.fna.gz | prodigal -d GCA_902782425.1_Rumen_uncultured_genome_RUG12772_genomic.fna/cds.fna -a GCA_902782425.1_Rumen_uncultured_genome_RUG12772_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 02:27:35,491] [INFO] Task succeeded: Prodigal
[2023-06-05 02:27:35,492] [INFO] Task started: HMMsearch
[2023-06-05 02:27:35,492] [INFO] Running command: hmmsearch --tblout GCA_902782425.1_Rumen_uncultured_genome_RUG12772_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57a58aed-c1e3-49dd-8001-4f102141e81e/dqc_reference/reference_markers.hmm GCA_902782425.1_Rumen_uncultured_genome_RUG12772_genomic.fna/protein.faa > /dev/null
[2023-06-05 02:27:35,746] [INFO] Task succeeded: HMMsearch
[2023-06-05 02:27:35,748] [INFO] Found 6/6 markers.
[2023-06-05 02:27:35,778] [INFO] Query marker FASTA was written to GCA_902782425.1_Rumen_uncultured_genome_RUG12772_genomic.fna/markers.fasta
[2023-06-05 02:27:35,779] [INFO] Task started: Blastn
[2023-06-05 02:27:35,779] [INFO] Running command: blastn -query GCA_902782425.1_Rumen_uncultured_genome_RUG12772_genomic.fna/markers.fasta -db /var/lib/cwl/stg57a58aed-c1e3-49dd-8001-4f102141e81e/dqc_reference/reference_markers.fasta -out GCA_902782425.1_Rumen_uncultured_genome_RUG12772_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:27:36,358] [INFO] Task succeeded: Blastn
[2023-06-05 02:27:36,363] [INFO] Selected 26 target genomes.
[2023-06-05 02:27:36,364] [INFO] Target genome list was writen to GCA_902782425.1_Rumen_uncultured_genome_RUG12772_genomic.fna/target_genomes.txt
[2023-06-05 02:27:36,368] [INFO] Task started: fastANI
[2023-06-05 02:27:36,369] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ebfb8de-7323-4cbb-88d5-b70d9681226a/GCA_902782425.1_Rumen_uncultured_genome_RUG12772_genomic.fna.gz --refList GCA_902782425.1_Rumen_uncultured_genome_RUG12772_genomic.fna/target_genomes.txt --output GCA_902782425.1_Rumen_uncultured_genome_RUG12772_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 02:27:49,010] [INFO] Task succeeded: fastANI
[2023-06-05 02:27:49,011] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57a58aed-c1e3-49dd-8001-4f102141e81e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 02:27:49,011] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57a58aed-c1e3-49dd-8001-4f102141e81e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 02:27:49,013] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 02:27:49,014] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 02:27:49,014] [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 02:27:49,016] [INFO] DFAST Taxonomy check result was written to GCA_902782425.1_Rumen_uncultured_genome_RUG12772_genomic.fna/tc_result.tsv
[2023-06-05 02:27:49,017] [INFO] ===== Taxonomy check completed =====
[2023-06-05 02:27:49,017] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 02:27:49,018] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57a58aed-c1e3-49dd-8001-4f102141e81e/dqc_reference/checkm_data
[2023-06-05 02:27:49,022] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 02:27:49,052] [INFO] Task started: CheckM
[2023-06-05 02:27:49,052] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902782425.1_Rumen_uncultured_genome_RUG12772_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902782425.1_Rumen_uncultured_genome_RUG12772_genomic.fna/checkm_input GCA_902782425.1_Rumen_uncultured_genome_RUG12772_genomic.fna/checkm_result
[2023-06-05 02:28:41,606] [INFO] Task succeeded: CheckM
[2023-06-05 02:28:41,607] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 02:28:41,629] [INFO] ===== Completeness check finished =====
[2023-06-05 02:28:41,629] [INFO] ===== Start GTDB Search =====
[2023-06-05 02:28:41,630] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902782425.1_Rumen_uncultured_genome_RUG12772_genomic.fna/markers.fasta)
[2023-06-05 02:28:41,630] [INFO] Task started: Blastn
[2023-06-05 02:28:41,630] [INFO] Running command: blastn -query GCA_902782425.1_Rumen_uncultured_genome_RUG12772_genomic.fna/markers.fasta -db /var/lib/cwl/stg57a58aed-c1e3-49dd-8001-4f102141e81e/dqc_reference/reference_markers_gtdb.fasta -out GCA_902782425.1_Rumen_uncultured_genome_RUG12772_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:28:42,445] [INFO] Task succeeded: Blastn
[2023-06-05 02:28:42,451] [INFO] Selected 14 target genomes.
[2023-06-05 02:28:42,451] [INFO] Target genome list was writen to GCA_902782425.1_Rumen_uncultured_genome_RUG12772_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 02:28:42,461] [INFO] Task started: fastANI
[2023-06-05 02:28:42,461] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ebfb8de-7323-4cbb-88d5-b70d9681226a/GCA_902782425.1_Rumen_uncultured_genome_RUG12772_genomic.fna.gz --refList GCA_902782425.1_Rumen_uncultured_genome_RUG12772_genomic.fna/target_genomes_gtdb.txt --output GCA_902782425.1_Rumen_uncultured_genome_RUG12772_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 02:28:52,994] [INFO] Task succeeded: fastANI
[2023-06-05 02:28:53,007] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 02:28:53,007] [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_902790215.1	s__UBA1711 sp902790215	97.4859	830	946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	97.42	97.21	0.88	0.83	8	conclusive
GCA_900317125.1	s__UBA1711 sp900317125	82.7406	558	946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	96.93	96.01	0.87	0.83	22	-
GCA_017550405.1	s__UBA1711 sp017550405	82.5073	555	946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017530105.1	s__UBA1711 sp017530105	81.7624	465	946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317955.1	s__UBA1711 sp900317955	81.4505	454	946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	98.66	97.32	0.93	0.86	3	-
GCA_900318175.1	s__UBA1711 sp900318175	81.3735	485	946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	98.21	97.84	0.90	0.87	10	-
GCA_002309955.1	s__UBA1711 sp002309955	81.0577	411	946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	97.92	97.92	0.81	0.81	2	-
GCA_017545365.1	s__UBA1711 sp017545365	80.7397	448	946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	98.41	98.41	0.93	0.93	2	-
GCA_017479705.1	s__UBA1711 sp017479705	80.6622	342	946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002354035.1	s__UBA1711 sp002354035	80.3705	464	946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	99.39	99.39	0.95	0.95	2	-
GCA_017509045.1	s__UBA1711 sp017509045	80.3073	375	946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	97.14	97.14	0.86	0.86	2	-
GCA_016281475.1	s__UBA1711 sp016281475	80.2953	379	946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002368955.1	s__UBA1711 sp002368955	78.5972	297	946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017524785.1	s__UBA1711 sp017524785	77.7459	167	946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 02:28:53,009] [INFO] GTDB search result was written to GCA_902782425.1_Rumen_uncultured_genome_RUG12772_genomic.fna/result_gtdb.tsv
[2023-06-05 02:28:53,010] [INFO] ===== GTDB Search completed =====
[2023-06-05 02:28:53,013] [INFO] DFAST_QC result json was written to GCA_902782425.1_Rumen_uncultured_genome_RUG12772_genomic.fna/dqc_result.json
[2023-06-05 02:28:53,013] [INFO] DFAST_QC completed!
[2023-06-05 02:28:53,014] [INFO] Total running time: 0h1m37s