[2023-06-28 21:25:52,348] [INFO] DFAST_QC pipeline started.
[2023-06-28 21:25:52,350] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 21:25:52,350] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ca9152f-ce75-4a85-9ea1-a6f80dc0bcf7/dqc_reference
[2023-06-28 21:25:53,537] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 21:25:53,537] [INFO] Task started: Prodigal
[2023-06-28 21:25:53,538] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c7c9116-1edc-43c9-bcfa-613550fbb07b/GCA_017467535.1_ASM1746753v1_genomic.fna.gz | prodigal -d GCA_017467535.1_ASM1746753v1_genomic.fna/cds.fna -a GCA_017467535.1_ASM1746753v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 21:26:07,634] [INFO] Task succeeded: Prodigal
[2023-06-28 21:26:07,634] [INFO] Task started: HMMsearch
[2023-06-28 21:26:07,634] [INFO] Running command: hmmsearch --tblout GCA_017467535.1_ASM1746753v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ca9152f-ce75-4a85-9ea1-a6f80dc0bcf7/dqc_reference/reference_markers.hmm GCA_017467535.1_ASM1746753v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 21:26:07,862] [INFO] Task succeeded: HMMsearch
[2023-06-28 21:26:07,864] [INFO] Found 6/6 markers.
[2023-06-28 21:26:07,887] [INFO] Query marker FASTA was written to GCA_017467535.1_ASM1746753v1_genomic.fna/markers.fasta
[2023-06-28 21:26:07,888] [INFO] Task started: Blastn
[2023-06-28 21:26:07,888] [INFO] Running command: blastn -query GCA_017467535.1_ASM1746753v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ca9152f-ce75-4a85-9ea1-a6f80dc0bcf7/dqc_reference/reference_markers.fasta -out GCA_017467535.1_ASM1746753v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:26:08,520] [INFO] Task succeeded: Blastn
[2023-06-28 21:26:08,525] [INFO] Selected 15 target genomes.
[2023-06-28 21:26:08,525] [INFO] Target genome list was writen to GCA_017467535.1_ASM1746753v1_genomic.fna/target_genomes.txt
[2023-06-28 21:26:08,526] [INFO] Task started: fastANI
[2023-06-28 21:26:08,527] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c7c9116-1edc-43c9-bcfa-613550fbb07b/GCA_017467535.1_ASM1746753v1_genomic.fna.gz --refList GCA_017467535.1_ASM1746753v1_genomic.fna/target_genomes.txt --output GCA_017467535.1_ASM1746753v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 21:26:15,468] [INFO] Task succeeded: fastANI
[2023-06-28 21:26:15,468] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ca9152f-ce75-4a85-9ea1-a6f80dc0bcf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 21:26:15,468] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ca9152f-ce75-4a85-9ea1-a6f80dc0bcf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 21:26:15,479] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 21:26:15,479] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 21:26:15,480] [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 brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	78.5274	224	742	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	76.9877	145	742	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	76.9624	153	742	95	below_threshold
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	76.9556	151	742	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	76.9209	151	742	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	76.9129	150	742	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.6708	117	742	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.5818	77	742	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.4415	134	742	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	76.2007	94	742	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	76.0523	80	742	95	below_threshold
Prevotella bergensis	strain=DSM 17361	GCA_000160535.1	242750	242750	type	True	75.7018	58	742	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 21:26:15,482] [INFO] DFAST Taxonomy check result was written to GCA_017467535.1_ASM1746753v1_genomic.fna/tc_result.tsv
[2023-06-28 21:26:15,482] [INFO] ===== Taxonomy check completed =====
[2023-06-28 21:26:15,482] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 21:26:15,483] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ca9152f-ce75-4a85-9ea1-a6f80dc0bcf7/dqc_reference/checkm_data
[2023-06-28 21:26:15,484] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 21:26:15,509] [INFO] Task started: CheckM
[2023-06-28 21:26:15,510] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017467535.1_ASM1746753v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017467535.1_ASM1746753v1_genomic.fna/checkm_input GCA_017467535.1_ASM1746753v1_genomic.fna/checkm_result
[2023-06-28 21:26:57,735] [INFO] Task succeeded: CheckM
[2023-06-28 21:26:57,737] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.30%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 21:26:57,760] [INFO] ===== Completeness check finished =====
[2023-06-28 21:26:57,761] [INFO] ===== Start GTDB Search =====
[2023-06-28 21:26:57,761] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017467535.1_ASM1746753v1_genomic.fna/markers.fasta)
[2023-06-28 21:26:57,761] [INFO] Task started: Blastn
[2023-06-28 21:26:57,762] [INFO] Running command: blastn -query GCA_017467535.1_ASM1746753v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ca9152f-ce75-4a85-9ea1-a6f80dc0bcf7/dqc_reference/reference_markers_gtdb.fasta -out GCA_017467535.1_ASM1746753v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:26:58,779] [INFO] Task succeeded: Blastn
[2023-06-28 21:26:58,783] [INFO] Selected 13 target genomes.
[2023-06-28 21:26:58,784] [INFO] Target genome list was writen to GCA_017467535.1_ASM1746753v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 21:26:58,785] [INFO] Task started: fastANI
[2023-06-28 21:26:58,785] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c7c9116-1edc-43c9-bcfa-613550fbb07b/GCA_017467535.1_ASM1746753v1_genomic.fna.gz --refList GCA_017467535.1_ASM1746753v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017467535.1_ASM1746753v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 21:27:06,292] [INFO] Task succeeded: fastANI
[2023-06-28 21:27:06,309] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 21:27:06,309] [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_017467535.1	s__Prevotella sp017467535	100.0	735	742	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017483805.1	s__Prevotella sp017483805	92.5571	565	742	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002361655.1	s__Prevotella sp002361655	82.1132	336	742	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902799905.1	s__Prevotella sp902799905	81.3541	428	742	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.33	98.29	0.89	0.87	3	-
GCA_017478085.1	s__Prevotella sp017478085	80.3821	337	742	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017455845.1	s__Prevotella sp017455845	80.1856	295	742	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902775475.1	s__Prevotella sp902775475	80.0687	365	742	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.69	98.51	0.89	0.87	7	-
GCA_902786565.1	s__Prevotella sp902786565	79.5069	364	742	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.07	98.05	0.87	0.85	3	-
GCA_905235325.1	s__Prevotella sp905235325	79.5046	294	742	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017470345.1	s__Prevotella sp017470345	79.4416	223	742	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902790625.1	s__Prevotella sp902790625	79.2557	336	742	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.16	96.49	0.84	0.82	3	-
GCA_902768105.1	s__Prevotella sp902768105	77.9245	212	742	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017483785.1	s__Prevotella sp017483785	77.022	105	742	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 21:27:06,311] [INFO] GTDB search result was written to GCA_017467535.1_ASM1746753v1_genomic.fna/result_gtdb.tsv
[2023-06-28 21:27:06,312] [INFO] ===== GTDB Search completed =====
[2023-06-28 21:27:06,316] [INFO] DFAST_QC result json was written to GCA_017467535.1_ASM1746753v1_genomic.fna/dqc_result.json
[2023-06-28 21:27:06,316] [INFO] DFAST_QC completed!
[2023-06-28 21:27:06,316] [INFO] Total running time: 0h1m14s