[2024-01-24 14:19:46,425] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:46,428] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:46,429] [INFO] DQC Reference Directory: /var/lib/cwl/stg4aabfb0c-3c28-4ada-8b50-8edf0e297bed/dqc_reference
[2024-01-24 14:19:47,808] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:47,809] [INFO] Task started: Prodigal
[2024-01-24 14:19:47,810] [INFO] Running command: gunzip -c /var/lib/cwl/stg28162247-7f15-4634-8d14-b6af987e6c96/GCF_008016795.1_ASM801679v1_genomic.fna.gz | prodigal -d GCF_008016795.1_ASM801679v1_genomic.fna/cds.fna -a GCF_008016795.1_ASM801679v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:02,901] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:02,902] [INFO] Task started: HMMsearch
[2024-01-24 14:20:02,902] [INFO] Running command: hmmsearch --tblout GCF_008016795.1_ASM801679v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4aabfb0c-3c28-4ada-8b50-8edf0e297bed/dqc_reference/reference_markers.hmm GCF_008016795.1_ASM801679v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:03,155] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:03,156] [INFO] Found 6/6 markers.
[2024-01-24 14:20:03,197] [INFO] Query marker FASTA was written to GCF_008016795.1_ASM801679v1_genomic.fna/markers.fasta
[2024-01-24 14:20:03,198] [INFO] Task started: Blastn
[2024-01-24 14:20:03,198] [INFO] Running command: blastn -query GCF_008016795.1_ASM801679v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4aabfb0c-3c28-4ada-8b50-8edf0e297bed/dqc_reference/reference_markers.fasta -out GCF_008016795.1_ASM801679v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:03,773] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:03,778] [INFO] Selected 21 target genomes.
[2024-01-24 14:20:03,779] [INFO] Target genome list was writen to GCF_008016795.1_ASM801679v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:03,791] [INFO] Task started: fastANI
[2024-01-24 14:20:03,792] [INFO] Running command: fastANI --query /var/lib/cwl/stg28162247-7f15-4634-8d14-b6af987e6c96/GCF_008016795.1_ASM801679v1_genomic.fna.gz --refList GCF_008016795.1_ASM801679v1_genomic.fna/target_genomes.txt --output GCF_008016795.1_ASM801679v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:14,922] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:14,923] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4aabfb0c-3c28-4ada-8b50-8edf0e297bed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:14,923] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4aabfb0c-3c28-4ada-8b50-8edf0e297bed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:14,939] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:14,939] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:14,939] [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 brunnea	strain=A2672	GCA_008016795.1	2508867	2508867	type	True	100.0	794	802	95	conclusive
Prevotella corporis	strain=JCM 8529	GCA_000613365.1	28128	28128	type	True	84.9342	337	802	95	below_threshold
Prevotella corporis	strain=DSM 18810	GCA_000430525.1	28128	28128	type	True	84.7532	340	802	95	below_threshold
Prevotella disiens	strain=NCTC11157	GCA_900454955.1	28130	28130	type	True	83.0693	170	802	95	below_threshold
Prevotella pallens	strain=DSM 18710	GCA_003269195.1	60133	60133	type	True	81.277	108	802	95	below_threshold
Prevotella pallens	strain=ATCC 700821	GCA_000220255.1	60133	60133	type	True	81.2173	116	802	95	below_threshold
Prevotella ihumii	strain=Marseille-P3385	GCA_900155655.1	1917878	1917878	type	True	80.9913	153	802	95	below_threshold
Prevotella fusca	strain=W1435	GCA_018128145.1	589436	589436	type	True	80.792	93	802	95	below_threshold
Prevotella disiens	strain=ATCC 29426	GCA_000467875.1	28130	28130	type	True	80.7168	133	802	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	80.5932	97	802	95	below_threshold
Prevotella veroralis	strain=DSM 19559	GCA_000377625.1	28137	28137	type	True	80.5706	93	802	95	below_threshold
Prevotella fusca	strain=JCM 17724	GCA_000614245.1	589436	589436	type	True	80.4739	94	802	95	below_threshold
Prevotella melaninogenica	strain=FDAARGOS_1566	GCA_020735785.1	28132	28132	suspected-type	True	80.1868	99	802	95	below_threshold
Prevotella melaninogenica	strain=ATCC 25845	GCA_000144405.1	28132	28132	suspected-type	True	80.0641	96	802	95	below_threshold
Prevotella aurantiaca	strain=JCM 15754	GCA_000614025.1	596085	596085	type	True	79.9642	107	802	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	79.5871	53	802	95	below_threshold
Prevotella vespertina	strain=A2879	GCA_009728485.1	2608404	2608404	type	True	79.4732	90	802	95	below_threshold
Prevotella oris	strain=DSM 18711	GCA_000377685.1	28135	28135	type	True	79.239	68	802	95	below_threshold
Prevotella micans	strain=JCM 16134	GCA_000614105.1	189723	189723	type	True	78.0615	64	802	95	below_threshold
Prevotella micans	strain=DSM 21469	GCA_000373705.1	189723	189723	type	True	77.8029	64	802	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:14,941] [INFO] DFAST Taxonomy check result was written to GCF_008016795.1_ASM801679v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:14,942] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:14,942] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:14,942] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4aabfb0c-3c28-4ada-8b50-8edf0e297bed/dqc_reference/checkm_data
[2024-01-24 14:20:14,944] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:14,975] [INFO] Task started: CheckM
[2024-01-24 14:20:14,975] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008016795.1_ASM801679v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008016795.1_ASM801679v1_genomic.fna/checkm_input GCF_008016795.1_ASM801679v1_genomic.fna/checkm_result
[2024-01-24 14:20:58,188] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:58,189] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:58,206] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:58,206] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:58,207] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008016795.1_ASM801679v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:58,207] [INFO] Task started: Blastn
[2024-01-24 14:20:58,207] [INFO] Running command: blastn -query GCF_008016795.1_ASM801679v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4aabfb0c-3c28-4ada-8b50-8edf0e297bed/dqc_reference/reference_markers_gtdb.fasta -out GCF_008016795.1_ASM801679v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:59,002] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:59,006] [INFO] Selected 23 target genomes.
[2024-01-24 14:20:59,006] [INFO] Target genome list was writen to GCF_008016795.1_ASM801679v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:59,049] [INFO] Task started: fastANI
[2024-01-24 14:20:59,049] [INFO] Running command: fastANI --query /var/lib/cwl/stg28162247-7f15-4634-8d14-b6af987e6c96/GCF_008016795.1_ASM801679v1_genomic.fna.gz --refList GCF_008016795.1_ASM801679v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008016795.1_ASM801679v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:11,275] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:11,287] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:11,288] [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_008016795.1	s__Prevotella brunnea	100.0	794	802	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.23	99.23	0.96	0.96	2	conclusive
GCF_000430525.1	s__Prevotella corporis	84.726	343	802	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.63	97.78	0.92	0.87	4	-
GCF_000220255.1	s__Prevotella pallens	81.2173	116	802	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.33	96.89	0.94	0.88	40	-
GCF_000257925.1	s__Prevotella sp000257925	81.0965	87	802	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.40	96.99	0.92	0.83	10	-
GCF_900155655.1	s__Prevotella ihumii	80.9887	152	802	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001262015.1	s__Prevotella fusca	80.6505	95	802	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.98	99.97	1.00	1.00	3	-
GCF_018127925.1	s__Prevotella melaninogenica_C	80.4433	92	802	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018128065.1	s__Prevotella sp000467895	80.1063	90	802	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.71	96.42	0.91	0.83	4	-
GCF_000144405.1	s__Prevotella melaninogenica	80.0641	96	802	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.46	95.36	0.87	0.78	36	-
GCF_000614025.1	s__Prevotella aurantiaca	79.9642	107	802	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.47	98.39	0.93	0.91	4	-
GCF_900113305.1	s__Prevotella sp900113305	79.462	50	802	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000688375.1	s__Prevotella sp000688375	78.6112	172	802	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613945.1	s__Prevotella falsenii	78.2889	138	802	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016901395.1	s__Prevotella sp016901395	78.1131	55	802	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000614105.1	s__Prevotella micans	78.0057	65	802	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.39	98.24	0.98	0.95	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:11,290] [INFO] GTDB search result was written to GCF_008016795.1_ASM801679v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:11,290] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:11,294] [INFO] DFAST_QC result json was written to GCF_008016795.1_ASM801679v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:11,294] [INFO] DFAST_QC completed!
[2024-01-24 14:21:11,294] [INFO] Total running time: 0h1m25s