[2024-01-24 12:40:20,631] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:20,633] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:20,633] [INFO] DQC Reference Directory: /var/lib/cwl/stg05982bde-cc74-4898-ad05-5f819c55341e/dqc_reference
[2024-01-24 12:40:21,848] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:21,849] [INFO] Task started: Prodigal
[2024-01-24 12:40:21,849] [INFO] Running command: gunzip -c /var/lib/cwl/stge116d09e-d095-4dd9-9858-b2dda32317ff/GCF_000011965.2_ASM1196v2_genomic.fna.gz | prodigal -d GCF_000011965.2_ASM1196v2_genomic.fna/cds.fna -a GCF_000011965.2_ASM1196v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:37,603] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:37,604] [INFO] Task started: HMMsearch
[2024-01-24 12:40:37,604] [INFO] Running command: hmmsearch --tblout GCF_000011965.2_ASM1196v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05982bde-cc74-4898-ad05-5f819c55341e/dqc_reference/reference_markers.hmm GCF_000011965.2_ASM1196v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:37,863] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:37,865] [INFO] Found 6/6 markers.
[2024-01-24 12:40:37,904] [INFO] Query marker FASTA was written to GCF_000011965.2_ASM1196v2_genomic.fna/markers.fasta
[2024-01-24 12:40:37,904] [INFO] Task started: Blastn
[2024-01-24 12:40:37,904] [INFO] Running command: blastn -query GCF_000011965.2_ASM1196v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg05982bde-cc74-4898-ad05-5f819c55341e/dqc_reference/reference_markers.fasta -out GCF_000011965.2_ASM1196v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:38,862] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:38,866] [INFO] Selected 18 target genomes.
[2024-01-24 12:40:38,867] [INFO] Target genome list was writen to GCF_000011965.2_ASM1196v2_genomic.fna/target_genomes.txt
[2024-01-24 12:40:38,874] [INFO] Task started: fastANI
[2024-01-24 12:40:38,874] [INFO] Running command: fastANI --query /var/lib/cwl/stge116d09e-d095-4dd9-9858-b2dda32317ff/GCF_000011965.2_ASM1196v2_genomic.fna.gz --refList GCF_000011965.2_ASM1196v2_genomic.fna/target_genomes.txt --output GCF_000011965.2_ASM1196v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:55,168] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:55,168] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05982bde-cc74-4898-ad05-5f819c55341e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:55,169] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05982bde-cc74-4898-ad05-5f819c55341e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:55,187] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:40:55,188] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:55,188] [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
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	100.0	1529	1532	95	conclusive
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	84.3661	987	1532	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	81.5722	768	1532	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	81.483	783	1532	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	81.1274	802	1532	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	81.1246	806	1532	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	81.071	813	1532	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	80.8256	777	1532	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	80.4198	772	1532	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	79.687	636	1532	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	79.6303	696	1532	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	78.6736	571	1532	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.6484	451	1532	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	78.4784	522	1532	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	78.4668	459	1532	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.4292	497	1532	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	78.1053	501	1532	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.809	410	1532	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:55,192] [INFO] DFAST Taxonomy check result was written to GCF_000011965.2_ASM1196v2_genomic.fna/tc_result.tsv
[2024-01-24 12:40:55,192] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:55,192] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:55,193] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05982bde-cc74-4898-ad05-5f819c55341e/dqc_reference/checkm_data
[2024-01-24 12:40:55,194] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:55,242] [INFO] Task started: CheckM
[2024-01-24 12:40:55,242] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000011965.2_ASM1196v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000011965.2_ASM1196v2_genomic.fna/checkm_input GCF_000011965.2_ASM1196v2_genomic.fna/checkm_result
[2024-01-24 12:41:45,960] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:45,961] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:45,982] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:45,983] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:45,983] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000011965.2_ASM1196v2_genomic.fna/markers.fasta)
[2024-01-24 12:41:45,983] [INFO] Task started: Blastn
[2024-01-24 12:41:45,984] [INFO] Running command: blastn -query GCF_000011965.2_ASM1196v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg05982bde-cc74-4898-ad05-5f819c55341e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000011965.2_ASM1196v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:47,640] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:47,644] [INFO] Selected 13 target genomes.
[2024-01-24 12:41:47,644] [INFO] Target genome list was writen to GCF_000011965.2_ASM1196v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:47,654] [INFO] Task started: fastANI
[2024-01-24 12:41:47,654] [INFO] Running command: fastANI --query /var/lib/cwl/stge116d09e-d095-4dd9-9858-b2dda32317ff/GCF_000011965.2_ASM1196v2_genomic.fna.gz --refList GCF_000011965.2_ASM1196v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000011965.2_ASM1196v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:59,590] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:59,605] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:59,605] [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_000011965.2	s__Ruegeria_B pomeroyi	100.0	1531	1532	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	conclusive
GCF_010500245.1	s__Ruegeria_B sp010500245	86.5547	1103	1532	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101475.1	s__Ruegeria_B marina	84.3528	989	1532	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129345.1	s__Ruegeria intermedia	81.5764	767	1532	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	81.4886	783	1532	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013031405.1	s__Ruegeria sp013031405	81.4686	887	1532	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	81.4335	745	1532	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_900109035.1	s__Cribrihabitans marinus	81.1446	805	1532	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_005938215.1	s__Ruegeria sediminis	81.1382	800	1532	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	80.8595	772	1532	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	79.6752	638	1532	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006227805.1	s__Aestuariivita sp006227805	79.461	440	1532	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032025.1	s__Ruegeria atlantica_C	79.2286	607	1532	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:59,607] [INFO] GTDB search result was written to GCF_000011965.2_ASM1196v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:59,607] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:59,611] [INFO] DFAST_QC result json was written to GCF_000011965.2_ASM1196v2_genomic.fna/dqc_result.json
[2024-01-24 12:41:59,611] [INFO] DFAST_QC completed!
[2024-01-24 12:41:59,611] [INFO] Total running time: 0h1m39s