[2024-01-24 12:46:56,025] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:56,026] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:56,027] [INFO] DQC Reference Directory: /var/lib/cwl/stgd71f60db-93bb-4343-bd93-d1ad8cde8780/dqc_reference
[2024-01-24 12:46:57,374] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:57,375] [INFO] Task started: Prodigal
[2024-01-24 12:46:57,375] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b7f09db-8566-48aa-b790-cdf17ee7ad44/GCF_000423645.1_ASM42364v1_genomic.fna.gz | prodigal -d GCF_000423645.1_ASM42364v1_genomic.fna/cds.fna -a GCF_000423645.1_ASM42364v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:08,560] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:08,560] [INFO] Task started: HMMsearch
[2024-01-24 12:47:08,560] [INFO] Running command: hmmsearch --tblout GCF_000423645.1_ASM42364v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd71f60db-93bb-4343-bd93-d1ad8cde8780/dqc_reference/reference_markers.hmm GCF_000423645.1_ASM42364v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:08,814] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:08,816] [INFO] Found 6/6 markers.
[2024-01-24 12:47:08,853] [INFO] Query marker FASTA was written to GCF_000423645.1_ASM42364v1_genomic.fna/markers.fasta
[2024-01-24 12:47:08,854] [INFO] Task started: Blastn
[2024-01-24 12:47:08,854] [INFO] Running command: blastn -query GCF_000423645.1_ASM42364v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd71f60db-93bb-4343-bd93-d1ad8cde8780/dqc_reference/reference_markers.fasta -out GCF_000423645.1_ASM42364v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:09,809] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:09,812] [INFO] Selected 32 target genomes.
[2024-01-24 12:47:09,812] [INFO] Target genome list was writen to GCF_000423645.1_ASM42364v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:09,826] [INFO] Task started: fastANI
[2024-01-24 12:47:09,826] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b7f09db-8566-48aa-b790-cdf17ee7ad44/GCF_000423645.1_ASM42364v1_genomic.fna.gz --refList GCF_000423645.1_ASM42364v1_genomic.fna/target_genomes.txt --output GCF_000423645.1_ASM42364v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:32,227] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:32,228] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd71f60db-93bb-4343-bd93-d1ad8cde8780/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:32,228] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd71f60db-93bb-4343-bd93-d1ad8cde8780/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:32,253] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:47:32,254] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:47:32,254] [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
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	79.3121	447	1152	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	79.2715	445	1152	95	below_threshold
Roseovarius nitratireducens	strain=TFZ	GCA_002925845.1	2044597	2044597	type	True	79.1366	445	1152	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	78.9897	447	1152	95	below_threshold
Roseovarius halotolerans	strain=CECT 8110	GCA_900172255.1	505353	505353	type	True	78.9887	446	1152	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.9465	478	1152	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	78.902	453	1152	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	78.8896	457	1152	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	78.8484	420	1152	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.8428	515	1152	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	78.8346	410	1152	95	below_threshold
Salibaculum halophilum	strain=WDS1C4	GCA_002094885.1	1914408	1914408	type	True	78.4859	349	1152	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	78.3757	365	1152	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	78.3664	401	1152	95	below_threshold
Salinihabitans flavidus	strain=DSM 27842	GCA_900110425.1	569882	569882	type	True	78.3134	421	1152	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	78.2933	333	1152	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.2784	361	1152	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	78.2124	414	1152	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	78.2031	378	1152	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	78.1775	377	1152	95	below_threshold
Pontibaca methylaminivorans	strain=DSM 21219	GCA_900156525.1	515897	515897	type	True	78.1751	263	1152	95	below_threshold
Allosediminivita pacifica	strain=CGMCC 1.12410	GCA_014637495.1	1267769	1267769	type	True	78.1674	352	1152	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	78.1655	367	1152	95	below_threshold
Allosediminivita pacifica	strain=DSM 29329	GCA_003054175.1	1267769	1267769	type	True	78.1345	347	1152	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	78.1075	454	1152	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.9561	300	1152	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	77.9323	388	1152	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	77.7499	405	1152	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	77.5947	300	1152	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	77.3241	298	1152	95	below_threshold
Pararhodobacter aggregans	strain=D1-19	GCA_003075525.1	404875	404875	type	True	77.1138	333	1152	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	77.0849	255	1152	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:32,256] [INFO] DFAST Taxonomy check result was written to GCF_000423645.1_ASM42364v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:32,256] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:32,256] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:32,257] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd71f60db-93bb-4343-bd93-d1ad8cde8780/dqc_reference/checkm_data
[2024-01-24 12:47:32,258] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:32,296] [INFO] Task started: CheckM
[2024-01-24 12:47:32,297] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000423645.1_ASM42364v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000423645.1_ASM42364v1_genomic.fna/checkm_input GCF_000423645.1_ASM42364v1_genomic.fna/checkm_result
[2024-01-24 12:48:08,101] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:08,102] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:08,124] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:08,124] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:08,125] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000423645.1_ASM42364v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:08,125] [INFO] Task started: Blastn
[2024-01-24 12:48:08,125] [INFO] Running command: blastn -query GCF_000423645.1_ASM42364v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd71f60db-93bb-4343-bd93-d1ad8cde8780/dqc_reference/reference_markers_gtdb.fasta -out GCF_000423645.1_ASM42364v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:09,866] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:09,872] [INFO] Selected 26 target genomes.
[2024-01-24 12:48:09,872] [INFO] Target genome list was writen to GCF_000423645.1_ASM42364v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:09,892] [INFO] Task started: fastANI
[2024-01-24 12:48:09,893] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b7f09db-8566-48aa-b790-cdf17ee7ad44/GCF_000423645.1_ASM42364v1_genomic.fna.gz --refList GCF_000423645.1_ASM42364v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000423645.1_ASM42364v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:28,611] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:28,631] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:28,632] [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_000423645.1	s__Sediminimonas qiaohouensis	100.0	1148	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sediminimonas	95.0	97.45	97.45	0.91	0.91	2	conclusive
GCA_011389955.1	s__Sediminimonas sp011389955	84.3634	414	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sediminimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	80.2976	592	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002786325.1	s__Pseudooceanicola_C lipolyticus	79.1519	458	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789075.1	s__Pseudooceanicola pacificus	79.1177	316	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	79.0878	455	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172255.1	s__Roseovarius halotolerans	79.0062	443	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002720475.1	s__Roseovarius sp002720475	78.9353	349	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.80	99.74	0.82	0.71	3	-
GCF_900109035.1	s__Cribrihabitans marinus	78.9227	453	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003651245.1	s__Roseovarius spongiae	78.806	418	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016278295.1	s__Roseovarius sp016278295	78.7464	376	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002166865.1	s__Roseovarius sp002166865	78.683	446	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107235.1	s__Citreimonas salinaria	78.6331	418	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Citreimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344785.1	s__Puniceibacterium profundi	78.5515	444	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314705.1	s__Aquicoccus sp001314705	78.5447	401	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aquicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003944755.1	s__Rhodovulum robiginosum	78.5096	434	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442255.1	s__Salipiger mucosus	78.468	440	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018224955.1	s__Aestuariicoccus sp018224955	78.3799	429	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792425.1	s__Thalassobius sp017792425	78.3649	409	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938215.1	s__Ruegeria sediminis	78.3558	403	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110425.1	s__Salinihabitans flavidus	78.3227	420	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salinihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003646465.1	s__Chachezhania antarctica	78.289	373	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Chachezhania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005887615.1	s__Sulfitobacter_E sabulilitoris	78.204	415	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003111685.1	s__Salipiger pacificus_A	78.1257	360	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.69	97.64	0.90	0.89	3	-
GCF_004348975.1	s__Antarcticimicrobium sediminis	78.0916	456	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709085.1	s__Pseudooceanicola sp002709085	77.9041	242	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:28,633] [INFO] GTDB search result was written to GCF_000423645.1_ASM42364v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:28,634] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:28,641] [INFO] DFAST_QC result json was written to GCF_000423645.1_ASM42364v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:28,641] [INFO] DFAST_QC completed!
[2024-01-24 12:48:28,641] [INFO] Total running time: 0h1m33s