[2024-01-24 11:44:38,160] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:38,163] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:38,163] [INFO] DQC Reference Directory: /var/lib/cwl/stg28feaf45-8576-425b-bc0f-097915c63e76/dqc_reference
[2024-01-24 11:44:41,487] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:41,488] [INFO] Task started: Prodigal
[2024-01-24 11:44:41,488] [INFO] Running command: gunzip -c /var/lib/cwl/stga351c776-7c19-4d03-82d4-410933c33c1c/GCF_006385685.1_ASM638568v1_genomic.fna.gz | prodigal -d GCF_006385685.1_ASM638568v1_genomic.fna/cds.fna -a GCF_006385685.1_ASM638568v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:53,024] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:53,024] [INFO] Task started: HMMsearch
[2024-01-24 11:44:53,024] [INFO] Running command: hmmsearch --tblout GCF_006385685.1_ASM638568v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28feaf45-8576-425b-bc0f-097915c63e76/dqc_reference/reference_markers.hmm GCF_006385685.1_ASM638568v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:53,303] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:53,305] [INFO] Found 6/6 markers.
[2024-01-24 11:44:53,349] [INFO] Query marker FASTA was written to GCF_006385685.1_ASM638568v1_genomic.fna/markers.fasta
[2024-01-24 11:44:53,349] [INFO] Task started: Blastn
[2024-01-24 11:44:53,349] [INFO] Running command: blastn -query GCF_006385685.1_ASM638568v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28feaf45-8576-425b-bc0f-097915c63e76/dqc_reference/reference_markers.fasta -out GCF_006385685.1_ASM638568v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:54,277] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:54,281] [INFO] Selected 19 target genomes.
[2024-01-24 11:44:54,282] [INFO] Target genome list was writen to GCF_006385685.1_ASM638568v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:54,401] [INFO] Task started: fastANI
[2024-01-24 11:44:54,402] [INFO] Running command: fastANI --query /var/lib/cwl/stga351c776-7c19-4d03-82d4-410933c33c1c/GCF_006385685.1_ASM638568v1_genomic.fna.gz --refList GCF_006385685.1_ASM638568v1_genomic.fna/target_genomes.txt --output GCF_006385685.1_ASM638568v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:45:10,471] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:10,471] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28feaf45-8576-425b-bc0f-097915c63e76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:45:10,472] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28feaf45-8576-425b-bc0f-097915c63e76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:45:10,490] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:45:10,490] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:45:10,491] [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
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	100.0	1555	1561	95	conclusive
Amaricoccus macauensis	strain=DSM 101730	GCA_014201905.1	57001	57001	type	True	79.6537	684	1561	95	below_threshold
Cereibacter johrii	strain=JA192	GCA_001720585.1	445629	445629	type	True	78.6062	473	1561	95	below_threshold
Cereibacter johrii	strain=JA192	GCA_003046325.1	445629	445629	type	True	78.457	504	1561	95	below_threshold
Cereibacter sphaeroides	strain=2.4.1	GCA_000273405.1	1063	1063	type	True	78.4093	521	1561	95	below_threshold
Sinirhodobacter hankyongi	strain=BO-81	GCA_003664585.1	2294033	2294033	type	True	78.3159	474	1561	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	78.2936	534	1561	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	78.1975	427	1561	95	below_threshold
Pontivivens ytuae	strain=MT2928	GCA_015679265.1	2789856	2789856	type	True	78.0247	425	1561	95	below_threshold
Oceanomicrobium pacificus	strain=KN286	GCA_009833495.1	2692916	2692916	type	True	77.9533	324	1561	95	below_threshold
Meinhardsimonia xiamenensis	strain=DSM 24422	GCA_003001835.1	990712	990712	type	True	77.9278	342	1561	95	below_threshold
Meinhardsimonia xiamenensis	strain=CGMCC 1.10789	GCA_900102905.1	990712	990712	type	True	77.9253	337	1561	95	below_threshold
Paroceanicella profunda	strain=D4M1	GCA_005887635.2	2579971	2579971	type	True	77.7904	513	1561	95	below_threshold
Mangrovicoccus ximenensis	strain=T1lg56	GCA_003056725.1	1911570	1911570	type	True	77.7422	531	1561	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	77.6758	491	1561	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	77.4643	447	1561	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	77.4033	250	1561	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	77.4023	447	1561	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	77.1537	351	1561	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:45:10,503] [INFO] DFAST Taxonomy check result was written to GCF_006385685.1_ASM638568v1_genomic.fna/tc_result.tsv
[2024-01-24 11:45:10,504] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:45:10,505] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:45:10,505] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28feaf45-8576-425b-bc0f-097915c63e76/dqc_reference/checkm_data
[2024-01-24 11:45:10,507] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:45:10,559] [INFO] Task started: CheckM
[2024-01-24 11:45:10,559] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006385685.1_ASM638568v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006385685.1_ASM638568v1_genomic.fna/checkm_input GCF_006385685.1_ASM638568v1_genomic.fna/checkm_result
[2024-01-24 11:46:01,839] [INFO] Task succeeded: CheckM
[2024-01-24 11:46:01,841] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:46:01,865] [INFO] ===== Completeness check finished =====
[2024-01-24 11:46:01,865] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:46:01,866] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006385685.1_ASM638568v1_genomic.fna/markers.fasta)
[2024-01-24 11:46:01,866] [INFO] Task started: Blastn
[2024-01-24 11:46:01,866] [INFO] Running command: blastn -query GCF_006385685.1_ASM638568v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28feaf45-8576-425b-bc0f-097915c63e76/dqc_reference/reference_markers_gtdb.fasta -out GCF_006385685.1_ASM638568v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:46:03,582] [INFO] Task succeeded: Blastn
[2024-01-24 11:46:03,587] [INFO] Selected 13 target genomes.
[2024-01-24 11:46:03,587] [INFO] Target genome list was writen to GCF_006385685.1_ASM638568v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:46:03,599] [INFO] Task started: fastANI
[2024-01-24 11:46:03,599] [INFO] Running command: fastANI --query /var/lib/cwl/stga351c776-7c19-4d03-82d4-410933c33c1c/GCF_006385685.1_ASM638568v1_genomic.fna.gz --refList GCF_006385685.1_ASM638568v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006385685.1_ASM638568v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:15,215] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:15,233] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:15,234] [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_006385685.1	s__Amaricoccus solimangrovi	100.0	1555	1561	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003241785.1	s__Amaricoccus sp003241785	85.6631	967	1561	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017993425.1	s__Amaricoccus sp017993425	80.0479	731	1561	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201905.1	s__Amaricoccus macauensis	79.6529	685	1561	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017995835.1	s__Amaricoccus sp017995835	79.6346	566	1561	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003258405.1	s__Amaricoccus sp003258405	79.3212	586	1561	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013093415.1	s__Halovulum dunhuangense	78.2148	425	1561	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153305.1	s__Oceanicola granulosus	77.7932	506	1561	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056725.1	s__Mangrovicoccus ximenensis	77.7355	533	1561	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007131685.1	s__Rhodobaculum sp007131685	77.0434	292	1561	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	99.44	99.41	0.86	0.86	3	-
GCA_018241455.1	s__FEN-1191 sp018241455	74.9412	89	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__FEN-1191	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903828805.1	s__Sandaracinus sp903828805	74.8445	168	1561	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Sandaracinaceae;g__Sandaracinus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:46:15,235] [INFO] GTDB search result was written to GCF_006385685.1_ASM638568v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:15,236] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:15,241] [INFO] DFAST_QC result json was written to GCF_006385685.1_ASM638568v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:15,241] [INFO] DFAST_QC completed!
[2024-01-24 11:46:15,241] [INFO] Total running time: 0h1m37s