[2024-01-25 20:19:50,510] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:19:50,512] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:19:50,512] [INFO] DQC Reference Directory: /var/lib/cwl/stga3d1370d-3a9a-4a47-83e0-522fe6c1c634/dqc_reference
[2024-01-25 20:19:51,602] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:19:51,602] [INFO] Task started: Prodigal
[2024-01-25 20:19:51,603] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc1fd77b-db93-4305-b012-355d6f3ec94a/GCF_009833495.1_ASM983349v1_genomic.fna.gz | prodigal -d GCF_009833495.1_ASM983349v1_genomic.fna/cds.fna -a GCF_009833495.1_ASM983349v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:20:00,724] [INFO] Task succeeded: Prodigal
[2024-01-25 20:20:00,725] [INFO] Task started: HMMsearch
[2024-01-25 20:20:00,725] [INFO] Running command: hmmsearch --tblout GCF_009833495.1_ASM983349v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3d1370d-3a9a-4a47-83e0-522fe6c1c634/dqc_reference/reference_markers.hmm GCF_009833495.1_ASM983349v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:20:00,924] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:20:00,926] [INFO] Found 6/6 markers.
[2024-01-25 20:20:00,954] [INFO] Query marker FASTA was written to GCF_009833495.1_ASM983349v1_genomic.fna/markers.fasta
[2024-01-25 20:20:00,954] [INFO] Task started: Blastn
[2024-01-25 20:20:00,954] [INFO] Running command: blastn -query GCF_009833495.1_ASM983349v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3d1370d-3a9a-4a47-83e0-522fe6c1c634/dqc_reference/reference_markers.fasta -out GCF_009833495.1_ASM983349v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:01,866] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:01,870] [INFO] Selected 23 target genomes.
[2024-01-25 20:20:01,870] [INFO] Target genome list was writen to GCF_009833495.1_ASM983349v1_genomic.fna/target_genomes.txt
[2024-01-25 20:20:01,880] [INFO] Task started: fastANI
[2024-01-25 20:20:01,880] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc1fd77b-db93-4305-b012-355d6f3ec94a/GCF_009833495.1_ASM983349v1_genomic.fna.gz --refList GCF_009833495.1_ASM983349v1_genomic.fna/target_genomes.txt --output GCF_009833495.1_ASM983349v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:20:19,255] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:19,256] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3d1370d-3a9a-4a47-83e0-522fe6c1c634/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:20:19,256] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3d1370d-3a9a-4a47-83e0-522fe6c1c634/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:20:19,269] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:20:19,269] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:20:19,269] [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
Oceanomicrobium pacificus	strain=KN286	GCA_009833495.1	2692916	2692916	type	True	100.0	1078	1079	95	conclusive
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	78.4667	365	1079	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	77.9981	385	1079	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	77.9878	327	1079	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	77.9167	286	1079	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.9036	290	1079	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	77.8882	290	1079	95	below_threshold
Maritimibacter harenae	strain=DP07	GCA_009882975.1	2606218	2606218	type	True	77.8439	267	1079	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	77.8056	329	1079	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	77.6744	347	1079	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	77.6716	346	1079	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	77.6659	291	1079	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	77.6236	283	1079	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	77.5977	327	1079	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	77.5644	327	1079	95	below_threshold
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	77.5534	263	1079	95	below_threshold
Defluviimonas aquaemixtae	strain=CECT 8626	GCA_900302475.1	1542388	1542388	type	True	77.2991	229	1079	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	77.2678	242	1079	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.2385	224	1079	95	below_threshold
Amaricoccus macauensis	strain=DSM 101730	GCA_014201905.1	57001	57001	type	True	77.2013	253	1079	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	77.2009	255	1079	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.1101	259	1079	95	below_threshold
Phaeobacter porticola	strain=P97	GCA_001888185.1	1844006	1844006	type	True	76.7785	137	1079	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:20:19,275] [INFO] DFAST Taxonomy check result was written to GCF_009833495.1_ASM983349v1_genomic.fna/tc_result.tsv
[2024-01-25 20:20:19,276] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:20:19,276] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:20:19,276] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3d1370d-3a9a-4a47-83e0-522fe6c1c634/dqc_reference/checkm_data
[2024-01-25 20:20:19,277] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:20:19,315] [INFO] Task started: CheckM
[2024-01-25 20:20:19,315] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009833495.1_ASM983349v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009833495.1_ASM983349v1_genomic.fna/checkm_input GCF_009833495.1_ASM983349v1_genomic.fna/checkm_result
[2024-01-25 20:20:53,594] [INFO] Task succeeded: CheckM
[2024-01-25 20:20:53,595] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:20:53,627] [INFO] ===== Completeness check finished =====
[2024-01-25 20:20:53,627] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:20:53,628] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009833495.1_ASM983349v1_genomic.fna/markers.fasta)
[2024-01-25 20:20:53,628] [INFO] Task started: Blastn
[2024-01-25 20:20:53,628] [INFO] Running command: blastn -query GCF_009833495.1_ASM983349v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3d1370d-3a9a-4a47-83e0-522fe6c1c634/dqc_reference/reference_markers_gtdb.fasta -out GCF_009833495.1_ASM983349v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:55,465] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:55,468] [INFO] Selected 25 target genomes.
[2024-01-25 20:20:55,468] [INFO] Target genome list was writen to GCF_009833495.1_ASM983349v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:20:55,491] [INFO] Task started: fastANI
[2024-01-25 20:20:55,491] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc1fd77b-db93-4305-b012-355d6f3ec94a/GCF_009833495.1_ASM983349v1_genomic.fna.gz --refList GCF_009833495.1_ASM983349v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009833495.1_ASM983349v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:21:15,005] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:15,020] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:21:15,021] [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_009833495.1	s__Oceanomicrobium pacificus	100.0	1078	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanomicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013093415.1	s__Halovulum dunhuangense	78.4777	363	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172235.1	s__Pseudoruegeria aquimaris	78.0613	334	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003265325.1	s__Halovulum sediminis	78.0088	347	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009697225.1	s__Halovulum marinum	77.9775	386	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002073975.1	s__Rhodovulum sp002073975	77.9726	300	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129345.1	s__Ruegeria intermedia	77.8911	289	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009882975.1	s__Maritimibacter harenae	77.8565	266	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003993775.1	s__Frigidibacter sp003993775	77.8171	322	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188335.1	s__Tropicimonas sediminicola	77.7821	327	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003258405.1	s__Amaricoccus sp003258405	77.7272	270	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000688295.1	s__Pseudooceanicola nanhaiensis	77.71	342	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCA_011620265.1	s__Albidovulum sp011620265	77.6358	303	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124525.1	s__Oceanicella actignis	77.6213	295	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicella	95.0	98.87	98.87	0.96	0.96	3	-
GCF_900112685.1	s__Roseivivax sediminis	77.5884	296	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	77.5837	325	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCA_009830125.1	s__GH1-50 sp009830125	77.5772	261	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GH1-50	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814095.1	s__Sagittula sp002814095	77.5065	312	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003789055.1	s__Oceanicola lentulus	77.4846	263	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015485375.1	s__UBA3077 sp015485375	77.4841	205	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3077	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003448965.1	s__Paroceanicella sp003448965	77.4672	355	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763785.1	s__SZUA-611 sp014763785	77.462	241	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SZUA-611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002695005.1	s__Maritimibacter sp002695005	77.3193	239	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014201905.1	s__Amaricoccus macauensis	77.223	251	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005887615.1	s__Sulfitobacter_E sabulilitoris	77.2009	255	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:21:15,022] [INFO] GTDB search result was written to GCF_009833495.1_ASM983349v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:21:15,023] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:21:15,027] [INFO] DFAST_QC result json was written to GCF_009833495.1_ASM983349v1_genomic.fna/dqc_result.json
[2024-01-25 20:21:15,027] [INFO] DFAST_QC completed!
[2024-01-25 20:21:15,027] [INFO] Total running time: 0h1m25s