[2024-01-24 13:13:38,308] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:38,313] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:38,313] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d7ffa30-2810-405f-8d69-8d797427d5fe/dqc_reference
[2024-01-24 13:13:39,640] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:39,641] [INFO] Task started: Prodigal
[2024-01-24 13:13:39,641] [INFO] Running command: gunzip -c /var/lib/cwl/stgda506a56-d909-4959-b8de-b02359329f17/GCF_008630495.1_ASM863049v1_genomic.fna.gz | prodigal -d GCF_008630495.1_ASM863049v1_genomic.fna/cds.fna -a GCF_008630495.1_ASM863049v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:48,696] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:48,697] [INFO] Task started: HMMsearch
[2024-01-24 13:13:48,697] [INFO] Running command: hmmsearch --tblout GCF_008630495.1_ASM863049v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d7ffa30-2810-405f-8d69-8d797427d5fe/dqc_reference/reference_markers.hmm GCF_008630495.1_ASM863049v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:48,903] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:48,904] [INFO] Found 6/6 markers.
[2024-01-24 13:13:48,927] [INFO] Query marker FASTA was written to GCF_008630495.1_ASM863049v1_genomic.fna/markers.fasta
[2024-01-24 13:13:48,928] [INFO] Task started: Blastn
[2024-01-24 13:13:48,928] [INFO] Running command: blastn -query GCF_008630495.1_ASM863049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d7ffa30-2810-405f-8d69-8d797427d5fe/dqc_reference/reference_markers.fasta -out GCF_008630495.1_ASM863049v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:49,879] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:49,883] [INFO] Selected 17 target genomes.
[2024-01-24 13:13:49,884] [INFO] Target genome list was writen to GCF_008630495.1_ASM863049v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:49,892] [INFO] Task started: fastANI
[2024-01-24 13:13:49,892] [INFO] Running command: fastANI --query /var/lib/cwl/stgda506a56-d909-4959-b8de-b02359329f17/GCF_008630495.1_ASM863049v1_genomic.fna.gz --refList GCF_008630495.1_ASM863049v1_genomic.fna/target_genomes.txt --output GCF_008630495.1_ASM863049v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:59,891] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:59,892] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d7ffa30-2810-405f-8d69-8d797427d5fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:59,892] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d7ffa30-2810-405f-8d69-8d797427d5fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:59,907] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:13:59,907] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:13:59,907] [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	78.8025	433	961	95	below_threshold
Marinicauda algicola	strain=JCM 31718	GCA_004793685.1	2029849	2029849	type	True	78.7698	432	961	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	78.7316	406	961	95	below_threshold
Glycocaulis alkaliphilus	strain=CGMCC 1.12428	GCA_014637625.1	1434191	1434191	type	True	78.6341	385	961	95	below_threshold
Glycocaulis alkaliphilus	strain=6B-8	GCA_004000605.1	1434191	1434191	type	True	78.5635	389	961	95	below_threshold
Glycocaulis albus	strain=CGMCC 1.12766	GCA_014639075.1	1382801	1382801	type	True	78.3686	376	961	95	below_threshold
Marinicauda pacifica	strain=CGMCC 1.11031	GCA_014636415.1	1133559	1133559	type	True	78.208	332	961	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_004793635.1	1133559	1133559	type	True	78.2028	333	961	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_009806145.1	1133559	1133559	type	True	78.1558	324	961	95	below_threshold
Maricaulis salignorans	strain=DSM 16077	GCA_900103475.1	144026	144026	type	True	77.2366	183	961	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	76.7312	153	961	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_022559625.1	1526572	1526572	type	True	76.5806	112	961	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	76.5756	106	961	95	below_threshold
Alsobacter metallidurans	strain=CGMCC 1.12214	GCA_014636935.1	340221	340221	type	True	76.281	120	961	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	76.2763	92	961	95	below_threshold
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	76.1914	83	961	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	76.1316	99	961	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:59,909] [INFO] DFAST Taxonomy check result was written to GCF_008630495.1_ASM863049v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:59,910] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:59,910] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:59,910] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d7ffa30-2810-405f-8d69-8d797427d5fe/dqc_reference/checkm_data
[2024-01-24 13:13:59,912] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:59,942] [INFO] Task started: CheckM
[2024-01-24 13:13:59,942] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008630495.1_ASM863049v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008630495.1_ASM863049v1_genomic.fna/checkm_input GCF_008630495.1_ASM863049v1_genomic.fna/checkm_result
[2024-01-24 13:14:29,387] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:29,388] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:29,449] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:29,450] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:29,450] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008630495.1_ASM863049v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:29,450] [INFO] Task started: Blastn
[2024-01-24 13:14:29,450] [INFO] Running command: blastn -query GCF_008630495.1_ASM863049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d7ffa30-2810-405f-8d69-8d797427d5fe/dqc_reference/reference_markers_gtdb.fasta -out GCF_008630495.1_ASM863049v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:31,242] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:31,244] [INFO] Selected 12 target genomes.
[2024-01-24 13:14:31,245] [INFO] Target genome list was writen to GCF_008630495.1_ASM863049v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:31,259] [INFO] Task started: fastANI
[2024-01-24 13:14:31,260] [INFO] Running command: fastANI --query /var/lib/cwl/stgda506a56-d909-4959-b8de-b02359329f17/GCF_008630495.1_ASM863049v1_genomic.fna.gz --refList GCF_008630495.1_ASM863049v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008630495.1_ASM863049v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:39,844] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:39,855] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:39,855] [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_008630495.1	s__Oceanicaulis satelles	100.0	961	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016124675.1	s__Oceanicaulis sp016124675	83.404	727	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007050995.1	s__Glycocaulis profundi	79.4757	499	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Glycocaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152745.1	s__Oceanicaulis sp000152745	79.0882	449	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	98.46	98.38	0.90	0.88	7	-
GCF_000420265.1	s__Oceanicaulis alexandrii	78.9413	400	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	97.56	97.05	0.94	0.85	5	-
GCF_017161425.1	s__Marinicauda algicola	78.7826	435	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Marinicauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003122085.1	s__WD6-1 sp003122085	78.7575	403	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__WD6-1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004000605.1	s__Glycocaulis alkaliphilus	78.5795	387	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Glycocaulis	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003046365.1	s__Oceanicaulis sp003046365	78.4212	362	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	96.56	96.56	0.93	0.93	2	-
GCF_014639075.1	s__Glycocaulis albus	78.3474	378	961	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	78.2139	332	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Marinicauda	95.0	100.00	100.00	1.00	1.00	3	-
GCF_014636935.1	s__Alsobacter metallidurans	76.2653	121	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Alsobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:39,857] [INFO] GTDB search result was written to GCF_008630495.1_ASM863049v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:39,858] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:39,863] [INFO] DFAST_QC result json was written to GCF_008630495.1_ASM863049v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:39,863] [INFO] DFAST_QC completed!
[2024-01-24 13:14:39,863] [INFO] Total running time: 0h1m2s