[2023-06-05 00:14:05,860] [INFO] DFAST_QC pipeline started.
[2023-06-05 00:14:05,862] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 00:14:05,862] [INFO] DQC Reference Directory: /var/lib/cwl/stgfee93103-a591-4c46-b19d-67fa18a18329/dqc_reference
[2023-06-05 00:14:07,486] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 00:14:07,487] [INFO] Task started: Prodigal
[2023-06-05 00:14:07,488] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a55ecda-b450-4c19-b6b3-09b69777d127/GCA_001657295.1_ASM165729v1_genomic.fna.gz | prodigal -d GCA_001657295.1_ASM165729v1_genomic.fna/cds.fna -a GCA_001657295.1_ASM165729v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 00:14:16,248] [INFO] Task succeeded: Prodigal
[2023-06-05 00:14:16,248] [INFO] Task started: HMMsearch
[2023-06-05 00:14:16,248] [INFO] Running command: hmmsearch --tblout GCA_001657295.1_ASM165729v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfee93103-a591-4c46-b19d-67fa18a18329/dqc_reference/reference_markers.hmm GCA_001657295.1_ASM165729v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 00:14:16,472] [INFO] Task succeeded: HMMsearch
[2023-06-05 00:14:16,473] [INFO] Found 6/6 markers.
[2023-06-05 00:14:16,503] [INFO] Query marker FASTA was written to GCA_001657295.1_ASM165729v1_genomic.fna/markers.fasta
[2023-06-05 00:14:16,503] [INFO] Task started: Blastn
[2023-06-05 00:14:16,504] [INFO] Running command: blastn -query GCA_001657295.1_ASM165729v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfee93103-a591-4c46-b19d-67fa18a18329/dqc_reference/reference_markers.fasta -out GCA_001657295.1_ASM165729v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:14:17,536] [INFO] Task succeeded: Blastn
[2023-06-05 00:14:17,540] [INFO] Selected 20 target genomes.
[2023-06-05 00:14:17,540] [INFO] Target genome list was writen to GCA_001657295.1_ASM165729v1_genomic.fna/target_genomes.txt
[2023-06-05 00:14:17,546] [INFO] Task started: fastANI
[2023-06-05 00:14:17,546] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a55ecda-b450-4c19-b6b3-09b69777d127/GCA_001657295.1_ASM165729v1_genomic.fna.gz --refList GCA_001657295.1_ASM165729v1_genomic.fna/target_genomes.txt --output GCA_001657295.1_ASM165729v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 00:14:33,624] [INFO] Task succeeded: fastANI
[2023-06-05 00:14:33,625] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfee93103-a591-4c46-b19d-67fa18a18329/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 00:14:33,625] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfee93103-a591-4c46-b19d-67fa18a18329/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 00:14:33,642] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 00:14:33,642] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 00:14:33,643] [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 algicola	strain=RMAR8-3	GCA_017161425.1	2029849	2029849	type	True	77.8393	369	1031	95	below_threshold
Marinicauda algicola	strain=JCM 31718	GCA_004793685.1	2029849	2029849	type	True	77.7947	372	1031	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	77.7811	357	1031	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_004793635.1	1133559	1133559	type	True	77.5521	281	1031	95	below_threshold
Marinicauda pacifica	strain=CGMCC 1.11031	GCA_014636415.1	1133559	1133559	type	True	77.5206	279	1031	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_009806145.1	1133559	1133559	type	True	77.5045	279	1031	95	below_threshold
Glycocaulis alkaliphilus	strain=CGMCC 1.12428	GCA_014637625.1	1434191	1434191	type	True	77.3878	241	1031	95	below_threshold
Glycocaulis alkaliphilus	strain=6B-8	GCA_004000605.1	1434191	1434191	type	True	77.3804	245	1031	95	below_threshold
Glycocaulis albus	strain=CGMCC 1.12766	GCA_014639075.1	1382801	1382801	type	True	77.3546	223	1031	95	below_threshold
Maricaulis salignorans	strain=DSM 16077	GCA_900103475.1	144026	144026	type	True	77.1544	156	1031	95	below_threshold
Maricaulis maris	strain=DSM 4734	GCA_003634045.1	74318	74318	type	True	77.0045	178	1031	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.306	70	1031	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	76.077	54	1031	95	below_threshold
Phenylobacterium hankyongense	strain=HKS-05	GCA_003254505.1	1813876	1813876	type	True	76.0332	146	1031	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	75.9083	105	1031	95	below_threshold
Caulobacter zeae	strain=410	GCA_002858925.1	2055137	2055137	type	True	75.8862	158	1031	95	below_threshold
Caulobacter endophyticus	strain=774	GCA_003116815.1	2172652	2172652	type	True	75.7983	146	1031	95	below_threshold
Hyphomonas sediminis	strain=WL0036	GCA_019679475.1	2866160	2866160	type	True	75.7966	69	1031	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	75.5584	143	1031	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.2213	103	1031	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 00:14:33,650] [INFO] DFAST Taxonomy check result was written to GCA_001657295.1_ASM165729v1_genomic.fna/tc_result.tsv
[2023-06-05 00:14:33,651] [INFO] ===== Taxonomy check completed =====
[2023-06-05 00:14:33,651] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 00:14:33,652] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfee93103-a591-4c46-b19d-67fa18a18329/dqc_reference/checkm_data
[2023-06-05 00:14:33,653] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 00:14:33,689] [INFO] Task started: CheckM
[2023-06-05 00:14:33,690] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001657295.1_ASM165729v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001657295.1_ASM165729v1_genomic.fna/checkm_input GCA_001657295.1_ASM165729v1_genomic.fna/checkm_result
[2023-06-05 00:15:02,716] [INFO] Task succeeded: CheckM
[2023-06-05 00:15:02,717] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 00:15:02,734] [INFO] ===== Completeness check finished =====
[2023-06-05 00:15:02,734] [INFO] ===== Start GTDB Search =====
[2023-06-05 00:15:02,735] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001657295.1_ASM165729v1_genomic.fna/markers.fasta)
[2023-06-05 00:15:02,735] [INFO] Task started: Blastn
[2023-06-05 00:15:02,735] [INFO] Running command: blastn -query GCA_001657295.1_ASM165729v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfee93103-a591-4c46-b19d-67fa18a18329/dqc_reference/reference_markers_gtdb.fasta -out GCA_001657295.1_ASM165729v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:15:04,286] [INFO] Task succeeded: Blastn
[2023-06-05 00:15:04,289] [INFO] Selected 14 target genomes.
[2023-06-05 00:15:04,290] [INFO] Target genome list was writen to GCA_001657295.1_ASM165729v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 00:15:04,562] [INFO] Task started: fastANI
[2023-06-05 00:15:04,562] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a55ecda-b450-4c19-b6b3-09b69777d127/GCA_001657295.1_ASM165729v1_genomic.fna.gz --refList GCA_001657295.1_ASM165729v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001657295.1_ASM165729v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 00:15:13,043] [INFO] Task succeeded: fastANI
[2023-06-05 00:15:13,055] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 00:15:13,055] [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
GCA_001657295.1	s__Oceanicaulis sp001657295	100.0	1027	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000152745.1	s__Oceanicaulis sp000152745	78.836	390	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	98.46	98.38	0.90	0.88	7	-
GCF_008630495.1	s__Oceanicaulis satelles	78.5344	423	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420265.1	s__Oceanicaulis alexandrii	78.3368	371	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	97.56	97.05	0.94	0.85	5	-
GCA_016124675.1	s__Oceanicaulis sp016124675	78.2063	392	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003046365.1	s__Oceanicaulis sp003046365	78.1558	363	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	96.56	96.56	0.93	0.93	2	-
GCF_007050995.1	s__Glycocaulis profundi	78.0057	325	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Glycocaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017161425.1	s__Marinicauda algicola	77.8481	368	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Marinicauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004793635.1	s__Marinicauda pacifica	77.5521	281	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Marinicauda	95.0	100.00	100.00	1.00	1.00	3	-
GCF_004000605.1	s__Glycocaulis alkaliphilus	77.357	247	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Glycocaulis	95.0	100.00	100.00	0.99	0.99	2	-
GCA_017642925.1	s__Maricaulis sp017642925	77.1337	234	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707795.1	s__Maricaulis sp002707795	77.0882	157	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	99.42	99.36	0.71	0.69	3	-
GCF_003634045.1	s__Maricaulis maris	76.9761	180	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	98.04	98.04	0.96	0.96	2	-
GCA_003576705.1	s__SYSU-D60015 sp003576705	75.7758	135	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__SYSU-D60015	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 00:15:13,057] [INFO] GTDB search result was written to GCA_001657295.1_ASM165729v1_genomic.fna/result_gtdb.tsv
[2023-06-05 00:15:13,057] [INFO] ===== GTDB Search completed =====
[2023-06-05 00:15:13,061] [INFO] DFAST_QC result json was written to GCA_001657295.1_ASM165729v1_genomic.fna/dqc_result.json
[2023-06-05 00:15:13,061] [INFO] DFAST_QC completed!
[2023-06-05 00:15:13,061] [INFO] Total running time: 0h1m7s