[2024-01-24 13:40:33,921] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:33,924] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:33,924] [INFO] DQC Reference Directory: /var/lib/cwl/stg67aa1996-8f46-4b6d-b3d9-8fa58f819f0c/dqc_reference
[2024-01-24 13:40:35,211] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:35,212] [INFO] Task started: Prodigal
[2024-01-24 13:40:35,213] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e52cafe-c435-4ac5-9a35-b13882912a43/GCF_003122085.1_ASM312208v1_genomic.fna.gz | prodigal -d GCF_003122085.1_ASM312208v1_genomic.fna/cds.fna -a GCF_003122085.1_ASM312208v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:42,730] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:42,730] [INFO] Task started: HMMsearch
[2024-01-24 13:40:42,731] [INFO] Running command: hmmsearch --tblout GCF_003122085.1_ASM312208v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67aa1996-8f46-4b6d-b3d9-8fa58f819f0c/dqc_reference/reference_markers.hmm GCF_003122085.1_ASM312208v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:42,990] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:42,991] [INFO] Found 6/6 markers.
[2024-01-24 13:40:43,018] [INFO] Query marker FASTA was written to GCF_003122085.1_ASM312208v1_genomic.fna/markers.fasta
[2024-01-24 13:40:43,018] [INFO] Task started: Blastn
[2024-01-24 13:40:43,018] [INFO] Running command: blastn -query GCF_003122085.1_ASM312208v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67aa1996-8f46-4b6d-b3d9-8fa58f819f0c/dqc_reference/reference_markers.fasta -out GCF_003122085.1_ASM312208v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:44,094] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:44,098] [INFO] Selected 19 target genomes.
[2024-01-24 13:40:44,098] [INFO] Target genome list was writen to GCF_003122085.1_ASM312208v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:44,110] [INFO] Task started: fastANI
[2024-01-24 13:40:44,110] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e52cafe-c435-4ac5-9a35-b13882912a43/GCF_003122085.1_ASM312208v1_genomic.fna.gz --refList GCF_003122085.1_ASM312208v1_genomic.fna/target_genomes.txt --output GCF_003122085.1_ASM312208v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:58,281] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:58,282] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67aa1996-8f46-4b6d-b3d9-8fa58f819f0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:58,282] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67aa1996-8f46-4b6d-b3d9-8fa58f819f0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:58,298] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:40:58,299] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:58,299] [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
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	100.0	958	958	95	conclusive
Marinicauda algicola	strain=JCM 31718	GCA_004793685.1	2029849	2029849	type	True	80.8333	600	958	95	below_threshold
Marinicauda algicola	strain=RMAR8-3	GCA_017161425.1	2029849	2029849	type	True	80.7977	612	958	95	below_threshold
Marinicauda pacifica	strain=CGMCC 1.11031	GCA_014636415.1	1133559	1133559	type	True	78.7044	405	958	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_004793635.1	1133559	1133559	type	True	78.6879	409	958	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_009806145.1	1133559	1133559	type	True	78.6052	412	958	95	below_threshold
Glycocaulis alkaliphilus	strain=CGMCC 1.12428	GCA_014637625.1	1434191	1434191	type	True	77.6647	300	958	95	below_threshold
Glycocaulis alkaliphilus	strain=6B-8	GCA_004000605.1	1434191	1434191	type	True	77.6385	301	958	95	below_threshold
Maricaulis maris	strain=DSM 4734	GCA_003634045.1	74318	74318	type	True	77.2564	243	958	95	below_threshold
Maricaulis salignorans	strain=DSM 16077	GCA_900103475.1	144026	144026	type	True	77.0811	202	958	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_003258835.1	34017	34017	type	True	76.983	215	958	95	below_threshold
Phenylobacterium hankyongense	strain=HKS-05	GCA_003254505.1	1813876	1813876	type	True	76.9688	246	958	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	76.8971	133	958	95	below_threshold
Aureimonas mangrovi	strain=LMG 31693	GCA_014058705.1	2758041	2758041	type	True	76.7285	170	958	95	below_threshold
Limimaricola variabilis	strain=CECT 8572	GCA_014195545.1	1492771	1492771	type	True	76.532	171	958	95	below_threshold
Salinarimonas rosea	strain=DSM 21201	GCA_000429045.1	552063	552063	type	True	76.4917	305	958	95	below_threshold
Acuticoccus mangrovi	strain=B2012	GCA_016411865.1	2796142	2796142	type	True	76.2331	217	958	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	76.1244	134	958	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	75.7717	148	958	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:58,302] [INFO] DFAST Taxonomy check result was written to GCF_003122085.1_ASM312208v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:58,303] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:58,303] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:58,303] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67aa1996-8f46-4b6d-b3d9-8fa58f819f0c/dqc_reference/checkm_data
[2024-01-24 13:40:58,305] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:58,336] [INFO] Task started: CheckM
[2024-01-24 13:40:58,336] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003122085.1_ASM312208v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003122085.1_ASM312208v1_genomic.fna/checkm_input GCF_003122085.1_ASM312208v1_genomic.fna/checkm_result
[2024-01-24 13:41:25,840] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:25,841] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:25,864] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:25,864] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:25,865] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003122085.1_ASM312208v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:25,865] [INFO] Task started: Blastn
[2024-01-24 13:41:25,866] [INFO] Running command: blastn -query GCF_003122085.1_ASM312208v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67aa1996-8f46-4b6d-b3d9-8fa58f819f0c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003122085.1_ASM312208v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:28,306] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:28,310] [INFO] Selected 11 target genomes.
[2024-01-24 13:41:28,310] [INFO] Target genome list was writen to GCF_003122085.1_ASM312208v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:28,402] [INFO] Task started: fastANI
[2024-01-24 13:41:28,403] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e52cafe-c435-4ac5-9a35-b13882912a43/GCF_003122085.1_ASM312208v1_genomic.fna.gz --refList GCF_003122085.1_ASM312208v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003122085.1_ASM312208v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:36,755] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:36,765] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:36,765] [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_003122085.1	s__WD6-1 sp003122085	100.0	958	958	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__WD6-1	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017161425.1	s__Marinicauda algicola	80.7971	613	958	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Marinicauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007050995.1	s__Glycocaulis profundi	79.5758	490	958	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Glycocaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004793635.1	s__Marinicauda pacifica	78.7088	407	958	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Marinicauda	95.0	100.00	100.00	1.00	1.00	3	-
GCF_008630495.1	s__Oceanicaulis satelles	78.5631	410	958	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124675.1	s__Oceanicaulis sp016124675	78.4428	381	958	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152745.1	s__Oceanicaulis sp000152745	78.1986	382	958	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	98.46	98.38	0.90	0.88	7	-
GCA_017642925.1	s__Maricaulis sp017642925	77.9463	330	958	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004296955.1	s__Brevundimonas sp004296955	76.7387	208	958	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.84	95.71	0.82	0.76	6	-
GCF_014195545.1	s__Limimaricola variabilis	76.5098	173	958	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009882975.1	s__Maritimibacter harenae	75.9517	141	958	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:36,766] [INFO] GTDB search result was written to GCF_003122085.1_ASM312208v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:36,767] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:36,772] [INFO] DFAST_QC result json was written to GCF_003122085.1_ASM312208v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:36,772] [INFO] DFAST_QC completed!
[2024-01-24 13:41:36,772] [INFO] Total running time: 0h1m3s