[2024-01-25 19:12:35,784] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:12:35,785] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:12:35,785] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a12e4c8-99d6-4f94-bdf2-b48e242255a4/dqc_reference
[2024-01-25 19:12:36,929] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:12:36,929] [INFO] Task started: Prodigal
[2024-01-25 19:12:36,930] [INFO] Running command: gunzip -c /var/lib/cwl/stg0e37ecd3-189d-4726-9a13-d5ec4225c0ea/GCF_028023675.1_ASM2802367v1_genomic.fna.gz | prodigal -d GCF_028023675.1_ASM2802367v1_genomic.fna/cds.fna -a GCF_028023675.1_ASM2802367v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:12:49,302] [INFO] Task succeeded: Prodigal
[2024-01-25 19:12:49,303] [INFO] Task started: HMMsearch
[2024-01-25 19:12:49,303] [INFO] Running command: hmmsearch --tblout GCF_028023675.1_ASM2802367v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a12e4c8-99d6-4f94-bdf2-b48e242255a4/dqc_reference/reference_markers.hmm GCF_028023675.1_ASM2802367v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:12:49,574] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:12:49,575] [INFO] Found 6/6 markers.
[2024-01-25 19:12:49,622] [INFO] Query marker FASTA was written to GCF_028023675.1_ASM2802367v1_genomic.fna/markers.fasta
[2024-01-25 19:12:49,623] [INFO] Task started: Blastn
[2024-01-25 19:12:49,623] [INFO] Running command: blastn -query GCF_028023675.1_ASM2802367v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a12e4c8-99d6-4f94-bdf2-b48e242255a4/dqc_reference/reference_markers.fasta -out GCF_028023675.1_ASM2802367v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:12:50,560] [INFO] Task succeeded: Blastn
[2024-01-25 19:12:50,564] [INFO] Selected 31 target genomes.
[2024-01-25 19:12:50,564] [INFO] Target genome list was writen to GCF_028023675.1_ASM2802367v1_genomic.fna/target_genomes.txt
[2024-01-25 19:12:50,586] [INFO] Task started: fastANI
[2024-01-25 19:12:50,586] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e37ecd3-189d-4726-9a13-d5ec4225c0ea/GCF_028023675.1_ASM2802367v1_genomic.fna.gz --refList GCF_028023675.1_ASM2802367v1_genomic.fna/target_genomes.txt --output GCF_028023675.1_ASM2802367v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:13:14,256] [INFO] Task succeeded: fastANI
[2024-01-25 19:13:14,257] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a12e4c8-99d6-4f94-bdf2-b48e242255a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:13:14,257] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a12e4c8-99d6-4f94-bdf2-b48e242255a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:13:14,273] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:13:14,274] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:13:14,274] [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
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.8862	532	1410	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	78.7016	514	1410	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	78.7014	508	1410	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	78.6902	556	1410	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.6748	494	1410	95	below_threshold
Marivita lacus	strain=CGMCC 1.12478	GCA_014637725.1	1323742	1323742	type	True	78.6382	501	1410	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.5238	515	1410	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	78.518	474	1410	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	78.502	487	1410	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	78.4368	467	1410	95	below_threshold
Pseudooceanicola nitratireducens	strain=DSM 29619	GCA_900112545.1	517719	517719	type	True	78.4361	469	1410	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	78.4276	470	1410	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	78.426	448	1410	95	below_threshold
Pseudooceanicola nitratireducens	strain=CGMCC 1.7292	GCA_900109195.1	517719	517719	type	True	78.3952	460	1410	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	78.3861	484	1410	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	78.353	568	1410	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	78.3515	564	1410	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	78.303	473	1410	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	78.2353	367	1410	95	below_threshold
Roseovarius gaetbuli	strain=CECT 8370	GCA_900172365.1	1356575	1356575	type	True	78.2021	414	1410	95	below_threshold
Marivita hallyeonensis	strain=DSM 29431	GCA_900129875.1	996342	996342	type	True	77.9479	367	1410	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	77.9159	409	1410	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	77.9006	398	1410	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.8584	381	1410	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	77.8559	325	1410	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	77.814	387	1410	95	below_threshold
Roseivivax halotolerans	strain=JCM 10271	GCA_900115815.1	93684	93684	type	True	77.654	336	1410	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	77.6393	353	1410	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.4429	321	1410	95	below_threshold
Paracoccus lutimaris	strain=CECT 8525	GCA_003337565.1	1490030	1490030	type	True	77.2803	319	1410	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	77.0078	173	1410	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:13:14,275] [INFO] DFAST Taxonomy check result was written to GCF_028023675.1_ASM2802367v1_genomic.fna/tc_result.tsv
[2024-01-25 19:13:14,275] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:13:14,276] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:13:14,276] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a12e4c8-99d6-4f94-bdf2-b48e242255a4/dqc_reference/checkm_data
[2024-01-25 19:13:14,276] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:13:14,318] [INFO] Task started: CheckM
[2024-01-25 19:13:14,319] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028023675.1_ASM2802367v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028023675.1_ASM2802367v1_genomic.fna/checkm_input GCF_028023675.1_ASM2802367v1_genomic.fna/checkm_result
[2024-01-25 19:13:55,747] [INFO] Task succeeded: CheckM
[2024-01-25 19:13:55,748] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:13:55,779] [INFO] ===== Completeness check finished =====
[2024-01-25 19:13:55,779] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:13:55,780] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028023675.1_ASM2802367v1_genomic.fna/markers.fasta)
[2024-01-25 19:13:55,780] [INFO] Task started: Blastn
[2024-01-25 19:13:55,780] [INFO] Running command: blastn -query GCF_028023675.1_ASM2802367v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a12e4c8-99d6-4f94-bdf2-b48e242255a4/dqc_reference/reference_markers_gtdb.fasta -out GCF_028023675.1_ASM2802367v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:13:57,549] [INFO] Task succeeded: Blastn
[2024-01-25 19:13:57,553] [INFO] Selected 28 target genomes.
[2024-01-25 19:13:57,554] [INFO] Target genome list was writen to GCF_028023675.1_ASM2802367v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:13:57,582] [INFO] Task started: fastANI
[2024-01-25 19:13:57,583] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e37ecd3-189d-4726-9a13-d5ec4225c0ea/GCF_028023675.1_ASM2802367v1_genomic.fna.gz --refList GCF_028023675.1_ASM2802367v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028023675.1_ASM2802367v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:14:19,916] [INFO] Task succeeded: fastANI
[2024-01-25 19:14:19,935] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:14:19,936] [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_900109145.1	s__Marinovum algicola	80.1876	737	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	99.11	98.22	0.94	0.88	3	-
GCA_006226775.1	s__Marinovum sp006226775	79.9086	704	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017311415.1	s__Salipiger abyssi_A	79.0204	521	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	78.9258	540	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152625.1	s__Roseovarius nubinhibens	78.8757	474	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.78	96.50	0.89	0.84	4	-
GCF_004358185.1	s__Antarcticimicrobium luteum	78.8666	534	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019104745.1	s__CAU-1522 sp019104745	78.7755	509	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1522	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344785.1	s__Puniceibacterium profundi	78.7151	566	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	78.7022	513	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_009857745.1	s__Thalassobius mangrovi	78.6616	496	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014637725.1	s__Marivita lacus	78.638	501	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100085.1	s__Salipiger marinus	78.5425	511	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.13	98.13	0.95	0.95	2	-
GCF_900100005.1	s__Lutimaribacter saemankumensis	78.4249	469	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458395.1	s__Leisingera aquaemixtae	78.4167	472	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	97.55	97.51	0.94	0.92	3	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	78.3901	455	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_018139985.1	s__JAGSOU01 sp018139985	78.3712	439	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016888515.1	s__Shimia_A biformata	78.355	497	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348975.1	s__Antarcticimicrobium sediminis	78.3004	474	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789075.1	s__Pseudooceanicola pacificus	78.2736	313	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003313245.1	s__Primorskyibacter marinus	78.2493	395	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172365.1	s__Roseovarius gaetbuli	78.1901	416	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521865.1	s__Roseivivax isoporae	78.1279	373	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860705.1	s__Salipiger sp018860705	78.0615	423	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003651245.1	s__Roseovarius spongiae	77.9798	415	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000590925.1	s__Roseicyclus elongatus	77.8749	379	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908505.1	s__Salibaculum sp009908505	77.8657	380	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428225.1	s__Roseovarius sp002428225	77.7156	269	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.12	96.12	0.88	0.88	2	-
GCF_005870025.1	s__Mangrovicoccus sp005870025	77.3792	375	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:14:19,937] [INFO] GTDB search result was written to GCF_028023675.1_ASM2802367v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:14:19,939] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:14:19,944] [INFO] DFAST_QC result json was written to GCF_028023675.1_ASM2802367v1_genomic.fna/dqc_result.json
[2024-01-25 19:14:19,945] [INFO] DFAST_QC completed!
[2024-01-25 19:14:19,945] [INFO] Total running time: 0h1m44s