[2024-01-24 13:58:10,266] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:10,268] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:10,268] [INFO] DQC Reference Directory: /var/lib/cwl/stg80cf64ec-cff7-4a27-b29c-98b4b8235507/dqc_reference
[2024-01-24 13:58:11,431] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:11,432] [INFO] Task started: Prodigal
[2024-01-24 13:58:11,432] [INFO] Running command: gunzip -c /var/lib/cwl/stge75b826a-a904-4767-a29a-7fc00aba9082/GCF_019973375.1_ASM1997337v1_genomic.fna.gz | prodigal -d GCF_019973375.1_ASM1997337v1_genomic.fna/cds.fna -a GCF_019973375.1_ASM1997337v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:30,616] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:30,617] [INFO] Task started: HMMsearch
[2024-01-24 13:58:30,617] [INFO] Running command: hmmsearch --tblout GCF_019973375.1_ASM1997337v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80cf64ec-cff7-4a27-b29c-98b4b8235507/dqc_reference/reference_markers.hmm GCF_019973375.1_ASM1997337v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:30,821] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:30,822] [INFO] Found 6/6 markers.
[2024-01-24 13:58:30,851] [INFO] Query marker FASTA was written to GCF_019973375.1_ASM1997337v1_genomic.fna/markers.fasta
[2024-01-24 13:58:30,851] [INFO] Task started: Blastn
[2024-01-24 13:58:30,851] [INFO] Running command: blastn -query GCF_019973375.1_ASM1997337v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80cf64ec-cff7-4a27-b29c-98b4b8235507/dqc_reference/reference_markers.fasta -out GCF_019973375.1_ASM1997337v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:31,385] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:31,387] [INFO] Selected 19 target genomes.
[2024-01-24 13:58:31,387] [INFO] Target genome list was writen to GCF_019973375.1_ASM1997337v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:31,392] [INFO] Task started: fastANI
[2024-01-24 13:58:31,392] [INFO] Running command: fastANI --query /var/lib/cwl/stge75b826a-a904-4767-a29a-7fc00aba9082/GCF_019973375.1_ASM1997337v1_genomic.fna.gz --refList GCF_019973375.1_ASM1997337v1_genomic.fna/target_genomes.txt --output GCF_019973375.1_ASM1997337v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:43,652] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:43,653] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80cf64ec-cff7-4a27-b29c-98b4b8235507/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:43,653] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80cf64ec-cff7-4a27-b29c-98b4b8235507/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:43,661] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:43,661] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:43,661] [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 lacticifex	strain=R5019	GCA_019973375.1	2854755	2854755	type	True	100.0	1388	1388	95	conclusive
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	79.1522	263	1388	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	77.5764	109	1388	95	below_threshold
Prevotella fusca	strain=W1435	GCA_018128145.1	589436	589436	type	True	77.4564	103	1388	95	below_threshold
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	77.28	92	1388	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	77.0748	150	1388	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.8151	116	1388	95	below_threshold
Prevotella bergensis	strain=DSM 17361	GCA_000160535.1	242750	242750	type	True	76.7269	72	1388	95	below_threshold
Prevotella dentasini	strain=JCM 15908	GCA_000614065.1	589537	589537	type	True	76.6864	126	1388	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	76.6293	122	1388	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	76.4854	88	1388	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:43,662] [INFO] DFAST Taxonomy check result was written to GCF_019973375.1_ASM1997337v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:43,662] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:43,663] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:43,663] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80cf64ec-cff7-4a27-b29c-98b4b8235507/dqc_reference/checkm_data
[2024-01-24 13:58:43,663] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:43,703] [INFO] Task started: CheckM
[2024-01-24 13:58:43,704] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019973375.1_ASM1997337v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019973375.1_ASM1997337v1_genomic.fna/checkm_input GCF_019973375.1_ASM1997337v1_genomic.fna/checkm_result
[2024-01-24 13:59:37,164] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:37,165] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:37,180] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:37,180] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:37,181] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019973375.1_ASM1997337v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:37,181] [INFO] Task started: Blastn
[2024-01-24 13:59:37,181] [INFO] Running command: blastn -query GCF_019973375.1_ASM1997337v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80cf64ec-cff7-4a27-b29c-98b4b8235507/dqc_reference/reference_markers_gtdb.fasta -out GCF_019973375.1_ASM1997337v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:37,969] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:37,972] [INFO] Selected 18 target genomes.
[2024-01-24 13:59:37,972] [INFO] Target genome list was writen to GCF_019973375.1_ASM1997337v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:37,982] [INFO] Task started: fastANI
[2024-01-24 13:59:37,982] [INFO] Running command: fastANI --query /var/lib/cwl/stge75b826a-a904-4767-a29a-7fc00aba9082/GCF_019973375.1_ASM1997337v1_genomic.fna.gz --refList GCF_019973375.1_ASM1997337v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019973375.1_ASM1997337v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:48,257] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:48,268] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:48,269] [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_900314945.1	s__Prevotella sp900314945	97.5741	890	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.87	98.30	0.92	0.89	7	conclusive
GCA_900315635.1	s__Prevotella sp900315635	79.1519	409	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.69	99.39	0.92	0.85	3	-
GCA_900314195.1	s__Prevotella sp900314195	79.0745	150	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	100.00	100.00	0.99	0.99	2	-
GCA_900316565.1	s__Prevotella sp900316565	78.9381	378	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.52	96.90	0.84	0.79	9	-
GCA_002481295.1	s__Prevotella sp002481295	78.8218	170	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.83	96.70	0.87	0.78	4	-
GCA_002353825.1	s__Prevotella sp002353825	78.8078	186	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.40	98.85	0.91	0.85	4	-
GCA_900546345.1	s__Prevotella sp900546345	78.4799	168	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900314455.1	s__Prevotella sp900314455	78.0372	270	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003609775.1	s__Prevotella melaninogenica_A	77.7028	81	1388	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	77.6205	210	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.59	98.19	0.88	0.85	9	-
GCF_001262015.1	s__Prevotella fusca	77.498	107	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.98	99.97	1.00	1.00	3	-
GCA_000431975.1	s__Prevotella sp000431975	76.8454	111	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.89	99.89	0.92	0.91	3	-
GCA_002437285.1	s__Prevotella sp002437285	76.6697	124	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.68	99.38	0.93	0.88	13	-
GCA_902779455.1	s__Prevotella sp902779455	76.6386	129	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318915.1	s__Prevotella sp900318915	76.4086	122	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.05	95.26	0.87	0.81	11	-
GCA_017459445.1	s__Prevotella sp017459445	76.3992	61	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017548275.1	s__Prevotella sp017548275	76.3176	79	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553155.1	s__Prevotella sp900553155	76.2031	64	1388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.04	96.93	0.80	0.75	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:48,270] [INFO] GTDB search result was written to GCF_019973375.1_ASM1997337v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:48,270] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:48,273] [INFO] DFAST_QC result json was written to GCF_019973375.1_ASM1997337v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:48,273] [INFO] DFAST_QC completed!
[2024-01-24 13:59:48,273] [INFO] Total running time: 0h1m38s