[2024-01-24 12:44:11,072] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:11,081] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:11,081] [INFO] DQC Reference Directory: /var/lib/cwl/stg89fc48d4-0bf4-4486-9876-93a882f349b7/dqc_reference
[2024-01-24 12:44:12,391] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:12,392] [INFO] Task started: Prodigal
[2024-01-24 12:44:12,393] [INFO] Running command: gunzip -c /var/lib/cwl/stg362140e3-d63c-4621-b219-b2d3f1df191a/GCF_014903745.1_ASM1490374v1_genomic.fna.gz | prodigal -d GCF_014903745.1_ASM1490374v1_genomic.fna/cds.fna -a GCF_014903745.1_ASM1490374v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:24,264] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:24,265] [INFO] Task started: HMMsearch
[2024-01-24 12:44:24,265] [INFO] Running command: hmmsearch --tblout GCF_014903745.1_ASM1490374v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89fc48d4-0bf4-4486-9876-93a882f349b7/dqc_reference/reference_markers.hmm GCF_014903745.1_ASM1490374v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:24,604] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:24,606] [INFO] Found 6/6 markers.
[2024-01-24 12:44:24,645] [INFO] Query marker FASTA was written to GCF_014903745.1_ASM1490374v1_genomic.fna/markers.fasta
[2024-01-24 12:44:24,645] [INFO] Task started: Blastn
[2024-01-24 12:44:24,645] [INFO] Running command: blastn -query GCF_014903745.1_ASM1490374v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89fc48d4-0bf4-4486-9876-93a882f349b7/dqc_reference/reference_markers.fasta -out GCF_014903745.1_ASM1490374v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:25,691] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:25,694] [INFO] Selected 22 target genomes.
[2024-01-24 12:44:25,694] [INFO] Target genome list was writen to GCF_014903745.1_ASM1490374v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:25,704] [INFO] Task started: fastANI
[2024-01-24 12:44:25,704] [INFO] Running command: fastANI --query /var/lib/cwl/stg362140e3-d63c-4621-b219-b2d3f1df191a/GCF_014903745.1_ASM1490374v1_genomic.fna.gz --refList GCF_014903745.1_ASM1490374v1_genomic.fna/target_genomes.txt --output GCF_014903745.1_ASM1490374v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:44,383] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:44,384] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89fc48d4-0bf4-4486-9876-93a882f349b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:44,384] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89fc48d4-0bf4-4486-9876-93a882f349b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:44,408] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:44:44,409] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:44,409] [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
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	100.0	1384	1389	95	conclusive
Mangrovicoccus ximenensis	strain=T1lg56	GCA_003056725.1	1911570	1911570	type	True	84.2773	925	1389	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	79.0586	506	1389	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_000520135.2	35806	35806	type	True	78.9195	518	1389	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_001633165.1	35806	35806	type	True	78.8902	529	1389	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	78.8658	550	1389	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	78.76	473	1389	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.7147	482	1389	95	below_threshold
Phaeovulum vinaykumarii	strain=DSM 18714	GCA_900156695.1	407234	407234	type	True	78.603	436	1389	95	below_threshold
Phaeovulum vinaykumarii	strain=JA123	GCA_900217755.1	407234	407234	type	True	78.602	434	1389	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	78.5958	471	1389	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.5049	573	1389	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	78.3986	387	1389	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.2999	483	1389	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	78.1987	399	1389	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	78.1986	397	1389	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	78.164	477	1389	95	below_threshold
Salibaculum griseiflavum	strain=WDS4C29	GCA_003129565.1	1914409	1914409	type	True	78.1618	351	1389	95	below_threshold
Jannaschia seohaensis	strain=DSM 25227	GCA_900116765.1	475081	475081	type	True	77.9217	405	1389	95	below_threshold
Pararhodobacter aggregans	strain=DSM 18938	GCA_003054005.1	404875	404875	type	True	77.842	499	1389	95	below_threshold
Pararhodobacter aggregans	strain=D1-19	GCA_003075525.1	404875	404875	type	True	77.8036	505	1389	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	77.6168	433	1389	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:44,411] [INFO] DFAST Taxonomy check result was written to GCF_014903745.1_ASM1490374v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:44,411] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:44,412] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:44,412] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89fc48d4-0bf4-4486-9876-93a882f349b7/dqc_reference/checkm_data
[2024-01-24 12:44:44,413] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:44,456] [INFO] Task started: CheckM
[2024-01-24 12:44:44,457] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014903745.1_ASM1490374v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014903745.1_ASM1490374v1_genomic.fna/checkm_input GCF_014903745.1_ASM1490374v1_genomic.fna/checkm_result
[2024-01-24 12:45:42,295] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:42,296] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:42,318] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:42,318] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:42,319] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014903745.1_ASM1490374v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:42,319] [INFO] Task started: Blastn
[2024-01-24 12:45:42,319] [INFO] Running command: blastn -query GCF_014903745.1_ASM1490374v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89fc48d4-0bf4-4486-9876-93a882f349b7/dqc_reference/reference_markers_gtdb.fasta -out GCF_014903745.1_ASM1490374v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:44,281] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:44,285] [INFO] Selected 13 target genomes.
[2024-01-24 12:45:44,285] [INFO] Target genome list was writen to GCF_014903745.1_ASM1490374v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:44,300] [INFO] Task started: fastANI
[2024-01-24 12:45:44,300] [INFO] Running command: fastANI --query /var/lib/cwl/stg362140e3-d63c-4621-b219-b2d3f1df191a/GCF_014903745.1_ASM1490374v1_genomic.fna.gz --refList GCF_014903745.1_ASM1490374v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014903745.1_ASM1490374v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:57,888] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:57,912] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:57,912] [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_014903745.1	s__Mangrovicoccus sp014903745	100.0	1384	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005870025.1	s__Mangrovicoccus sp005870025	85.1533	1084	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013184745.1	s__Mangrovicoccus sp013184745	85.1471	1035	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056725.1	s__Mangrovicoccus ximenensis	84.3089	921	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365965.1	s__Rhodovulum visakhapatnamense	79.0815	503	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.55	98.44	0.90	0.89	5	-
GCF_003053725.1	s__Rhodovulum kholense	79.019	517	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.27	98.27	0.96	0.96	2	-
GCF_002073975.1	s__Rhodovulum sp002073975	78.9414	498	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	78.7521	475	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009649175.1	s__Rhodovulum strictum	78.5707	474	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001447385.1	s__Paracoccus sp001447385	78.5355	486	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000763885.1	s__Paracoccus versutus	78.5311	497	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	98.67	98.17	0.87	0.76	7	-
GCF_000153305.1	s__Oceanicola granulosus	77.9432	469	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075525.1	s__Pararhodobacter aggregans	77.7981	506	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:57,915] [INFO] GTDB search result was written to GCF_014903745.1_ASM1490374v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:57,916] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:57,920] [INFO] DFAST_QC result json was written to GCF_014903745.1_ASM1490374v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:57,921] [INFO] DFAST_QC completed!
[2024-01-24 12:45:57,921] [INFO] Total running time: 0h1m47s