[2024-01-25 20:13:20,548] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:13:20,550] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:13:20,550] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c879a86-2c9d-4762-b2d6-e16cf02f433a/dqc_reference
[2024-01-25 20:13:21,679] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:13:21,680] [INFO] Task started: Prodigal
[2024-01-25 20:13:21,680] [INFO] Running command: gunzip -c /var/lib/cwl/stg0936a115-66ed-4bcb-aa8c-36caaf4f1fd1/GCF_016623495.1_ASM1662349v1_genomic.fna.gz | prodigal -d GCF_016623495.1_ASM1662349v1_genomic.fna/cds.fna -a GCF_016623495.1_ASM1662349v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:13:32,063] [INFO] Task succeeded: Prodigal
[2024-01-25 20:13:32,063] [INFO] Task started: HMMsearch
[2024-01-25 20:13:32,063] [INFO] Running command: hmmsearch --tblout GCF_016623495.1_ASM1662349v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c879a86-2c9d-4762-b2d6-e16cf02f433a/dqc_reference/reference_markers.hmm GCF_016623495.1_ASM1662349v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:13:32,289] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:13:32,290] [INFO] Found 6/6 markers.
[2024-01-25 20:13:32,324] [INFO] Query marker FASTA was written to GCF_016623495.1_ASM1662349v1_genomic.fna/markers.fasta
[2024-01-25 20:13:32,324] [INFO] Task started: Blastn
[2024-01-25 20:13:32,324] [INFO] Running command: blastn -query GCF_016623495.1_ASM1662349v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c879a86-2c9d-4762-b2d6-e16cf02f433a/dqc_reference/reference_markers.fasta -out GCF_016623495.1_ASM1662349v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:33,161] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:33,163] [INFO] Selected 22 target genomes.
[2024-01-25 20:13:33,164] [INFO] Target genome list was writen to GCF_016623495.1_ASM1662349v1_genomic.fna/target_genomes.txt
[2024-01-25 20:13:33,186] [INFO] Task started: fastANI
[2024-01-25 20:13:33,186] [INFO] Running command: fastANI --query /var/lib/cwl/stg0936a115-66ed-4bcb-aa8c-36caaf4f1fd1/GCF_016623495.1_ASM1662349v1_genomic.fna.gz --refList GCF_016623495.1_ASM1662349v1_genomic.fna/target_genomes.txt --output GCF_016623495.1_ASM1662349v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:13:49,640] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:49,641] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c879a86-2c9d-4762-b2d6-e16cf02f433a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:13:49,641] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c879a86-2c9d-4762-b2d6-e16cf02f433a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:13:49,653] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:13:49,653] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:13:49,654] [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
Thermohalobaculum xanthum	strain=M0105	GCA_016623495.1	2753746	2753746	type	True	100.0	1335	1336	95	conclusive
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	78.8973	424	1336	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	78.2685	365	1336	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	78.1355	443	1336	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	78.1087	404	1336	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	78.091	385	1336	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.0385	330	1336	95	below_threshold
Coraliihabitans acroporae	strain=NNCM2	GCA_019891535.1	2834412	2834412	type	True	77.9993	404	1336	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	77.8982	349	1336	95	below_threshold
Paroceanicella profunda	strain=D4M1	GCA_005887635.2	2579971	2579971	type	True	77.8618	428	1336	95	below_threshold
Meinhardsimonia xiamenensis	strain=DSM 24422	GCA_003001835.1	990712	990712	type	True	77.8181	306	1336	95	below_threshold
Phaeovulum vinaykumarii	strain=JA123	GCA_900217755.1	407234	407234	type	True	77.7741	279	1336	95	below_threshold
Rubrimonas cliftonensis	strain=DSM 15345	GCA_900107585.1	89524	89524	type	True	77.749	457	1336	95	below_threshold
Phaeovulum vinaykumarii	strain=DSM 18714	GCA_900156695.1	407234	407234	type	True	77.7242	283	1336	95	below_threshold
Limimaricola cinnabarinus	strain=LL-001	GCA_000466965.1	1125964	1125964	type	True	77.6972	281	1336	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	77.5663	342	1336	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	77.5573	311	1336	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	77.4874	293	1336	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	77.3122	277	1336	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	77.277	300	1336	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	77.1586	263	1336	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	77.1218	271	1336	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:13:49,655] [INFO] DFAST Taxonomy check result was written to GCF_016623495.1_ASM1662349v1_genomic.fna/tc_result.tsv
[2024-01-25 20:13:49,655] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:13:49,655] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:13:49,655] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c879a86-2c9d-4762-b2d6-e16cf02f433a/dqc_reference/checkm_data
[2024-01-25 20:13:49,656] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:13:49,698] [INFO] Task started: CheckM
[2024-01-25 20:13:49,698] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016623495.1_ASM1662349v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016623495.1_ASM1662349v1_genomic.fna/checkm_input GCF_016623495.1_ASM1662349v1_genomic.fna/checkm_result
[2024-01-25 20:14:26,806] [INFO] Task succeeded: CheckM
[2024-01-25 20:14:26,807] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:14:26,824] [INFO] ===== Completeness check finished =====
[2024-01-25 20:14:26,825] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:14:26,826] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016623495.1_ASM1662349v1_genomic.fna/markers.fasta)
[2024-01-25 20:14:26,826] [INFO] Task started: Blastn
[2024-01-25 20:14:26,826] [INFO] Running command: blastn -query GCF_016623495.1_ASM1662349v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c879a86-2c9d-4762-b2d6-e16cf02f433a/dqc_reference/reference_markers_gtdb.fasta -out GCF_016623495.1_ASM1662349v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:28,365] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:28,368] [INFO] Selected 24 target genomes.
[2024-01-25 20:14:28,368] [INFO] Target genome list was writen to GCF_016623495.1_ASM1662349v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:14:28,380] [INFO] Task started: fastANI
[2024-01-25 20:14:28,380] [INFO] Running command: fastANI --query /var/lib/cwl/stg0936a115-66ed-4bcb-aa8c-36caaf4f1fd1/GCF_016623495.1_ASM1662349v1_genomic.fna.gz --refList GCF_016623495.1_ASM1662349v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016623495.1_ASM1662349v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:14:46,346] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:46,360] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:14:46,360] [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_016623495.1	s__Limibaculum sp016623495	100.0	1335	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limibaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008124525.1	s__Oceanicella actignis	78.8729	427	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicella	95.0	98.87	98.87	0.96	0.96	3	-
GCF_900113695.1	s__Albimonas pacifica	78.2261	489	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009697225.1	s__Halovulum marinum	78.1686	439	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003448965.1	s__Paroceanicella sp003448965	78.1423	458	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102015.1	s__Limimaricola pyoseonensis	78.1302	403	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385685.1	s__Amaricoccus solimangrovi	78.0996	384	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002723615.1	s__Limimaricola cinnabarinus_B	77.9553	344	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005887635.2	s__Paroceanicella profunda	77.8675	427	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241785.1	s__Amaricoccus sp003241785	77.8628	393	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664585.1	s__Paenirhodobacter hankyongi	77.8435	333	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017995835.1	s__Amaricoccus sp017995835	77.8253	315	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003298775.1	s__Rhodosalinus sp003298775	77.7575	356	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodosalinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156695.1	s__Bieblia_A vinaykumarii	77.7023	285	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Bieblia_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000466965.1	s__Limimaricola cinnabarinus	77.6989	281	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365965.1	s__Rhodovulum visakhapatnamense	77.5756	341	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.55	98.44	0.90	0.89	5	-
GCF_004010155.1	s__Solirhodobacter olei	77.5425	339	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Solirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002073975.1	s__Rhodovulum sp002073975	77.5381	307	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003258405.1	s__Amaricoccus sp003258405	77.5272	313	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215355.1	s__Pseudooceanicola antarcticus	77.3239	272	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009649175.1	s__Rhodovulum strictum	77.2892	298	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003550665.1	s__Rhodobaculum sp003550665	77.264	251	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	99.32	99.19	0.86	0.85	4	-
GCF_002786295.1	s__Pseudooceanicola marinus	77.1578	264	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.99	0.99	2	-
GCA_007134805.1	s__Roseinatronobacter sp007134805	76.8478	149	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	99.08	99.08	0.63	0.63	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:14:46,361] [INFO] GTDB search result was written to GCF_016623495.1_ASM1662349v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:14:46,362] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:14:46,366] [INFO] DFAST_QC result json was written to GCF_016623495.1_ASM1662349v1_genomic.fna/dqc_result.json
[2024-01-25 20:14:46,367] [INFO] DFAST_QC completed!
[2024-01-25 20:14:46,367] [INFO] Total running time: 0h1m26s