[2024-01-24 13:32:41,179] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:41,180] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:41,180] [INFO] DQC Reference Directory: /var/lib/cwl/stg82160d55-77c2-46ec-90d1-107ff14f703d/dqc_reference
[2024-01-24 13:32:42,397] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:42,398] [INFO] Task started: Prodigal
[2024-01-24 13:32:42,399] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4fdefa6-8424-4d5f-aaf7-1e127cb6cbc6/GCF_000613565.1_ASM61356v1_genomic.fna.gz | prodigal -d GCF_000613565.1_ASM61356v1_genomic.fna/cds.fna -a GCF_000613565.1_ASM61356v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:58,932] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:58,933] [INFO] Task started: HMMsearch
[2024-01-24 13:32:58,933] [INFO] Running command: hmmsearch --tblout GCF_000613565.1_ASM61356v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg82160d55-77c2-46ec-90d1-107ff14f703d/dqc_reference/reference_markers.hmm GCF_000613565.1_ASM61356v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:59,246] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:59,247] [INFO] Found 6/6 markers.
[2024-01-24 13:32:59,271] [INFO] Query marker FASTA was written to GCF_000613565.1_ASM61356v1_genomic.fna/markers.fasta
[2024-01-24 13:32:59,271] [INFO] Task started: Blastn
[2024-01-24 13:32:59,271] [INFO] Running command: blastn -query GCF_000613565.1_ASM61356v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82160d55-77c2-46ec-90d1-107ff14f703d/dqc_reference/reference_markers.fasta -out GCF_000613565.1_ASM61356v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:59,903] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:59,906] [INFO] Selected 18 target genomes.
[2024-01-24 13:32:59,906] [INFO] Target genome list was writen to GCF_000613565.1_ASM61356v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:59,911] [INFO] Task started: fastANI
[2024-01-24 13:32:59,911] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4fdefa6-8424-4d5f-aaf7-1e127cb6cbc6/GCF_000613565.1_ASM61356v1_genomic.fna.gz --refList GCF_000613565.1_ASM61356v1_genomic.fna/target_genomes.txt --output GCF_000613565.1_ASM61356v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:11,072] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:11,073] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg82160d55-77c2-46ec-90d1-107ff14f703d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:11,073] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg82160d55-77c2-46ec-90d1-107ff14f703d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:11,083] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:33:11,083] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:11,083] [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 baroniae	strain=JCM 13447	GCA_000613565.1	305719	305719	type	True	100.0	984	992	95	conclusive
Prevotella baroniae	strain=DSM 16972	GCA_000426585.1	305719	305719	type	True	99.9463	982	992	95	conclusive
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	84.3111	585	992	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	80.7265	50	992	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	80.4621	234	992	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	79.2828	107	992	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	78.8168	204	992	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	78.5758	220	992	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	78.4769	214	992	95	below_threshold
Prevotella maculosa	strain=JCM 15638	GCA_000613965.1	439703	439703	type	True	77.8444	134	992	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	77.4476	91	992	95	below_threshold
Prevotella bergensis	strain=DSM 17361	GCA_000160535.1	242750	242750	type	True	77.236	89	992	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	77.0914	95	992	95	below_threshold
Prevotella loescheii	strain=DSM 19665	GCA_000378085.1	840	840	type	True	76.8148	77	992	95	below_threshold
Prevotella loescheii	strain=ATCC 15930	GCA_000698925.1	840	840	type	True	76.7709	68	992	95	below_threshold
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	76.6356	79	992	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:11,084] [INFO] DFAST Taxonomy check result was written to GCF_000613565.1_ASM61356v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:11,085] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:11,085] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:11,085] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg82160d55-77c2-46ec-90d1-107ff14f703d/dqc_reference/checkm_data
[2024-01-24 13:33:11,086] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:11,116] [INFO] Task started: CheckM
[2024-01-24 13:33:11,116] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000613565.1_ASM61356v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000613565.1_ASM61356v1_genomic.fna/checkm_input GCF_000613565.1_ASM61356v1_genomic.fna/checkm_result
[2024-01-24 13:33:56,640] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:56,641] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:56,655] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:56,656] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:56,656] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000613565.1_ASM61356v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:56,656] [INFO] Task started: Blastn
[2024-01-24 13:33:56,656] [INFO] Running command: blastn -query GCF_000613565.1_ASM61356v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82160d55-77c2-46ec-90d1-107ff14f703d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000613565.1_ASM61356v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:57,857] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:57,859] [INFO] Selected 22 target genomes.
[2024-01-24 13:33:57,859] [INFO] Target genome list was writen to GCF_000613565.1_ASM61356v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:57,871] [INFO] Task started: fastANI
[2024-01-24 13:33:57,872] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4fdefa6-8424-4d5f-aaf7-1e127cb6cbc6/GCF_000613565.1_ASM61356v1_genomic.fna.gz --refList GCF_000613565.1_ASM61356v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000613565.1_ASM61356v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:10,766] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:10,779] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:10,779] [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_000426585.1	s__Prevotella baroniae	99.9463	982	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.79	98.01	0.95	0.92	4	conclusive
GCF_003043925.1	s__Prevotella sp003043925	84.1975	586	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.98	99.98	0.98	0.98	2	-
GCF_000599605.1	s__Prevotella sp000599605	82.3376	132	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.66	96.63	0.93	0.92	3	-
GCF_000184945.1	s__Prevotella buccae	80.4628	234	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.38	98.24	0.91	0.87	7	-
GCF_003043945.1	s__Prevotella sp003043945	79.4638	169	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.81	99.81	0.99	0.99	2	-
GCF_900079775.1	s__Prevotella lascolaii	79.3839	107	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.26	98.20	0.94	0.92	5	-
GCF_900113305.1	s__Prevotella sp900113305	78.0909	152	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016899955.1	s__Prevotella sp900540415	77.2661	137	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.44	98.08	0.94	0.91	6	-
GCF_002251365.1	s__Prevotella sp002251365	77.1012	103	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.20	97.97	0.85	0.80	5	-
GCA_900769055.1	s__Prevotella sp900769055	77.0401	88	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553595.1	s__Prevotella sp900553595	77.0116	97	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.96	97.92	0.92	0.85	3	-
GCA_017458125.1	s__Prevotella sp017458125	76.9572	125	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.42	97.42	0.81	0.81	2	-
GCA_902779455.1	s__Prevotella sp902779455	76.94	136	992	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	76.9245	164	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.59	98.19	0.88	0.85	9	-
GCA_003447235.1	s__Prevotella sp003447235	76.8557	99	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.02	97.84	0.85	0.82	13	-
GCA_000436915.1	s__Prevotella sp000436915	76.7665	56	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.18	97.08	0.77	0.76	4	-
GCA_902775475.1	s__Prevotella sp902775475	76.7215	157	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.69	98.51	0.89	0.87	7	-
GCF_004535825.1	s__Prevotella hominis	76.6663	79	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.52	95.16	0.76	0.66	13	-
GCA_900317545.1	s__Prevotella sp900317545	76.6465	90	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.65	99.65	0.96	0.96	2	-
GCA_002440225.1	s__Prevotella sp002440225	76.5617	80	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.88	98.88	0.81	0.81	2	-
GCA_900543975.1	s__Prevotella sp900543975	76.5588	93	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.48	97.34	0.84	0.79	5	-
GCA_017428055.1	s__Prevotella sp017428055	76.4828	97	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.50	98.50	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:10,782] [INFO] GTDB search result was written to GCF_000613565.1_ASM61356v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:10,782] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:10,785] [INFO] DFAST_QC result json was written to GCF_000613565.1_ASM61356v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:10,786] [INFO] DFAST_QC completed!
[2024-01-24 13:34:10,786] [INFO] Total running time: 0h1m30s