[2023-06-16 19:09:58,816] [INFO] DFAST_QC pipeline started.
[2023-06-16 19:09:58,818] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 19:09:58,818] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8f766a7-cb82-484e-86df-34a05c1aff86/dqc_reference
[2023-06-16 19:09:59,896] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 19:09:59,896] [INFO] Task started: Prodigal
[2023-06-16 19:09:59,897] [INFO] Running command: gunzip -c /var/lib/cwl/stg37d83d93-030c-467a-85a8-ece72169dfad/GCA_905193025.1_ERR1600656-mag-bin.69_genomic.fna.gz | prodigal -d GCA_905193025.1_ERR1600656-mag-bin.69_genomic.fna/cds.fna -a GCA_905193025.1_ERR1600656-mag-bin.69_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 19:10:18,075] [INFO] Task succeeded: Prodigal
[2023-06-16 19:10:18,075] [INFO] Task started: HMMsearch
[2023-06-16 19:10:18,076] [INFO] Running command: hmmsearch --tblout GCA_905193025.1_ERR1600656-mag-bin.69_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8f766a7-cb82-484e-86df-34a05c1aff86/dqc_reference/reference_markers.hmm GCA_905193025.1_ERR1600656-mag-bin.69_genomic.fna/protein.faa > /dev/null
[2023-06-16 19:10:18,260] [INFO] Task succeeded: HMMsearch
[2023-06-16 19:10:18,261] [INFO] Found 6/6 markers.
[2023-06-16 19:10:18,286] [INFO] Query marker FASTA was written to GCA_905193025.1_ERR1600656-mag-bin.69_genomic.fna/markers.fasta
[2023-06-16 19:10:18,287] [INFO] Task started: Blastn
[2023-06-16 19:10:18,287] [INFO] Running command: blastn -query GCA_905193025.1_ERR1600656-mag-bin.69_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8f766a7-cb82-484e-86df-34a05c1aff86/dqc_reference/reference_markers.fasta -out GCA_905193025.1_ERR1600656-mag-bin.69_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:10:18,845] [INFO] Task succeeded: Blastn
[2023-06-16 19:10:18,848] [INFO] Selected 14 target genomes.
[2023-06-16 19:10:18,848] [INFO] Target genome list was writen to GCA_905193025.1_ERR1600656-mag-bin.69_genomic.fna/target_genomes.txt
[2023-06-16 19:10:18,851] [INFO] Task started: fastANI
[2023-06-16 19:10:18,851] [INFO] Running command: fastANI --query /var/lib/cwl/stg37d83d93-030c-467a-85a8-ece72169dfad/GCA_905193025.1_ERR1600656-mag-bin.69_genomic.fna.gz --refList GCA_905193025.1_ERR1600656-mag-bin.69_genomic.fna/target_genomes.txt --output GCA_905193025.1_ERR1600656-mag-bin.69_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 19:10:26,659] [INFO] Task succeeded: fastANI
[2023-06-16 19:10:26,659] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8f766a7-cb82-484e-86df-34a05c1aff86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 19:10:26,659] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8f766a7-cb82-484e-86df-34a05c1aff86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 19:10:26,667] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2023-06-16 19:10:26,668] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-16 19:10:26,668] [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
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	99.0168	875	973	95	conclusive
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	77.7806	194	973	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	77.6995	271	973	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	77.6129	271	973	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	77.4516	283	973	95	below_threshold
Prevotella lacticifex	strain=R5019	GCA_019973375.1	2854755	2854755	type	True	77.0949	142	973	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	77.0413	111	973	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	77.0205	152	973	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	77.0098	86	973	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	76.9465	120	973	95	below_threshold
Prevotella bergensis	strain=DSM 17361	GCA_000160535.1	242750	242750	type	True	76.814	135	973	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 19:10:26,669] [INFO] DFAST Taxonomy check result was written to GCA_905193025.1_ERR1600656-mag-bin.69_genomic.fna/tc_result.tsv
[2023-06-16 19:10:26,670] [INFO] ===== Taxonomy check completed =====
[2023-06-16 19:10:26,670] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 19:10:26,670] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8f766a7-cb82-484e-86df-34a05c1aff86/dqc_reference/checkm_data
[2023-06-16 19:10:26,671] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 19:10:26,703] [INFO] Task started: CheckM
[2023-06-16 19:10:26,703] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905193025.1_ERR1600656-mag-bin.69_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905193025.1_ERR1600656-mag-bin.69_genomic.fna/checkm_input GCA_905193025.1_ERR1600656-mag-bin.69_genomic.fna/checkm_result
[2023-06-16 19:11:17,813] [INFO] Task succeeded: CheckM
[2023-06-16 19:11:17,814] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 19:11:17,832] [INFO] ===== Completeness check finished =====
[2023-06-16 19:11:17,832] [INFO] ===== Start GTDB Search =====
[2023-06-16 19:11:17,833] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905193025.1_ERR1600656-mag-bin.69_genomic.fna/markers.fasta)
[2023-06-16 19:11:17,834] [INFO] Task started: Blastn
[2023-06-16 19:11:17,834] [INFO] Running command: blastn -query GCA_905193025.1_ERR1600656-mag-bin.69_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8f766a7-cb82-484e-86df-34a05c1aff86/dqc_reference/reference_markers_gtdb.fasta -out GCA_905193025.1_ERR1600656-mag-bin.69_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:11:18,763] [INFO] Task succeeded: Blastn
[2023-06-16 19:11:18,767] [INFO] Selected 14 target genomes.
[2023-06-16 19:11:18,767] [INFO] Target genome list was writen to GCA_905193025.1_ERR1600656-mag-bin.69_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 19:11:18,796] [INFO] Task started: fastANI
[2023-06-16 19:11:18,796] [INFO] Running command: fastANI --query /var/lib/cwl/stg37d83d93-030c-467a-85a8-ece72169dfad/GCA_905193025.1_ERR1600656-mag-bin.69_genomic.fna.gz --refList GCA_905193025.1_ERR1600656-mag-bin.69_genomic.fna/target_genomes_gtdb.txt --output GCA_905193025.1_ERR1600656-mag-bin.69_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 19:11:27,085] [INFO] Task succeeded: fastANI
[2023-06-16 19:11:27,095] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 19:11:27,095] [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
GCF_018789675.1	s__Prevotella sp002300055	99.0168	875	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.15	99.02	0.92	0.90	6	conclusive
GCA_002437285.1	s__Prevotella sp002437285	81.8419	488	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.68	99.38	0.93	0.88	13	-
GCA_002437115.1	s__Prevotella sp002437115	80.5071	438	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315835.1	s__Prevotella sp900315835	78.2742	237	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.59	98.19	0.88	0.85	9	-
GCA_900762125.1	s__Prevotella sp900762125	78.2371	218	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317685.1	s__Prevotella sp900317685	77.8586	201	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.13	96.10	0.84	0.76	12	-
GCF_009695775.1	s__Prevotella mizrahii	77.7918	194	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.15	96.87	0.87	0.84	6	-
GCA_002317385.1	s__Prevotella sp002317385	77.6741	244	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000431975.1	s__Prevotella sp000431975	77.6663	146	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.89	99.89	0.92	0.91	3	-
GCA_900546345.1	s__Prevotella sp900546345	77.6357	164	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016901395.1	s__Prevotella sp016901395	77.5447	216	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002481295.1	s__Prevotella sp002481295	77.4977	203	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.83	96.70	0.87	0.78	4	-
GCF_000518545.1	s__Prevotella seregens	77.4516	283	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.68	98.64	0.90	0.90	3	-
--------------------------------------------------------------------------------
[2023-06-16 19:11:27,097] [INFO] GTDB search result was written to GCA_905193025.1_ERR1600656-mag-bin.69_genomic.fna/result_gtdb.tsv
[2023-06-16 19:11:27,097] [INFO] ===== GTDB Search completed =====
[2023-06-16 19:11:27,100] [INFO] DFAST_QC result json was written to GCA_905193025.1_ERR1600656-mag-bin.69_genomic.fna/dqc_result.json
[2023-06-16 19:11:27,100] [INFO] DFAST_QC completed!
[2023-06-16 19:11:27,100] [INFO] Total running time: 0h1m28s