[2024-01-24 13:56:58,362] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:58,364] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:58,364] [INFO] DQC Reference Directory: /var/lib/cwl/stgea1cae57-71b6-4a67-b640-548f0fa47613/dqc_reference
[2024-01-24 13:56:59,638] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:59,639] [INFO] Task started: Prodigal
[2024-01-24 13:56:59,639] [INFO] Running command: gunzip -c /var/lib/cwl/stg49591646-78d3-4e6d-bd9c-3b1e48ec72f7/GCF_028463845.1_ASM2846384v1_genomic.fna.gz | prodigal -d GCF_028463845.1_ASM2846384v1_genomic.fna/cds.fna -a GCF_028463845.1_ASM2846384v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:10,995] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:10,996] [INFO] Task started: HMMsearch
[2024-01-24 13:57:10,996] [INFO] Running command: hmmsearch --tblout GCF_028463845.1_ASM2846384v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea1cae57-71b6-4a67-b640-548f0fa47613/dqc_reference/reference_markers.hmm GCF_028463845.1_ASM2846384v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:11,287] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:11,288] [INFO] Found 6/6 markers.
[2024-01-24 13:57:11,323] [INFO] Query marker FASTA was written to GCF_028463845.1_ASM2846384v1_genomic.fna/markers.fasta
[2024-01-24 13:57:11,323] [INFO] Task started: Blastn
[2024-01-24 13:57:11,323] [INFO] Running command: blastn -query GCF_028463845.1_ASM2846384v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea1cae57-71b6-4a67-b640-548f0fa47613/dqc_reference/reference_markers.fasta -out GCF_028463845.1_ASM2846384v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:12,276] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:12,280] [INFO] Selected 26 target genomes.
[2024-01-24 13:57:12,281] [INFO] Target genome list was writen to GCF_028463845.1_ASM2846384v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:12,292] [INFO] Task started: fastANI
[2024-01-24 13:57:12,292] [INFO] Running command: fastANI --query /var/lib/cwl/stg49591646-78d3-4e6d-bd9c-3b1e48ec72f7/GCF_028463845.1_ASM2846384v1_genomic.fna.gz --refList GCF_028463845.1_ASM2846384v1_genomic.fna/target_genomes.txt --output GCF_028463845.1_ASM2846384v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:28,595] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:28,596] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea1cae57-71b6-4a67-b640-548f0fa47613/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:28,596] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea1cae57-71b6-4a67-b640-548f0fa47613/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:28,615] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:57:28,615] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:57:28,615] [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
Kordiimonas marina	strain=A6E486	GCA_023006325.1	2872312	2872312	type	True	78.1054	354	1197	95	below_threshold
Kordiimonas lacus	strain=S3-22	GCA_001550055.1	637679	637679	type	True	77.7376	249	1197	95	below_threshold
Kordiimonas lacus	strain=CGMCC 1.9109	GCA_900101935.1	637679	637679	type	True	77.6815	246	1197	95	below_threshold
Kordiimonas gwangyangensis	strain=DSM 19435	GCA_000375545.1	288022	288022	type	True	77.663	249	1197	95	below_threshold
Kordiimonas lipolytica	strain=M41	GCA_001550065.1	1662421	1662421	type	True	77.6066	257	1197	95	below_threshold
Eilatimonas milleporae	strain=DSM 25217	GCA_003688555.1	911205	911205	type	True	76.8151	164	1197	95	below_threshold
Pedomonas mirosovicensis	strain=A1X5R2	GCA_022569295.1	2908641	2908641	type	True	76.6654	112	1197	95	below_threshold
Rhodothalassium salexigens	strain=DSM 2132	GCA_016583875.1	1086	1086	type	True	76.6545	123	1197	95	below_threshold
Rhodothalassium salexigens	strain=DSM 2132	GCA_014197775.1	1086	1086	type	True	76.4741	125	1197	95	below_threshold
Rhodothalassium salexigens	strain=DSM 2132	GCA_004341375.1	1086	1086	type	True	76.4524	125	1197	95	below_threshold
Sphingopyxis microcysteis	strain=Z10-6	GCA_012274265.1	2484145	2484145	type	True	76.4333	90	1197	95	below_threshold
Sphingomonas pokkalii	strain=L3B27	GCA_003096275.1	2175090	2175090	type	True	76.3748	108	1197	95	below_threshold
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_009789535.1	1166323	1166323	type	True	76.3225	101	1197	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	76.2879	58	1197	95	below_threshold
Roseovarius halotolerans	strain=CECT 8110	GCA_900172255.1	505353	505353	type	True	76.256	59	1197	95	below_threshold
Neorhizobium vignae	strain=CCBAU 05176	GCA_000732195.1	690585	690585	type	True	76.1807	86	1197	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.1783	94	1197	95	below_threshold
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_014197095.1	1166323	1166323	type	True	76.1576	100	1197	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	76.0958	99	1197	95	below_threshold
Rhizobium vallis	strain=CCBAU 65647	GCA_003985155.1	634290	634290	type	True	76.0432	90	1197	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	76.0255	80	1197	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.9898	79	1197	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	75.9888	80	1197	95	below_threshold
Paracoccus thiocyanatus	strain=ATCC 700171	GCA_900156255.1	34006	34006	type	True	75.987	80	1197	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	75.7181	59	1197	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:28,617] [INFO] DFAST Taxonomy check result was written to GCF_028463845.1_ASM2846384v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:28,620] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:28,620] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:28,621] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea1cae57-71b6-4a67-b640-548f0fa47613/dqc_reference/checkm_data
[2024-01-24 13:57:28,622] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:28,664] [INFO] Task started: CheckM
[2024-01-24 13:57:28,664] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028463845.1_ASM2846384v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028463845.1_ASM2846384v1_genomic.fna/checkm_input GCF_028463845.1_ASM2846384v1_genomic.fna/checkm_result
[2024-01-24 13:58:06,577] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:06,578] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:06,595] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:06,595] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:06,596] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028463845.1_ASM2846384v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:06,596] [INFO] Task started: Blastn
[2024-01-24 13:58:06,596] [INFO] Running command: blastn -query GCF_028463845.1_ASM2846384v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea1cae57-71b6-4a67-b640-548f0fa47613/dqc_reference/reference_markers_gtdb.fasta -out GCF_028463845.1_ASM2846384v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:08,359] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:08,363] [INFO] Selected 23 target genomes.
[2024-01-24 13:58:08,364] [INFO] Target genome list was writen to GCF_028463845.1_ASM2846384v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:08,384] [INFO] Task started: fastANI
[2024-01-24 13:58:08,385] [INFO] Running command: fastANI --query /var/lib/cwl/stg49591646-78d3-4e6d-bd9c-3b1e48ec72f7/GCF_028463845.1_ASM2846384v1_genomic.fna.gz --refList GCF_028463845.1_ASM2846384v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028463845.1_ASM2846384v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:25,097] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:25,117] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:58:25,117] [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_006226495.1	s__Kordiimonas sp006226495	78.4104	383	1197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001550055.1	s__Kordiimonas lacus	77.7229	249	1197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	98.68	97.35	0.95	0.90	3	-
GCF_000375545.1	s__Kordiimonas gwangyangensis	77.663	249	1197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	99.96	99.96	1.00	1.00	2	-
GCF_001550065.1	s__Kordiimonas lipolytica	77.5711	255	1197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688555.1	s__Eilatimonas milleporae	76.8151	164	1197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Eilatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961745.1	s__BRH-c57 sp000961745	76.7588	72	1197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__BRH-c57	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010994245.1	s__Sandarakinorhabdus rubra	76.6207	87	1197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandarakinorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013372925.1	s__Kordiimonas sp013372925	76.5788	109	1197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013317235.1	s__Leisingera sp013317235	76.4783	67	1197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001695835.1	s__Ensifer sp001695835	76.4577	73	1197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	100.00	100.00	1.00	0.99	4	-
GCF_004341375.1	s__Rhodothalassium salexigens	76.4524	125	1197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Rhodothalassiaceae;g__Rhodothalassium	95.0	97.98	95.92	0.96	0.92	5	-
GCF_012274265.1	s__Sphingopyxis microcysteis	76.4333	90	1197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	96.26	96.26	0.86	0.86	2	-
GCF_900184795.1	s__Phaeospirillum sp900184795	76.3992	81	1197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018987265.1	s__Rhizobium sp018987265	76.3598	80	1197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017877055.1	s__Neorhizobium galegae_D	76.1956	88	1197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009915765.1	s__Pannonibacter sp009915765	76.1385	107	1197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter	95.0	98.76	98.76	0.96	0.96	2	-
GCF_012650175.1	s__Sphingomonas sp012650175	76.0753	108	1197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420765.1	s__Sandarakinorhabdus limnophila	76.0603	88	1197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandarakinorhabdus	95.0	96.49	96.49	0.92	0.92	2	-
GCF_000282895.1	s__Sphingomonas sp000282895	76.0244	99	1197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900176475.1	s__Tropicibacter naphthalenivorans	75.7826	54	1197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicibacter	95.0	99.99	99.99	0.99	0.99	2	-
GCA_003695555.1	s__J084 sp003695555	75.4669	60	1197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Rhodothalassiaceae;g__J084	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007131945.1	s__Pararhodobacter sp007131945	75.3523	70	1197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	99.16	99.15	0.86	0.82	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:25,119] [INFO] GTDB search result was written to GCF_028463845.1_ASM2846384v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:25,120] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:25,126] [INFO] DFAST_QC result json was written to GCF_028463845.1_ASM2846384v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:25,126] [INFO] DFAST_QC completed!
[2024-01-24 13:58:25,127] [INFO] Total running time: 0h1m27s