[2024-01-24 13:57:44,002] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:44,004] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:44,004] [INFO] DQC Reference Directory: /var/lib/cwl/stg275bbef1-ce90-4b30-b95c-05a92ed35e75/dqc_reference
[2024-01-24 13:57:45,252] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:45,252] [INFO] Task started: Prodigal
[2024-01-24 13:57:45,253] [INFO] Running command: gunzip -c /var/lib/cwl/stgad122f8e-6c3f-4ebf-ab04-14291af49469/GCF_900100085.1_IMG-taxon_2615840707_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900100085.1_IMG-taxon_2615840707_annotated_assembly_genomic.fna/cds.fna -a GCF_900100085.1_IMG-taxon_2615840707_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:01,884] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:01,885] [INFO] Task started: HMMsearch
[2024-01-24 13:58:01,885] [INFO] Running command: hmmsearch --tblout GCF_900100085.1_IMG-taxon_2615840707_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg275bbef1-ce90-4b30-b95c-05a92ed35e75/dqc_reference/reference_markers.hmm GCF_900100085.1_IMG-taxon_2615840707_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:02,200] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:02,201] [INFO] Found 6/6 markers.
[2024-01-24 13:58:02,249] [INFO] Query marker FASTA was written to GCF_900100085.1_IMG-taxon_2615840707_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:58:02,250] [INFO] Task started: Blastn
[2024-01-24 13:58:02,250] [INFO] Running command: blastn -query GCF_900100085.1_IMG-taxon_2615840707_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg275bbef1-ce90-4b30-b95c-05a92ed35e75/dqc_reference/reference_markers.fasta -out GCF_900100085.1_IMG-taxon_2615840707_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:03,298] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:03,301] [INFO] Selected 17 target genomes.
[2024-01-24 13:58:03,301] [INFO] Target genome list was writen to GCF_900100085.1_IMG-taxon_2615840707_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:58:03,326] [INFO] Task started: fastANI
[2024-01-24 13:58:03,327] [INFO] Running command: fastANI --query /var/lib/cwl/stgad122f8e-6c3f-4ebf-ab04-14291af49469/GCF_900100085.1_IMG-taxon_2615840707_annotated_assembly_genomic.fna.gz --refList GCF_900100085.1_IMG-taxon_2615840707_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900100085.1_IMG-taxon_2615840707_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:20,378] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:20,378] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg275bbef1-ce90-4b30-b95c-05a92ed35e75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:20,379] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg275bbef1-ce90-4b30-b95c-05a92ed35e75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:20,397] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:20,397] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:20,397] [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
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	100.0	1810	1816	95	conclusive
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	80.815	918	1816	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	80.7831	930	1816	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	80.7004	884	1816	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	80.65	864	1816	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	80.1423	809	1816	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	80.1271	836	1816	95	below_threshold
Salipiger aestuarii	strain=AD8	GCA_008930655.1	568098	568098	type	True	80.059	745	1816	95	below_threshold
Salipiger aestuarii	strain=DSM 22011	GCA_003259905.1	568098	568098	type	True	80.0583	754	1816	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	79.7799	688	1816	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	79.0536	537	1816	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.9355	563	1816	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	78.5346	559	1816	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	78.5166	562	1816	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.1438	485	1816	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.8392	443	1816	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.0472	326	1816	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:20,399] [INFO] DFAST Taxonomy check result was written to GCF_900100085.1_IMG-taxon_2615840707_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:58:20,399] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:20,399] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:20,400] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg275bbef1-ce90-4b30-b95c-05a92ed35e75/dqc_reference/checkm_data
[2024-01-24 13:58:20,401] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:20,461] [INFO] Task started: CheckM
[2024-01-24 13:58:20,461] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900100085.1_IMG-taxon_2615840707_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900100085.1_IMG-taxon_2615840707_annotated_assembly_genomic.fna/checkm_input GCF_900100085.1_IMG-taxon_2615840707_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:59:31,854] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:31,856] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:31,876] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:31,876] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:31,877] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900100085.1_IMG-taxon_2615840707_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:59:31,877] [INFO] Task started: Blastn
[2024-01-24 13:59:31,877] [INFO] Running command: blastn -query GCF_900100085.1_IMG-taxon_2615840707_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg275bbef1-ce90-4b30-b95c-05a92ed35e75/dqc_reference/reference_markers_gtdb.fasta -out GCF_900100085.1_IMG-taxon_2615840707_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:33,817] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:33,821] [INFO] Selected 11 target genomes.
[2024-01-24 13:59:33,821] [INFO] Target genome list was writen to GCF_900100085.1_IMG-taxon_2615840707_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:33,959] [INFO] Task started: fastANI
[2024-01-24 13:59:33,959] [INFO] Running command: fastANI --query /var/lib/cwl/stgad122f8e-6c3f-4ebf-ab04-14291af49469/GCF_900100085.1_IMG-taxon_2615840707_annotated_assembly_genomic.fna.gz --refList GCF_900100085.1_IMG-taxon_2615840707_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900100085.1_IMG-taxon_2615840707_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:48,682] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:48,696] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:48,696] [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_900100085.1	s__Salipiger marinus	100.0	1808	1816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.13	98.13	0.95	0.95	2	conclusive
GCF_017311415.1	s__Salipiger abyssi_A	81.5673	854	1816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	81.5557	859	1816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687105.1	s__Salipiger sp001687105	81.2979	930	1816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	96.47	96.47	0.82	0.82	2	-
GCF_015223355.1	s__Salipiger pacificus_B	81.1402	923	1816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002300555.1	s__Salipiger sp002300555	80.8684	674	1816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003111685.1	s__Salipiger pacificus_A	80.8362	890	1816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.69	97.64	0.90	0.89	3	-
GCF_900116195.1	s__Salipiger pacificus	80.8343	915	1816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000153725.1	s__Salipiger bermudensis	80.687	886	1816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.06	97.75	0.87	0.75	4	-
GCF_900102075.1	s__Salipiger thiooxidans	80.6314	868	1816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
GCF_000442255.1	s__Salipiger mucosus	80.1471	797	1816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:48,698] [INFO] GTDB search result was written to GCF_900100085.1_IMG-taxon_2615840707_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:48,699] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:48,702] [INFO] DFAST_QC result json was written to GCF_900100085.1_IMG-taxon_2615840707_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:59:48,702] [INFO] DFAST_QC completed!
[2024-01-24 13:59:48,702] [INFO] Total running time: 0h2m5s