[2024-01-24 13:46:17,519] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:17,522] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:17,522] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf9804b6-f316-4c40-b7c4-e59384bba33f/dqc_reference
[2024-01-24 13:46:18,879] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:18,881] [INFO] Task started: Prodigal
[2024-01-24 13:46:18,881] [INFO] Running command: gunzip -c /var/lib/cwl/stgc6d2c5ab-bf88-42b7-9c19-25ae3e5f12bb/GCF_014656375.1_ASM1465637v1_genomic.fna.gz | prodigal -d GCF_014656375.1_ASM1465637v1_genomic.fna/cds.fna -a GCF_014656375.1_ASM1465637v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:30,580] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:30,580] [INFO] Task started: HMMsearch
[2024-01-24 13:46:30,580] [INFO] Running command: hmmsearch --tblout GCF_014656375.1_ASM1465637v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf9804b6-f316-4c40-b7c4-e59384bba33f/dqc_reference/reference_markers.hmm GCF_014656375.1_ASM1465637v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:30,903] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:30,904] [INFO] Found 6/6 markers.
[2024-01-24 13:46:30,944] [INFO] Query marker FASTA was written to GCF_014656375.1_ASM1465637v1_genomic.fna/markers.fasta
[2024-01-24 13:46:30,944] [INFO] Task started: Blastn
[2024-01-24 13:46:30,944] [INFO] Running command: blastn -query GCF_014656375.1_ASM1465637v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf9804b6-f316-4c40-b7c4-e59384bba33f/dqc_reference/reference_markers.fasta -out GCF_014656375.1_ASM1465637v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:31,890] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:31,894] [INFO] Selected 18 target genomes.
[2024-01-24 13:46:31,895] [INFO] Target genome list was writen to GCF_014656375.1_ASM1465637v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:31,906] [INFO] Task started: fastANI
[2024-01-24 13:46:31,906] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6d2c5ab-bf88-42b7-9c19-25ae3e5f12bb/GCF_014656375.1_ASM1465637v1_genomic.fna.gz --refList GCF_014656375.1_ASM1465637v1_genomic.fna/target_genomes.txt --output GCF_014656375.1_ASM1465637v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:44,855] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:44,855] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf9804b6-f316-4c40-b7c4-e59384bba33f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:44,855] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf9804b6-f316-4c40-b7c4-e59384bba33f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:44,869] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:44,869] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:44,869] [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
Aliiroseovarius zhejiangensis	strain=KCTC 42443	GCA_014656375.1	1632025	1632025	type	True	100.0	1132	1132	95	conclusive
Aliiroseovarius sediminilitoris	strain=DSM 29439	GCA_900109955.1	1173584	1173584	type	True	83.6507	847	1132	95	below_threshold
Aliiroseovarius marinus	strain=A6024	GCA_004360145.1	2500159	2500159	type	True	79.8536	613	1132	95	below_threshold
Aliiroseovarius pelagivivens	strain=CECT 8811	GCA_900302485.1	1639690	1639690	type	True	79.7536	546	1132	95	below_threshold
Aliiroseovarius crassostreae	strain=CV919-312	GCA_001307765.1	154981	154981	type	True	79.591	456	1132	95	below_threshold
Aliiroseovarius halocynthiae	strain=MA1-10	GCA_007004645.1	985055	985055	type	True	79.5717	524	1132	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	78.2546	411	1132	95	below_threshold
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_008124775.1	404236	404236	type	True	77.9733	363	1132	95	below_threshold
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_000152805.1	404236	404236	type	True	77.8869	373	1132	95	below_threshold
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	77.8363	257	1132	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	77.6949	276	1132	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.6941	283	1132	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.6515	335	1132	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	77.3928	297	1132	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.3751	250	1132	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	77.314	253	1132	95	below_threshold
Celeribacter litoreus	strain=ASW11-22	GCA_020165855.1	2876714	2876714	type	True	77.1931	154	1132	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	76.9409	264	1132	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:44,871] [INFO] DFAST Taxonomy check result was written to GCF_014656375.1_ASM1465637v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:44,872] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:44,872] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:44,872] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf9804b6-f316-4c40-b7c4-e59384bba33f/dqc_reference/checkm_data
[2024-01-24 13:46:44,873] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:44,912] [INFO] Task started: CheckM
[2024-01-24 13:46:44,912] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014656375.1_ASM1465637v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014656375.1_ASM1465637v1_genomic.fna/checkm_input GCF_014656375.1_ASM1465637v1_genomic.fna/checkm_result
[2024-01-24 13:47:25,478] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:25,479] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:25,501] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:25,502] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:25,502] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014656375.1_ASM1465637v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:25,503] [INFO] Task started: Blastn
[2024-01-24 13:47:25,503] [INFO] Running command: blastn -query GCF_014656375.1_ASM1465637v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf9804b6-f316-4c40-b7c4-e59384bba33f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014656375.1_ASM1465637v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:27,227] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:27,233] [INFO] Selected 13 target genomes.
[2024-01-24 13:47:27,233] [INFO] Target genome list was writen to GCF_014656375.1_ASM1465637v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:27,252] [INFO] Task started: fastANI
[2024-01-24 13:47:27,252] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6d2c5ab-bf88-42b7-9c19-25ae3e5f12bb/GCF_014656375.1_ASM1465637v1_genomic.fna.gz --refList GCF_014656375.1_ASM1465637v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014656375.1_ASM1465637v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:36,768] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:36,779] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:36,780] [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_014656375.1	s__Aliiroseovarius zhejiangensis	100.0	1132	1132	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900109955.1	s__Aliiroseovarius sediminilitoris	83.6515	846	1132	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500215.1	s__Aliiroseovarius sp010500215	79.8604	588	1132	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004360145.1	s__Aliiroseovarius marinus	79.8531	613	1132	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302485.1	s__Aliiroseovarius pelagivivens	79.7536	546	1132	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001307765.1	s__Aliiroseovarius crassostreae	79.591	456	1132	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	96.06	95.64	0.88	0.84	18	-
GCF_007004645.1	s__Aliiroseovarius halocynthiae	79.5717	524	1132	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	78.1748	394	1132	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002367285.1	s__Aliiroseovarius sp002367285	78.1458	365	1132	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109145.1	s__Marinovum algicola	77.7293	347	1132	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	99.11	98.22	0.94	0.88	3	-
GCF_900100085.1	s__Salipiger marinus	77.6423	336	1132	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.13	98.13	0.95	0.95	2	-
GCF_016412875.1	s__Palleronia pontilimi	77.5833	301	1132	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153725.1	s__Salipiger bermudensis	77.3779	297	1132	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.06	97.75	0.87	0.75	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:36,782] [INFO] GTDB search result was written to GCF_014656375.1_ASM1465637v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:36,782] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:36,786] [INFO] DFAST_QC result json was written to GCF_014656375.1_ASM1465637v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:36,786] [INFO] DFAST_QC completed!
[2024-01-24 13:47:36,786] [INFO] Total running time: 0h1m19s