[2024-01-24 14:03:08,454] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:03:08,457] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:03:08,458] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8676673-5714-4c60-84de-d37d4f6e2a39/dqc_reference
[2024-01-24 14:03:09,937] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:03:09,938] [INFO] Task started: Prodigal
[2024-01-24 14:03:09,938] [INFO] Running command: gunzip -c /var/lib/cwl/stgf1d1f352-a82e-4a2b-86e3-adda5a3f0c04/GCF_014196965.1_ASM1419696v1_genomic.fna.gz | prodigal -d GCF_014196965.1_ASM1419696v1_genomic.fna/cds.fna -a GCF_014196965.1_ASM1419696v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:22,244] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:22,245] [INFO] Task started: HMMsearch
[2024-01-24 14:03:22,245] [INFO] Running command: hmmsearch --tblout GCF_014196965.1_ASM1419696v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8676673-5714-4c60-84de-d37d4f6e2a39/dqc_reference/reference_markers.hmm GCF_014196965.1_ASM1419696v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:22,578] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:22,579] [INFO] Found 6/6 markers.
[2024-01-24 14:03:22,627] [INFO] Query marker FASTA was written to GCF_014196965.1_ASM1419696v1_genomic.fna/markers.fasta
[2024-01-24 14:03:22,627] [INFO] Task started: Blastn
[2024-01-24 14:03:22,628] [INFO] Running command: blastn -query GCF_014196965.1_ASM1419696v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8676673-5714-4c60-84de-d37d4f6e2a39/dqc_reference/reference_markers.fasta -out GCF_014196965.1_ASM1419696v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:23,667] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:23,670] [INFO] Selected 26 target genomes.
[2024-01-24 14:03:23,670] [INFO] Target genome list was writen to GCF_014196965.1_ASM1419696v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:23,700] [INFO] Task started: fastANI
[2024-01-24 14:03:23,701] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1d1f352-a82e-4a2b-86e3-adda5a3f0c04/GCF_014196965.1_ASM1419696v1_genomic.fna.gz --refList GCF_014196965.1_ASM1419696v1_genomic.fna/target_genomes.txt --output GCF_014196965.1_ASM1419696v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:42,925] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:42,925] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8676673-5714-4c60-84de-d37d4f6e2a39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:42,926] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8676673-5714-4c60-84de-d37d4f6e2a39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:42,945] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:03:42,946] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:03:42,946] [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
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	80.4004	536	1343	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_004345735.1	35804	35804	type	True	80.3271	542	1343	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	80.2478	587	1343	95	below_threshold
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	80.2335	375	1343	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	79.8469	428	1343	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	79.736	551	1343	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	79.6209	558	1343	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	79.5141	524	1343	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	79.509	554	1343	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	79.4988	536	1343	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	79.3276	378	1343	95	below_threshold
Allgaiera indica	strain=CGMCC 1.10859	GCA_014653075.1	765699	765699	type	True	79.2165	476	1343	95	below_threshold
Allgaiera indica	strain=DSM 24802	GCA_900106675.1	765699	765699	type	True	79.191	474	1343	95	below_threshold
Actibacterium mucosum	strain=KCTC 23349	GCA_000647975.1	1087332	1087332	type	True	79.0833	430	1343	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	79.0286	433	1343	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	78.9944	469	1343	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	78.9566	485	1343	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_016653435.1	33049	33049	type	True	78.8646	420	1343	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_004363195.1	33049	33049	type	True	78.8348	439	1343	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_003034995.1	33049	33049	type	True	78.7521	428	1343	95	below_threshold
Actibacterium atlanticum	strain=22II-S11-z10	GCA_000671395.1	1461693	1461693	type	True	78.7518	409	1343	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	78.4266	404	1343	95	below_threshold
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	78.3903	338	1343	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	78.2702	363	1343	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	78.2568	400	1343	95	below_threshold
Pseudogemmobacter bohemicus	strain=Cd-10	GCA_003290025.1	2250708	2250708	type	True	77.3813	359	1343	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:42,947] [INFO] DFAST Taxonomy check result was written to GCF_014196965.1_ASM1419696v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:42,948] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:42,948] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:42,948] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8676673-5714-4c60-84de-d37d4f6e2a39/dqc_reference/checkm_data
[2024-01-24 14:03:42,950] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:42,996] [INFO] Task started: CheckM
[2024-01-24 14:03:42,997] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014196965.1_ASM1419696v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014196965.1_ASM1419696v1_genomic.fna/checkm_input GCF_014196965.1_ASM1419696v1_genomic.fna/checkm_result
[2024-01-24 14:04:24,035] [INFO] Task succeeded: CheckM
[2024-01-24 14:04:24,036] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:04:24,062] [INFO] ===== Completeness check finished =====
[2024-01-24 14:04:24,063] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:04:24,063] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014196965.1_ASM1419696v1_genomic.fna/markers.fasta)
[2024-01-24 14:04:24,064] [INFO] Task started: Blastn
[2024-01-24 14:04:24,064] [INFO] Running command: blastn -query GCF_014196965.1_ASM1419696v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8676673-5714-4c60-84de-d37d4f6e2a39/dqc_reference/reference_markers_gtdb.fasta -out GCF_014196965.1_ASM1419696v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:04:25,971] [INFO] Task succeeded: Blastn
[2024-01-24 14:04:25,976] [INFO] Selected 19 target genomes.
[2024-01-24 14:04:25,976] [INFO] Target genome list was writen to GCF_014196965.1_ASM1419696v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:04:25,999] [INFO] Task started: fastANI
[2024-01-24 14:04:25,999] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1d1f352-a82e-4a2b-86e3-adda5a3f0c04/GCF_014196965.1_ASM1419696v1_genomic.fna.gz --refList GCF_014196965.1_ASM1419696v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014196965.1_ASM1419696v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:04:41,497] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:41,514] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:04:41,515] [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_014196965.1	s__Actibacterium_A naphthalenivorans	100.0	1340	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium_A	95.0	98.28	97.38	0.93	0.89	4	conclusive
GCF_002285435.1	s__Actibacterium ureilyticum	81.3676	706	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	81.0175	635	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744955.1	s__Actibacterium sp000744955	80.4016	631	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343075.1	s__Rhodovulum marinum	80.2717	585	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938875.1	s__Rhodovulum sp016938875	80.1235	531	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016278325.1	s__JADQCB01 sp016278325	80.0658	524	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JADQCB01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797755.1	s__Brevirhabdus pacifica	79.8592	427	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Brevirhabdus	95.0	99.99	99.97	0.99	0.98	4	-
GCF_009649175.1	s__Rhodovulum strictum	79.7221	552	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339675.1	s__Rhodovulum steppense	79.6487	555	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342445.1	s__Rhodovulum euryhalinum	79.5431	521	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	79.4826	537	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053725.1	s__Rhodovulum kholense	79.3871	543	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.27	98.27	0.96	0.96	2	-
GCF_900142935.1	s__Rhodovulum sp900142935	79.2296	502	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000647975.1	s__Actibacterium mucosum	79.0833	430	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018219815.1	s__Thalassobius aquimarinus	78.9799	471	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019061145.1	s__ASV31 sp019061145	78.6769	455	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ASV31	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003122205.1	s__QEYE01 sp003122205	78.4301	435	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__QEYE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017592335.1	s__Sulfitobacter_F sp017592335	77.5467	238	1343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:04:41,517] [INFO] GTDB search result was written to GCF_014196965.1_ASM1419696v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:04:41,517] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:04:41,523] [INFO] DFAST_QC result json was written to GCF_014196965.1_ASM1419696v1_genomic.fna/dqc_result.json
[2024-01-24 14:04:41,524] [INFO] DFAST_QC completed!
[2024-01-24 14:04:41,524] [INFO] Total running time: 0h1m33s