[2023-06-28 15:14:57,245] [INFO] DFAST_QC pipeline started.
[2023-06-28 15:14:57,247] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 15:14:57,247] [INFO] DQC Reference Directory: /var/lib/cwl/stg099af322-336d-4b1a-a915-462d11551917/dqc_reference
[2023-06-28 15:14:58,455] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 15:14:58,463] [INFO] Task started: Prodigal
[2023-06-28 15:14:58,464] [INFO] Running command: gunzip -c /var/lib/cwl/stg09da68c5-5929-489f-9635-b43daf52c16e/GCA_015261705.1_ASM1526170v1_genomic.fna.gz | prodigal -d GCA_015261705.1_ASM1526170v1_genomic.fna/cds.fna -a GCA_015261705.1_ASM1526170v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 15:15:08,573] [INFO] Task succeeded: Prodigal
[2023-06-28 15:15:08,573] [INFO] Task started: HMMsearch
[2023-06-28 15:15:08,573] [INFO] Running command: hmmsearch --tblout GCA_015261705.1_ASM1526170v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg099af322-336d-4b1a-a915-462d11551917/dqc_reference/reference_markers.hmm GCA_015261705.1_ASM1526170v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 15:15:08,759] [INFO] Task succeeded: HMMsearch
[2023-06-28 15:15:08,760] [INFO] Found 6/6 markers.
[2023-06-28 15:15:08,781] [INFO] Query marker FASTA was written to GCA_015261705.1_ASM1526170v1_genomic.fna/markers.fasta
[2023-06-28 15:15:08,782] [INFO] Task started: Blastn
[2023-06-28 15:15:08,782] [INFO] Running command: blastn -query GCA_015261705.1_ASM1526170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg099af322-336d-4b1a-a915-462d11551917/dqc_reference/reference_markers.fasta -out GCA_015261705.1_ASM1526170v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:15:09,339] [INFO] Task succeeded: Blastn
[2023-06-28 15:15:09,343] [INFO] Selected 11 target genomes.
[2023-06-28 15:15:09,344] [INFO] Target genome list was writen to GCA_015261705.1_ASM1526170v1_genomic.fna/target_genomes.txt
[2023-06-28 15:15:09,344] [INFO] Task started: fastANI
[2023-06-28 15:15:09,345] [INFO] Running command: fastANI --query /var/lib/cwl/stg09da68c5-5929-489f-9635-b43daf52c16e/GCA_015261705.1_ASM1526170v1_genomic.fna.gz --refList GCA_015261705.1_ASM1526170v1_genomic.fna/target_genomes.txt --output GCA_015261705.1_ASM1526170v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 15:15:16,080] [INFO] Task succeeded: fastANI
[2023-06-28 15:15:16,080] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg099af322-336d-4b1a-a915-462d11551917/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 15:15:16,080] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg099af322-336d-4b1a-a915-462d11551917/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 15:15:16,090] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2023-06-28 15:15:16,090] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 15:15:16,090] [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 pallens	strain=DSM 18710	GCA_003269195.1	60133	60133	type	True	98.2993	762	822	95	conclusive
Prevotella pallens	strain=ATCC 700821	GCA_000220255.1	60133	60133	type	True	98.2058	784	822	95	conclusive
Prevotella nigrescens	strain=NCTC9336	GCA_900454985.1	28133	28133	type	True	83.9022	594	822	95	below_threshold
Prevotella nigrescens	strain=ATCC 33563	GCA_000220235.1	28133	28133	type	True	83.8353	592	822	95	below_threshold
Prevotella nigrescens	strain=FDAARGOS_1486	GCA_019930605.1	28133	28133	type	True	83.7526	593	822	95	below_threshold
Prevotella aurantiaca	strain=JCM 15754	GCA_000614025.1	596085	596085	type	True	82.1605	486	822	95	below_threshold
Prevotella intermedia	strain=ATCC 25611	GCA_000519165.1	28131	28131	type	True	80.6827	429	822	95	below_threshold
Prevotella intermedia	strain=DSM 20706	GCA_000439065.1	28131	28131	type	True	80.5624	436	822	95	below_threshold
Prevotella vespertina	strain=A2879	GCA_009728485.1	2608404	2608404	type	True	78.3865	86	822	95	below_threshold
Prevotella veroralis	strain=DSM 19559	GCA_000377625.1	28137	28137	type	True	77.9551	86	822	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 15:15:16,093] [INFO] DFAST Taxonomy check result was written to GCA_015261705.1_ASM1526170v1_genomic.fna/tc_result.tsv
[2023-06-28 15:15:16,093] [INFO] ===== Taxonomy check completed =====
[2023-06-28 15:15:16,094] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 15:15:16,094] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg099af322-336d-4b1a-a915-462d11551917/dqc_reference/checkm_data
[2023-06-28 15:15:16,095] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 15:15:16,138] [INFO] Task started: CheckM
[2023-06-28 15:15:16,138] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015261705.1_ASM1526170v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015261705.1_ASM1526170v1_genomic.fna/checkm_input GCA_015261705.1_ASM1526170v1_genomic.fna/checkm_result
[2023-06-28 15:15:48,113] [INFO] Task succeeded: CheckM
[2023-06-28 15:15:48,114] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 15:15:48,131] [INFO] ===== Completeness check finished =====
[2023-06-28 15:15:48,132] [INFO] ===== Start GTDB Search =====
[2023-06-28 15:15:48,132] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015261705.1_ASM1526170v1_genomic.fna/markers.fasta)
[2023-06-28 15:15:48,132] [INFO] Task started: Blastn
[2023-06-28 15:15:48,132] [INFO] Running command: blastn -query GCA_015261705.1_ASM1526170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg099af322-336d-4b1a-a915-462d11551917/dqc_reference/reference_markers_gtdb.fasta -out GCA_015261705.1_ASM1526170v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:15:48,836] [INFO] Task succeeded: Blastn
[2023-06-28 15:15:48,840] [INFO] Selected 15 target genomes.
[2023-06-28 15:15:48,840] [INFO] Target genome list was writen to GCA_015261705.1_ASM1526170v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 15:15:48,845] [INFO] Task started: fastANI
[2023-06-28 15:15:48,845] [INFO] Running command: fastANI --query /var/lib/cwl/stg09da68c5-5929-489f-9635-b43daf52c16e/GCA_015261705.1_ASM1526170v1_genomic.fna.gz --refList GCA_015261705.1_ASM1526170v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015261705.1_ASM1526170v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 15:15:56,977] [INFO] Task succeeded: fastANI
[2023-06-28 15:15:56,987] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 15:15:56,987] [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_000220255.1	s__Prevotella pallens	98.2058	784	822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.33	96.89	0.94	0.88	40	conclusive
GCF_000220235.1	s__Prevotella nigrescens	83.8284	592	822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.14	97.70	0.92	0.78	13	-
GCF_000614025.1	s__Prevotella aurantiaca	82.1394	488	822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.47	98.39	0.93	0.91	4	-
GCF_001953955.1	s__Prevotella intermedia	80.6133	434	822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.61	96.13	0.88	0.83	34	-
GCF_000613945.1	s__Prevotella falsenii	79.5739	406	822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000257925.1	s__Prevotella sp000257925	78.3939	90	822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.40	96.99	0.92	0.83	10	-
GCF_000144405.1	s__Prevotella melaninogenica	78.0735	101	822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.46	95.36	0.87	0.78	36	-
GCF_000377625.1	s__Prevotella veroralis	77.9557	86	822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.76	96.65	0.91	0.86	4	-
GCF_000613345.1	s__Prevotella disiens	77.8577	247	822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.74	97.99	0.90	0.82	7	-
GCF_900155655.1	s__Prevotella ihumii	77.654	173	822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000262545.1	s__Prevotella bivia	77.1158	93	822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.82	98.45	0.91	0.86	8	-
--------------------------------------------------------------------------------
[2023-06-28 15:15:56,989] [INFO] GTDB search result was written to GCA_015261705.1_ASM1526170v1_genomic.fna/result_gtdb.tsv
[2023-06-28 15:15:56,991] [INFO] ===== GTDB Search completed =====
[2023-06-28 15:15:56,994] [INFO] DFAST_QC result json was written to GCA_015261705.1_ASM1526170v1_genomic.fna/dqc_result.json
[2023-06-28 15:15:56,995] [INFO] DFAST_QC completed!
[2023-06-28 15:15:56,995] [INFO] Total running time: 0h0m60s