[2024-01-24 13:32:13,186] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:13,188] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:13,189] [INFO] DQC Reference Directory: /var/lib/cwl/stg8becf86f-c7ca-4da4-be28-3f1056c339b5/dqc_reference
[2024-01-24 13:32:14,395] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:14,396] [INFO] Task started: Prodigal
[2024-01-24 13:32:14,396] [INFO] Running command: gunzip -c /var/lib/cwl/stgb2aad145-3022-4452-aa50-a116104888ab/GCF_900172355.1_R.antarcticus_CECT7023_Spades_Prokka_genomic.fna.gz | prodigal -d GCF_900172355.1_R.antarcticus_CECT7023_Spades_Prokka_genomic.fna/cds.fna -a GCF_900172355.1_R.antarcticus_CECT7023_Spades_Prokka_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:31,572] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:31,573] [INFO] Task started: HMMsearch
[2024-01-24 13:32:31,573] [INFO] Running command: hmmsearch --tblout GCF_900172355.1_R.antarcticus_CECT7023_Spades_Prokka_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8becf86f-c7ca-4da4-be28-3f1056c339b5/dqc_reference/reference_markers.hmm GCF_900172355.1_R.antarcticus_CECT7023_Spades_Prokka_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:31,866] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:31,867] [INFO] Found 6/6 markers.
[2024-01-24 13:32:31,916] [INFO] Query marker FASTA was written to GCF_900172355.1_R.antarcticus_CECT7023_Spades_Prokka_genomic.fna/markers.fasta
[2024-01-24 13:32:31,916] [INFO] Task started: Blastn
[2024-01-24 13:32:31,916] [INFO] Running command: blastn -query GCF_900172355.1_R.antarcticus_CECT7023_Spades_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg8becf86f-c7ca-4da4-be28-3f1056c339b5/dqc_reference/reference_markers.fasta -out GCF_900172355.1_R.antarcticus_CECT7023_Spades_Prokka_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:32,845] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:32,850] [INFO] Selected 27 target genomes.
[2024-01-24 13:32:32,850] [INFO] Target genome list was writen to GCF_900172355.1_R.antarcticus_CECT7023_Spades_Prokka_genomic.fna/target_genomes.txt
[2024-01-24 13:32:32,860] [INFO] Task started: fastANI
[2024-01-24 13:32:32,860] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2aad145-3022-4452-aa50-a116104888ab/GCF_900172355.1_R.antarcticus_CECT7023_Spades_Prokka_genomic.fna.gz --refList GCF_900172355.1_R.antarcticus_CECT7023_Spades_Prokka_genomic.fna/target_genomes.txt --output GCF_900172355.1_R.antarcticus_CECT7023_Spades_Prokka_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:56,196] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:56,197] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8becf86f-c7ca-4da4-be28-3f1056c339b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:56,197] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8becf86f-c7ca-4da4-be28-3f1056c339b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:56,217] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:32:56,218] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:32:56,218] [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
Pelagovum pacificum	strain=SM1903	GCA_006363825.1	2588711	2588711	type	True	79.0373	605	1593	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	79.0105	532	1593	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	78.9462	540	1593	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	78.9091	577	1593	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	78.8607	580	1593	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	78.8279	586	1593	95	below_threshold
Wenxinia marina	strain=CGMCC 1.6105	GCA_014645075.1	390641	390641	type	True	78.8192	589	1593	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	78.72	523	1593	95	below_threshold
Limimaricola soesokkakensis	strain=DSM 29956	GCA_003014435.1	1343159	1343159	type	True	78.6684	462	1593	95	below_threshold
Limimaricola soesokkakensis	strain=CECT 8367	GCA_900172345.1	1343159	1343159	type	True	78.6649	471	1593	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.6338	463	1593	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	78.5931	499	1593	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	78.5896	496	1593	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	78.3873	498	1593	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	78.3592	518	1593	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	78.3206	494	1593	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	78.3069	475	1593	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	78.2785	492	1593	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	78.248	463	1593	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.2473	451	1593	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	78.2453	506	1593	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	78.226	458	1593	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	78.0055	409	1593	95	below_threshold
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	77.9731	392	1593	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	77.8428	433	1593	95	below_threshold
Hasllibacter halocynthiae	strain=DSM 29318	GCA_003003095.1	595589	595589	type	True	77.5942	327	1593	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.4466	354	1593	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:56,219] [INFO] DFAST Taxonomy check result was written to GCF_900172355.1_R.antarcticus_CECT7023_Spades_Prokka_genomic.fna/tc_result.tsv
[2024-01-24 13:32:56,220] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:56,220] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:56,220] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8becf86f-c7ca-4da4-be28-3f1056c339b5/dqc_reference/checkm_data
[2024-01-24 13:32:56,221] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:56,268] [INFO] Task started: CheckM
[2024-01-24 13:32:56,269] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900172355.1_R.antarcticus_CECT7023_Spades_Prokka_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900172355.1_R.antarcticus_CECT7023_Spades_Prokka_genomic.fna/checkm_input GCF_900172355.1_R.antarcticus_CECT7023_Spades_Prokka_genomic.fna/checkm_result
[2024-01-24 13:33:53,208] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:53,209] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:53,231] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:53,231] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:53,232] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900172355.1_R.antarcticus_CECT7023_Spades_Prokka_genomic.fna/markers.fasta)
[2024-01-24 13:33:53,232] [INFO] Task started: Blastn
[2024-01-24 13:33:53,233] [INFO] Running command: blastn -query GCF_900172355.1_R.antarcticus_CECT7023_Spades_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg8becf86f-c7ca-4da4-be28-3f1056c339b5/dqc_reference/reference_markers_gtdb.fasta -out GCF_900172355.1_R.antarcticus_CECT7023_Spades_Prokka_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:54,666] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:54,669] [INFO] Selected 19 target genomes.
[2024-01-24 13:33:54,669] [INFO] Target genome list was writen to GCF_900172355.1_R.antarcticus_CECT7023_Spades_Prokka_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:54,708] [INFO] Task started: fastANI
[2024-01-24 13:33:54,708] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2aad145-3022-4452-aa50-a116104888ab/GCF_900172355.1_R.antarcticus_CECT7023_Spades_Prokka_genomic.fna.gz --refList GCF_900172355.1_R.antarcticus_CECT7023_Spades_Prokka_genomic.fna/target_genomes_gtdb.txt --output GCF_900172355.1_R.antarcticus_CECT7023_Spades_Prokka_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:13,519] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:13,541] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:13,542] [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_900172355.1	s__Oceanicola antarcticus	100.0	1590	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000153305.1	s__Oceanicola granulosus	80.0148	647	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008710275.1	s__Oceanicola sp008710275	79.8034	672	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003789055.1	s__Oceanicola lentulus	79.7171	701	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016134045.1	s__Oceanicola pacificus_A	79.1045	598	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000688295.1	s__Pseudooceanicola nanhaiensis	78.9868	535	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900102015.1	s__Limimaricola pyoseonensis	78.8913	580	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379485.1	s__Wenxinia marina	78.831	584	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	99.99	99.99	0.99	0.99	3	-
GCF_900172345.1	s__Limimaricola soesokkakensis	78.6822	469	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900142185.1	s__Lutimaribacter pacificus	78.6391	503	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900109035.1	s__Cribrihabitans marinus	78.5843	495	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCA_006226775.1	s__Marinovum sp006226775	78.5526	533	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019061145.1	s__ASV31 sp019061145	78.5375	495	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ASV31	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521865.1	s__Roseivivax isoporae	78.3557	519	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004000435.1	s__Flavimaricola sp004000435	78.2376	508	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Flavimaricola	95.0	99.99	99.97	0.99	0.98	36	-
GCF_001205715.1	s__Pseudaestuariivita atlantica	78.2202	466	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudaestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003254465.1	s__Fluviibacterium sp003254465	78.1397	457	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fluviibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007131945.1	s__Pararhodobacter sp007131945	77.6177	328	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	99.16	99.15	0.86	0.82	3	-
GCF_003003095.1	s__Hasllibacter halocynthiae	77.595	327	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Hasllibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:13,543] [INFO] GTDB search result was written to GCF_900172355.1_R.antarcticus_CECT7023_Spades_Prokka_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:13,544] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:13,548] [INFO] DFAST_QC result json was written to GCF_900172355.1_R.antarcticus_CECT7023_Spades_Prokka_genomic.fna/dqc_result.json
[2024-01-24 13:34:13,549] [INFO] DFAST_QC completed!
[2024-01-24 13:34:13,549] [INFO] Total running time: 0h2m0s