[2024-01-25 19:08:20,429] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:08:20,430] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:08:20,430] [INFO] DQC Reference Directory: /var/lib/cwl/stg8aade623-b01b-4d3b-8e6c-f704ebb9c155/dqc_reference
[2024-01-25 19:08:21,571] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:08:21,571] [INFO] Task started: Prodigal
[2024-01-25 19:08:21,571] [INFO] Running command: gunzip -c /var/lib/cwl/stg3883acd5-145c-48b1-bbac-951eb776cac3/GCF_900302465.1_A.donghaensisCECT8599_Spades_Prokka_genomic.fna.gz | prodigal -d GCF_900302465.1_A.donghaensisCECT8599_Spades_Prokka_genomic.fna/cds.fna -a GCF_900302465.1_A.donghaensisCECT8599_Spades_Prokka_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:08:34,723] [INFO] Task succeeded: Prodigal
[2024-01-25 19:08:34,724] [INFO] Task started: HMMsearch
[2024-01-25 19:08:34,724] [INFO] Running command: hmmsearch --tblout GCF_900302465.1_A.donghaensisCECT8599_Spades_Prokka_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8aade623-b01b-4d3b-8e6c-f704ebb9c155/dqc_reference/reference_markers.hmm GCF_900302465.1_A.donghaensisCECT8599_Spades_Prokka_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:08:35,010] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:08:35,011] [INFO] Found 6/6 markers.
[2024-01-25 19:08:35,049] [INFO] Query marker FASTA was written to GCF_900302465.1_A.donghaensisCECT8599_Spades_Prokka_genomic.fna/markers.fasta
[2024-01-25 19:08:35,050] [INFO] Task started: Blastn
[2024-01-25 19:08:35,050] [INFO] Running command: blastn -query GCF_900302465.1_A.donghaensisCECT8599_Spades_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg8aade623-b01b-4d3b-8e6c-f704ebb9c155/dqc_reference/reference_markers.fasta -out GCF_900302465.1_A.donghaensisCECT8599_Spades_Prokka_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:08:35,674] [INFO] Task succeeded: Blastn
[2024-01-25 19:08:35,678] [INFO] Selected 25 target genomes.
[2024-01-25 19:08:35,678] [INFO] Target genome list was writen to GCF_900302465.1_A.donghaensisCECT8599_Spades_Prokka_genomic.fna/target_genomes.txt
[2024-01-25 19:08:35,712] [INFO] Task started: fastANI
[2024-01-25 19:08:35,713] [INFO] Running command: fastANI --query /var/lib/cwl/stg3883acd5-145c-48b1-bbac-951eb776cac3/GCF_900302465.1_A.donghaensisCECT8599_Spades_Prokka_genomic.fna.gz --refList GCF_900302465.1_A.donghaensisCECT8599_Spades_Prokka_genomic.fna/target_genomes.txt --output GCF_900302465.1_A.donghaensisCECT8599_Spades_Prokka_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:08:53,363] [INFO] Task succeeded: fastANI
[2024-01-25 19:08:53,364] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8aade623-b01b-4d3b-8e6c-f704ebb9c155/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:08:53,364] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8aade623-b01b-4d3b-8e6c-f704ebb9c155/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:08:53,378] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:08:53,378] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:08:53,378] [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
Ascidiaceihabitans donghaensis	strain=CECT 8599	GCA_900302465.1	1510460	1510460	type	True	100.0	1357	1357	95	conclusive
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	77.8515	257	1357	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	77.8369	250	1357	95	below_threshold
Sulfitobacter donghicola	strain=KCTC 12864	GCA_000622405.1	421000	421000	type	True	77.7978	222	1357	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	77.7207	275	1357	95	below_threshold
Sulfitobacter donghicola	strain=JCM 14565	GCA_000712275.1	421000	421000	type	True	77.5336	215	1357	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.5039	293	1357	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.4988	292	1357	95	below_threshold
Sulfitobacter noctilucicola	strain=NB-77	GCA_000622385.1	1342301	1342301	type	True	77.4781	223	1357	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	77.4073	230	1357	95	below_threshold
Sulfitobacter noctilucicola	strain=DSM 101015	GCA_014197555.1	1342301	1342301	type	True	77.3721	222	1357	95	below_threshold
Tateyamaria pelophila	strain=DSM 17270	GCA_019966495.1	328415	328415	type	True	77.2269	233	1357	95	below_threshold
Tateyamaria omphalii	strain=KCTC 12333	GCA_014651375.1	299262	299262	type	True	77.1442	233	1357	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	77.0892	232	1357	95	below_threshold
Roseovarius litorisediminis	strain=CECT 8287	GCA_900172295.1	1312363	1312363	type	True	77.0793	139	1357	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	76.9678	163	1357	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.8604	145	1357	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.7839	170	1357	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	76.7561	150	1357	95	below_threshold
Cochlodiniinecator piscidefendens	strain=M26A2M	GCA_011326755.1	2715756	2715756	type	True	76.6953	89	1357	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	76.5631	90	1357	95	below_threshold
Tritonibacter multivorans	strain=CECT 7557	GCA_001458415.1	928856	928856	type	True	76.5406	161	1357	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	76.3531	150	1357	95	below_threshold
Gemmobacter serpentinus	strain=HB-1	GCA_008973825.1	2652247	2652247	type	True	76.3187	67	1357	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	75.9441	92	1357	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:08:53,379] [INFO] DFAST Taxonomy check result was written to GCF_900302465.1_A.donghaensisCECT8599_Spades_Prokka_genomic.fna/tc_result.tsv
[2024-01-25 19:08:53,381] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:08:53,381] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:08:53,381] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8aade623-b01b-4d3b-8e6c-f704ebb9c155/dqc_reference/checkm_data
[2024-01-25 19:08:53,382] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:08:53,433] [INFO] Task started: CheckM
[2024-01-25 19:08:53,433] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900302465.1_A.donghaensisCECT8599_Spades_Prokka_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900302465.1_A.donghaensisCECT8599_Spades_Prokka_genomic.fna/checkm_input GCF_900302465.1_A.donghaensisCECT8599_Spades_Prokka_genomic.fna/checkm_result
[2024-01-25 19:09:34,223] [INFO] Task succeeded: CheckM
[2024-01-25 19:09:34,224] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:09:34,257] [INFO] ===== Completeness check finished =====
[2024-01-25 19:09:34,257] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:09:34,257] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900302465.1_A.donghaensisCECT8599_Spades_Prokka_genomic.fna/markers.fasta)
[2024-01-25 19:09:34,258] [INFO] Task started: Blastn
[2024-01-25 19:09:34,258] [INFO] Running command: blastn -query GCF_900302465.1_A.donghaensisCECT8599_Spades_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg8aade623-b01b-4d3b-8e6c-f704ebb9c155/dqc_reference/reference_markers_gtdb.fasta -out GCF_900302465.1_A.donghaensisCECT8599_Spades_Prokka_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:09:35,202] [INFO] Task succeeded: Blastn
[2024-01-25 19:09:35,206] [INFO] Selected 23 target genomes.
[2024-01-25 19:09:35,206] [INFO] Target genome list was writen to GCF_900302465.1_A.donghaensisCECT8599_Spades_Prokka_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:09:35,237] [INFO] Task started: fastANI
[2024-01-25 19:09:35,238] [INFO] Running command: fastANI --query /var/lib/cwl/stg3883acd5-145c-48b1-bbac-951eb776cac3/GCF_900302465.1_A.donghaensisCECT8599_Spades_Prokka_genomic.fna.gz --refList GCF_900302465.1_A.donghaensisCECT8599_Spades_Prokka_genomic.fna/target_genomes_gtdb.txt --output GCF_900302465.1_A.donghaensisCECT8599_Spades_Prokka_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:09:52,153] [INFO] Task succeeded: fastANI
[2024-01-25 19:09:52,166] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:09:52,166] [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_900302465.1	s__Ascidiaceihabitans donghaensis	100.0	1357	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000622405.1	s__Sulfitobacter donghicola	77.7832	223	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000622325.1	s__Sulfitobacter geojensis	77.7635	255	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.34	96.22	0.90	0.89	35	-
GCF_003054325.1	s__Sulfitobacter mediterraneus	77.7404	274	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.52	96.39	0.88	0.86	71	-
GCA_018647275.1	s__Ascidiaceihabitans sp018647275	77.5295	117	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	77.5039	293	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_000622385.1	s__Sulfitobacter noctilucicola	77.4781	223	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013282155.1	s__Sulfitobacter sp013282155	77.449	270	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.41	99.36	0.93	0.90	3	-
GCF_000622365.1	s__Sulfitobacter noctilucae	77.3431	228	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196805.1	s__Sulfitobacter undariae	77.3126	199	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969365.1	s__Tateyamaria omphalii_A	77.3049	248	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016801775.1	s__Sulfitobacter mediterraneus_A	77.2719	250	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	99.99	1.00	1.00	16	-
GCF_900112755.1	s__Sulfitobacter brevis	77.2618	192	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116285.1	s__Sulfitobacter marinus	77.2511	233	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363555.1	s__Sulfitobacter sp009363555	77.1784	213	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352045.1	s__JL08 sp003352045	77.1114	210	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JL08	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900537075.1	s__Ruegeria_E sp900537075	77.0887	202	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473165.1	s__Leisingera aquimarina	77.0636	162	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854855.1	s__Sulfitobacter sp017854855	77.0409	238	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650875.1	s__Sulfitobacter sp001650875	76.9886	232	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854415.1	s__Yoonia sp017854415	76.8881	115	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004123675.1	s__Leisingera sp004123675	76.8776	174	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.03	97.97	0.88	0.88	3	-
GCA_013215215.1	s__Cognatishimia sp013215215	76.4764	137	1357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatishimia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:09:52,168] [INFO] GTDB search result was written to GCF_900302465.1_A.donghaensisCECT8599_Spades_Prokka_genomic.fna/result_gtdb.tsv
[2024-01-25 19:09:52,168] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:09:52,174] [INFO] DFAST_QC result json was written to GCF_900302465.1_A.donghaensisCECT8599_Spades_Prokka_genomic.fna/dqc_result.json
[2024-01-25 19:09:52,174] [INFO] DFAST_QC completed!
[2024-01-25 19:09:52,174] [INFO] Total running time: 0h1m32s