[2024-01-25 20:22:35,694] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:22:35,696] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:22:35,696] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e8017f9-3ebd-453c-b7d9-4a11ed332aca/dqc_reference
[2024-01-25 20:22:36,819] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:22:36,820] [INFO] Task started: Prodigal
[2024-01-25 20:22:36,820] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3dc2910-088d-4bcd-a33e-84c52d5b16c4/GCF_030410045.1_ASM3041004v1_genomic.fna.gz | prodigal -d GCF_030410045.1_ASM3041004v1_genomic.fna/cds.fna -a GCF_030410045.1_ASM3041004v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:22:44,443] [INFO] Task succeeded: Prodigal
[2024-01-25 20:22:44,443] [INFO] Task started: HMMsearch
[2024-01-25 20:22:44,443] [INFO] Running command: hmmsearch --tblout GCF_030410045.1_ASM3041004v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e8017f9-3ebd-453c-b7d9-4a11ed332aca/dqc_reference/reference_markers.hmm GCF_030410045.1_ASM3041004v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:22:44,646] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:22:44,647] [INFO] Found 6/6 markers.
[2024-01-25 20:22:44,672] [INFO] Query marker FASTA was written to GCF_030410045.1_ASM3041004v1_genomic.fna/markers.fasta
[2024-01-25 20:22:44,672] [INFO] Task started: Blastn
[2024-01-25 20:22:44,672] [INFO] Running command: blastn -query GCF_030410045.1_ASM3041004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e8017f9-3ebd-453c-b7d9-4a11ed332aca/dqc_reference/reference_markers.fasta -out GCF_030410045.1_ASM3041004v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:45,395] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:45,398] [INFO] Selected 25 target genomes.
[2024-01-25 20:22:45,398] [INFO] Target genome list was writen to GCF_030410045.1_ASM3041004v1_genomic.fna/target_genomes.txt
[2024-01-25 20:22:45,440] [INFO] Task started: fastANI
[2024-01-25 20:22:45,440] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3dc2910-088d-4bcd-a33e-84c52d5b16c4/GCF_030410045.1_ASM3041004v1_genomic.fna.gz --refList GCF_030410045.1_ASM3041004v1_genomic.fna/target_genomes.txt --output GCF_030410045.1_ASM3041004v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:23:01,267] [INFO] Task succeeded: fastANI
[2024-01-25 20:23:01,268] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e8017f9-3ebd-453c-b7d9-4a11ed332aca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:23:01,268] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e8017f9-3ebd-453c-b7d9-4a11ed332aca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:23:01,282] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:23:01,282] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:23:01,283] [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
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	79.0521	393	938	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	79.0367	389	938	95	below_threshold
Celeribacter litoreus	strain=ASW11-22	GCA_020165855.1	2876714	2876714	type	True	77.846	189	938	95	below_threshold
Donghicola mangrovi	strain=B5-SW-15	GCA_013377535.1	2729614	2729614	type	True	77.6295	229	938	95	below_threshold
Thalassococcus halodurans	strain=DSM 26915	GCA_900108225.1	373675	373675	type	True	77.6076	208	938	95	below_threshold
Actibacterium pelagium	strain=JN33	GCA_002285415.1	2029103	2029103	type	True	77.5557	155	938	95	below_threshold
Actibacterium pelagium	strain=CGMCC 1.16012	GCA_014644355.1	2029103	2029103	type	True	77.547	157	938	95	below_threshold
Tritonibacter multivorans	strain=CECT 7557	GCA_001458415.1	928856	928856	type	True	77.3041	161	938	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	77.0602	168	938	95	below_threshold
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_000152805.1	404236	404236	type	True	76.9998	162	938	95	below_threshold
Cognatishimia maritima	strain=DSM 28223	GCA_900129685.1	870908	870908	type	True	76.9887	135	938	95	below_threshold
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_008124775.1	404236	404236	type	True	76.9849	162	938	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	76.9651	164	938	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	76.9444	139	938	95	below_threshold
Loktanella salsilacus	strain=DSM 16199	GCA_900114485.1	195913	195913	type	True	76.9441	186	938	95	below_threshold
Thioclava marina	strain=11.10-0-13	GCA_002020135.1	1915077	1915077	type	True	76.9105	130	938	95	below_threshold
Roseovarius albus	strain=CECT 7450	GCA_900172335.1	1247867	1247867	type	True	76.8875	92	938	95	below_threshold
Sagittula marina	strain=DSM 102235	GCA_014196795.1	943940	943940	type	True	76.8864	127	938	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	76.7631	91	938	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.7534	124	938	95	below_threshold
Limimaricola variabilis	strain=CECT 8572	GCA_014195545.1	1492771	1492771	type	True	76.7299	123	938	95	below_threshold
Primorskyibacter sedentarius	strain=DSM 104836	GCA_004342065.1	745311	745311	type	True	76.654	128	938	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.5764	138	938	95	below_threshold
Ascidiaceihabitans donghaensis	strain=CECT 8599	GCA_900302465.1	1510460	1510460	type	True	76.4059	82	938	95	below_threshold
Roseivivax jejudonensis	strain=CECT 8625	GCA_900172265.1	1529041	1529041	type	True	76.2694	101	938	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:23:01,284] [INFO] DFAST Taxonomy check result was written to GCF_030410045.1_ASM3041004v1_genomic.fna/tc_result.tsv
[2024-01-25 20:23:01,284] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:23:01,285] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:23:01,285] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e8017f9-3ebd-453c-b7d9-4a11ed332aca/dqc_reference/checkm_data
[2024-01-25 20:23:01,286] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:23:01,315] [INFO] Task started: CheckM
[2024-01-25 20:23:01,315] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030410045.1_ASM3041004v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030410045.1_ASM3041004v1_genomic.fna/checkm_input GCF_030410045.1_ASM3041004v1_genomic.fna/checkm_result
[2024-01-25 20:23:27,928] [INFO] Task succeeded: CheckM
[2024-01-25 20:23:27,929] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:23:27,944] [INFO] ===== Completeness check finished =====
[2024-01-25 20:23:27,944] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:23:27,945] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030410045.1_ASM3041004v1_genomic.fna/markers.fasta)
[2024-01-25 20:23:27,945] [INFO] Task started: Blastn
[2024-01-25 20:23:27,945] [INFO] Running command: blastn -query GCF_030410045.1_ASM3041004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e8017f9-3ebd-453c-b7d9-4a11ed332aca/dqc_reference/reference_markers_gtdb.fasta -out GCF_030410045.1_ASM3041004v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:29,240] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:29,243] [INFO] Selected 11 target genomes.
[2024-01-25 20:23:29,243] [INFO] Target genome list was writen to GCF_030410045.1_ASM3041004v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:23:29,251] [INFO] Task started: fastANI
[2024-01-25 20:23:29,252] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3dc2910-088d-4bcd-a33e-84c52d5b16c4/GCF_030410045.1_ASM3041004v1_genomic.fna.gz --refList GCF_030410045.1_ASM3041004v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030410045.1_ASM3041004v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:23:36,916] [INFO] Task succeeded: fastANI
[2024-01-25 20:23:36,924] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:23:36,924] [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_002850435.1	s__Marivivens zhoushanense	96.4302	872	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001908835.1	s__Marivivens sp001908835	92.1323	895	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	98.73	98.07	0.98	0.97	4	-
GCF_002150005.2	s__Marivivens niveibacter	79.0335	388	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015220045.1	s__Marivivens aquimaris	79.0292	395	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011806565.1	s__Marivivens donghaensis	79.0026	383	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108225.1	s__Thalassococcus halodurans	77.5929	209	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassococcus	95.0	96.13	96.13	0.95	0.95	2	-
GCA_013215215.1	s__Cognatishimia sp013215215	77.0374	126	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatishimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	77.0343	168	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017798205.1	s__Cognatishimia activa_A	77.0302	154	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatishimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002020135.1	s__Thioclava marina	76.8699	131	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	98.70	98.47	0.89	0.86	6	-
GCA_001730095.1	s__Leisingera sp001730095	76.8322	118	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:23:36,925] [INFO] GTDB search result was written to GCF_030410045.1_ASM3041004v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:23:36,926] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:23:36,929] [INFO] DFAST_QC result json was written to GCF_030410045.1_ASM3041004v1_genomic.fna/dqc_result.json
[2024-01-25 20:23:36,929] [INFO] DFAST_QC completed!
[2024-01-25 20:23:36,929] [INFO] Total running time: 0h1m1s