[2024-01-25 19:41:50,775] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:41:50,777] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:41:50,777] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a78e45a-b5e0-4357-b1e8-23d8cd306e06/dqc_reference
[2024-01-25 19:41:51,906] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:41:51,906] [INFO] Task started: Prodigal
[2024-01-25 19:41:51,907] [INFO] Running command: gunzip -c /var/lib/cwl/stgb7ebb116-3369-4da5-9155-9c0d0f1916d3/GCF_017161425.1_ASM1716142v1_genomic.fna.gz | prodigal -d GCF_017161425.1_ASM1716142v1_genomic.fna/cds.fna -a GCF_017161425.1_ASM1716142v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:42:00,136] [INFO] Task succeeded: Prodigal
[2024-01-25 19:42:00,136] [INFO] Task started: HMMsearch
[2024-01-25 19:42:00,136] [INFO] Running command: hmmsearch --tblout GCF_017161425.1_ASM1716142v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a78e45a-b5e0-4357-b1e8-23d8cd306e06/dqc_reference/reference_markers.hmm GCF_017161425.1_ASM1716142v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:42:00,364] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:42:00,365] [INFO] Found 6/6 markers.
[2024-01-25 19:42:00,407] [INFO] Query marker FASTA was written to GCF_017161425.1_ASM1716142v1_genomic.fna/markers.fasta
[2024-01-25 19:42:00,408] [INFO] Task started: Blastn
[2024-01-25 19:42:00,408] [INFO] Running command: blastn -query GCF_017161425.1_ASM1716142v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a78e45a-b5e0-4357-b1e8-23d8cd306e06/dqc_reference/reference_markers.fasta -out GCF_017161425.1_ASM1716142v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:42:01,279] [INFO] Task succeeded: Blastn
[2024-01-25 19:42:01,281] [INFO] Selected 15 target genomes.
[2024-01-25 19:42:01,282] [INFO] Target genome list was writen to GCF_017161425.1_ASM1716142v1_genomic.fna/target_genomes.txt
[2024-01-25 19:42:01,296] [INFO] Task started: fastANI
[2024-01-25 19:42:01,296] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7ebb116-3369-4da5-9155-9c0d0f1916d3/GCF_017161425.1_ASM1716142v1_genomic.fna.gz --refList GCF_017161425.1_ASM1716142v1_genomic.fna/target_genomes.txt --output GCF_017161425.1_ASM1716142v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:42:12,618] [INFO] Task succeeded: fastANI
[2024-01-25 19:42:12,618] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a78e45a-b5e0-4357-b1e8-23d8cd306e06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:42:12,619] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a78e45a-b5e0-4357-b1e8-23d8cd306e06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:42:12,628] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:42:12,628] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:42:12,628] [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	100.0	1138	1141	95	conclusive
Marinicauda algicola	strain=JCM 31718	GCA_004793685.1	2029849	2029849	type	True	99.987	1124	1141	95	conclusive
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	80.7524	604	1141	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_009806145.1	1133559	1133559	type	True	80.3828	583	1141	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_004793635.1	1133559	1133559	type	True	80.3602	577	1141	95	below_threshold
Marinicauda pacifica	strain=CGMCC 1.11031	GCA_014636415.1	1133559	1133559	type	True	80.3195	579	1141	95	below_threshold
Glycocaulis alkaliphilus	strain=CGMCC 1.12428	GCA_014637625.1	1434191	1434191	type	True	78.2772	335	1141	95	below_threshold
Glycocaulis albus	strain=CGMCC 1.12766	GCA_014639075.1	1382801	1382801	type	True	78.0257	340	1141	95	below_threshold
Paracoccus limosus	strain=JCM 17370	GCA_009711185.1	913252	913252	type	True	76.9917	108	1141	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	76.7052	154	1141	95	below_threshold
Acuticoccus mangrovi	strain=B2012	GCA_016411865.1	2796142	2796142	type	True	76.5184	201	1141	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	76.3641	266	1141	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	76.2889	277	1141	95	below_threshold
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	75.6333	93	1141	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:42:12,629] [INFO] DFAST Taxonomy check result was written to GCF_017161425.1_ASM1716142v1_genomic.fna/tc_result.tsv
[2024-01-25 19:42:12,630] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:42:12,630] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:42:12,630] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a78e45a-b5e0-4357-b1e8-23d8cd306e06/dqc_reference/checkm_data
[2024-01-25 19:42:12,631] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:42:12,666] [INFO] Task started: CheckM
[2024-01-25 19:42:12,666] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017161425.1_ASM1716142v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017161425.1_ASM1716142v1_genomic.fna/checkm_input GCF_017161425.1_ASM1716142v1_genomic.fna/checkm_result
[2024-01-25 19:42:40,758] [INFO] Task succeeded: CheckM
[2024-01-25 19:42:40,758] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:42:40,782] [INFO] ===== Completeness check finished =====
[2024-01-25 19:42:40,782] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:42:40,782] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017161425.1_ASM1716142v1_genomic.fna/markers.fasta)
[2024-01-25 19:42:40,783] [INFO] Task started: Blastn
[2024-01-25 19:42:40,783] [INFO] Running command: blastn -query GCF_017161425.1_ASM1716142v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a78e45a-b5e0-4357-b1e8-23d8cd306e06/dqc_reference/reference_markers_gtdb.fasta -out GCF_017161425.1_ASM1716142v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:42:42,398] [INFO] Task succeeded: Blastn
[2024-01-25 19:42:42,401] [INFO] Selected 14 target genomes.
[2024-01-25 19:42:42,401] [INFO] Target genome list was writen to GCF_017161425.1_ASM1716142v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:42:42,414] [INFO] Task started: fastANI
[2024-01-25 19:42:42,414] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7ebb116-3369-4da5-9155-9c0d0f1916d3/GCF_017161425.1_ASM1716142v1_genomic.fna.gz --refList GCF_017161425.1_ASM1716142v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017161425.1_ASM1716142v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:42:51,942] [INFO] Task succeeded: fastANI
[2024-01-25 19:42:51,951] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:42:51,951] [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_017161425.1	s__Marinicauda algicola	100.0	1139	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Marinicauda	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003122085.1	s__WD6-1 sp003122085	80.774	601	1141	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_004793635.1	s__Marinicauda pacifica	80.3607	577	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Marinicauda	95.0	100.00	100.00	1.00	1.00	3	-
GCF_007050995.1	s__Glycocaulis profundi	79.5352	493	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Glycocaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630495.1	s__Oceanicaulis satelles	78.842	418	1141	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	78.3574	442	1141	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	78.1907	408	1141	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	78.063	308	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	97.56	97.05	0.94	0.85	5	-
GCA_001657295.1	s__Oceanicaulis sp001657295	77.9217	378	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711185.1	s__Paracoccus limosus	77.0163	107	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016411865.1	s__Acuticoccus sp016411865	76.5157	201	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Amorphaceae;g__Acuticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689705.1	s__HKCCE3408 sp015689705	76.3268	144	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HKCCE3408	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002783145.1	s__Nioella sp002783145	75.9634	76	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:42:51,952] [INFO] GTDB search result was written to GCF_017161425.1_ASM1716142v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:42:51,953] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:42:51,955] [INFO] DFAST_QC result json was written to GCF_017161425.1_ASM1716142v1_genomic.fna/dqc_result.json
[2024-01-25 19:42:51,955] [INFO] DFAST_QC completed!
[2024-01-25 19:42:51,955] [INFO] Total running time: 0h1m1s