[2023-06-16 19:05:16,687] [INFO] DFAST_QC pipeline started.
[2023-06-16 19:05:16,689] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 19:05:16,689] [INFO] DQC Reference Directory: /var/lib/cwl/stge408535e-4883-4eaa-9468-71b55bc099e2/dqc_reference
[2023-06-16 19:05:17,812] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 19:05:17,812] [INFO] Task started: Prodigal
[2023-06-16 19:05:17,812] [INFO] Running command: gunzip -c /var/lib/cwl/stg6694a769-caf6-4e0f-bf3b-563729703e04/GCA_905199095.1_ERR1305892-mag-bin.20_genomic.fna.gz | prodigal -d GCA_905199095.1_ERR1305892-mag-bin.20_genomic.fna/cds.fna -a GCA_905199095.1_ERR1305892-mag-bin.20_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 19:05:28,826] [INFO] Task succeeded: Prodigal
[2023-06-16 19:05:28,826] [INFO] Task started: HMMsearch
[2023-06-16 19:05:28,826] [INFO] Running command: hmmsearch --tblout GCA_905199095.1_ERR1305892-mag-bin.20_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge408535e-4883-4eaa-9468-71b55bc099e2/dqc_reference/reference_markers.hmm GCA_905199095.1_ERR1305892-mag-bin.20_genomic.fna/protein.faa > /dev/null
[2023-06-16 19:05:29,015] [INFO] Task succeeded: HMMsearch
[2023-06-16 19:05:29,016] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6694a769-caf6-4e0f-bf3b-563729703e04/GCA_905199095.1_ERR1305892-mag-bin.20_genomic.fna.gz]
[2023-06-16 19:05:29,041] [INFO] Query marker FASTA was written to GCA_905199095.1_ERR1305892-mag-bin.20_genomic.fna/markers.fasta
[2023-06-16 19:05:29,042] [INFO] Task started: Blastn
[2023-06-16 19:05:29,042] [INFO] Running command: blastn -query GCA_905199095.1_ERR1305892-mag-bin.20_genomic.fna/markers.fasta -db /var/lib/cwl/stge408535e-4883-4eaa-9468-71b55bc099e2/dqc_reference/reference_markers.fasta -out GCA_905199095.1_ERR1305892-mag-bin.20_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:05:29,643] [INFO] Task succeeded: Blastn
[2023-06-16 19:05:29,647] [INFO] Selected 27 target genomes.
[2023-06-16 19:05:29,647] [INFO] Target genome list was writen to GCA_905199095.1_ERR1305892-mag-bin.20_genomic.fna/target_genomes.txt
[2023-06-16 19:05:29,649] [INFO] Task started: fastANI
[2023-06-16 19:05:29,649] [INFO] Running command: fastANI --query /var/lib/cwl/stg6694a769-caf6-4e0f-bf3b-563729703e04/GCA_905199095.1_ERR1305892-mag-bin.20_genomic.fna.gz --refList GCA_905199095.1_ERR1305892-mag-bin.20_genomic.fna/target_genomes.txt --output GCA_905199095.1_ERR1305892-mag-bin.20_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 19:05:42,572] [INFO] Task succeeded: fastANI
[2023-06-16 19:05:42,573] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge408535e-4883-4eaa-9468-71b55bc099e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 19:05:42,573] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge408535e-4883-4eaa-9468-71b55bc099e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 19:05:42,579] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 19:05:42,579] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 19:05:42,579] [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
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	76.9396	74	775	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	76.9158	75	775	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	76.9105	75	775	95	below_threshold
Palleniella intestinalis	strain=PINT	GCA_013166595.1	2736291	2736291	type	True	76.4426	65	775	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.2752	64	775	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	76.0469	74	775	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 19:05:42,580] [INFO] DFAST Taxonomy check result was written to GCA_905199095.1_ERR1305892-mag-bin.20_genomic.fna/tc_result.tsv
[2023-06-16 19:05:42,581] [INFO] ===== Taxonomy check completed =====
[2023-06-16 19:05:42,581] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 19:05:42,581] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge408535e-4883-4eaa-9468-71b55bc099e2/dqc_reference/checkm_data
[2023-06-16 19:05:42,582] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 19:05:42,636] [INFO] Task started: CheckM
[2023-06-16 19:05:42,636] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905199095.1_ERR1305892-mag-bin.20_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905199095.1_ERR1305892-mag-bin.20_genomic.fna/checkm_input GCA_905199095.1_ERR1305892-mag-bin.20_genomic.fna/checkm_result
[2023-06-16 19:06:17,497] [INFO] Task succeeded: CheckM
[2023-06-16 19:06:17,498] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.78%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 19:06:17,515] [INFO] ===== Completeness check finished =====
[2023-06-16 19:06:17,515] [INFO] ===== Start GTDB Search =====
[2023-06-16 19:06:17,516] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905199095.1_ERR1305892-mag-bin.20_genomic.fna/markers.fasta)
[2023-06-16 19:06:17,517] [INFO] Task started: Blastn
[2023-06-16 19:06:17,517] [INFO] Running command: blastn -query GCA_905199095.1_ERR1305892-mag-bin.20_genomic.fna/markers.fasta -db /var/lib/cwl/stge408535e-4883-4eaa-9468-71b55bc099e2/dqc_reference/reference_markers_gtdb.fasta -out GCA_905199095.1_ERR1305892-mag-bin.20_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:06:18,420] [INFO] Task succeeded: Blastn
[2023-06-16 19:06:18,423] [INFO] Selected 17 target genomes.
[2023-06-16 19:06:18,424] [INFO] Target genome list was writen to GCA_905199095.1_ERR1305892-mag-bin.20_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 19:06:18,433] [INFO] Task started: fastANI
[2023-06-16 19:06:18,434] [INFO] Running command: fastANI --query /var/lib/cwl/stg6694a769-caf6-4e0f-bf3b-563729703e04/GCA_905199095.1_ERR1305892-mag-bin.20_genomic.fna.gz --refList GCA_905199095.1_ERR1305892-mag-bin.20_genomic.fna/target_genomes_gtdb.txt --output GCA_905199095.1_ERR1305892-mag-bin.20_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 19:06:27,920] [INFO] Task succeeded: fastANI
[2023-06-16 19:06:27,928] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 19:06:27,929] [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_900548195.1	s__Prevotella sp900548195	95.3494	602	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.71	95.27	0.80	0.75	7	conclusive
GCA_900552965.1	s__Prevotella sp900552965	88.6863	454	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.78	99.78	0.83	0.83	2	-
GCA_900769275.1	s__Prevotella sp900769275	78.2907	212	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002317355.1	s__Prevotella sp002317355	78.2738	171	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315105.1	s__Prevotella sp900315105	78.1646	170	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.64	97.28	0.95	0.91	3	-
GCA_902801155.1	s__Prevotella sp902801155	77.8076	140	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.39	96.09	0.81	0.73	3	-
GCA_902798615.1	s__Prevotella sp902798615	77.7728	168	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.97	96.95	0.86	0.84	3	-
GCA_902801425.1	s__Prevotella sp902801425	77.4114	151	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.61	96.51	0.78	0.78	3	-
GCA_017478025.1	s__Prevotella sp017478025	76.4749	57	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.24	95.24	0.74	0.74	2	-
GCA_002297965.1	s__Prevotella sp002297965	76.3237	50	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.14	99.14	0.78	0.78	2	-
GCF_000687715.1	s__Prevotella ruminicola_B	76.131	51	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002394385.1	s__Prevotella sp002394385	75.7893	58	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.28	97.06	0.88	0.86	9	-
--------------------------------------------------------------------------------
[2023-06-16 19:06:27,930] [INFO] GTDB search result was written to GCA_905199095.1_ERR1305892-mag-bin.20_genomic.fna/result_gtdb.tsv
[2023-06-16 19:06:27,930] [INFO] ===== GTDB Search completed =====
[2023-06-16 19:06:27,933] [INFO] DFAST_QC result json was written to GCA_905199095.1_ERR1305892-mag-bin.20_genomic.fna/dqc_result.json
[2023-06-16 19:06:27,933] [INFO] DFAST_QC completed!
[2023-06-16 19:06:27,933] [INFO] Total running time: 0h1m11s