[2024-01-24 13:17:30,177] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:30,178] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:30,179] [INFO] DQC Reference Directory: /var/lib/cwl/stge7923160-541e-42a3-8471-ba14f730207e/dqc_reference
[2024-01-24 13:17:31,449] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:31,450] [INFO] Task started: Prodigal
[2024-01-24 13:17:31,451] [INFO] Running command: gunzip -c /var/lib/cwl/stgee8a0e88-4269-4dae-bb0c-662317cb03f3/GCF_003664585.1_ASM366458v1_genomic.fna.gz | prodigal -d GCF_003664585.1_ASM366458v1_genomic.fna/cds.fna -a GCF_003664585.1_ASM366458v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:42,061] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:42,061] [INFO] Task started: HMMsearch
[2024-01-24 13:17:42,061] [INFO] Running command: hmmsearch --tblout GCF_003664585.1_ASM366458v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7923160-541e-42a3-8471-ba14f730207e/dqc_reference/reference_markers.hmm GCF_003664585.1_ASM366458v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:42,360] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:42,361] [INFO] Found 6/6 markers.
[2024-01-24 13:17:42,401] [INFO] Query marker FASTA was written to GCF_003664585.1_ASM366458v1_genomic.fna/markers.fasta
[2024-01-24 13:17:42,401] [INFO] Task started: Blastn
[2024-01-24 13:17:42,401] [INFO] Running command: blastn -query GCF_003664585.1_ASM366458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7923160-541e-42a3-8471-ba14f730207e/dqc_reference/reference_markers.fasta -out GCF_003664585.1_ASM366458v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:43,532] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:43,538] [INFO] Selected 14 target genomes.
[2024-01-24 13:17:43,538] [INFO] Target genome list was writen to GCF_003664585.1_ASM366458v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:43,549] [INFO] Task started: fastANI
[2024-01-24 13:17:43,549] [INFO] Running command: fastANI --query /var/lib/cwl/stgee8a0e88-4269-4dae-bb0c-662317cb03f3/GCF_003664585.1_ASM366458v1_genomic.fna.gz --refList GCF_003664585.1_ASM366458v1_genomic.fna/target_genomes.txt --output GCF_003664585.1_ASM366458v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:55,785] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:55,785] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7923160-541e-42a3-8471-ba14f730207e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:55,786] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7923160-541e-42a3-8471-ba14f730207e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:55,797] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:55,797] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:55,797] [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
Sinirhodobacter hankyongi	strain=BO-81	GCA_003664585.1	2294033	2294033	type	True	100.0	1237	1239	95	conclusive
Sinirhodobacter ferrireducens	strain=CCTCC AB2012026	GCA_004022265.1	1215032	1215032	type	True	94.6831	1055	1239	95	below_threshold
Sinirhodobacter huangdaonensis	strain=CGMCC 1.12963	GCA_004022465.1	2501515	2501515	type	True	93.8857	1061	1239	95	below_threshold
Rhodobacter capsulatus	strain=DSM 1710	GCA_003254295.1	1061	1061	type	True	81.9404	696	1239	95	below_threshold
Rhodobacter viridis	strain=JA737	GCA_003217355.1	1054202	1054202	type	True	81.8452	690	1239	95	below_threshold
Thioclava nitratireducens	strain=25B10_4	GCA_001940525.2	1915078	1915078	type	True	80.1784	605	1239	95	below_threshold
Phaeovulum vinaykumarii	strain=DSM 18714	GCA_900156695.1	407234	407234	type	True	80.1731	596	1239	95	below_threshold
Phaeovulum vinaykumarii	strain=JA123	GCA_900217755.1	407234	407234	type	True	80.1669	591	1239	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	79.8511	581	1239	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	79.8378	536	1239	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	79.7558	546	1239	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	79.3557	482	1239	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	78.9811	488	1239	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	78.6038	447	1239	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:55,799] [INFO] DFAST Taxonomy check result was written to GCF_003664585.1_ASM366458v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:55,800] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:55,800] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:55,800] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7923160-541e-42a3-8471-ba14f730207e/dqc_reference/checkm_data
[2024-01-24 13:17:55,801] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:55,851] [INFO] Task started: CheckM
[2024-01-24 13:17:55,851] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003664585.1_ASM366458v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003664585.1_ASM366458v1_genomic.fna/checkm_input GCF_003664585.1_ASM366458v1_genomic.fna/checkm_result
[2024-01-24 13:18:58,857] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:58,858] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:58,879] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:58,880] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:58,880] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003664585.1_ASM366458v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:58,881] [INFO] Task started: Blastn
[2024-01-24 13:18:58,881] [INFO] Running command: blastn -query GCF_003664585.1_ASM366458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7923160-541e-42a3-8471-ba14f730207e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003664585.1_ASM366458v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:01,014] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:01,018] [INFO] Selected 8 target genomes.
[2024-01-24 13:19:01,018] [INFO] Target genome list was writen to GCF_003664585.1_ASM366458v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:01,030] [INFO] Task started: fastANI
[2024-01-24 13:19:01,030] [INFO] Running command: fastANI --query /var/lib/cwl/stgee8a0e88-4269-4dae-bb0c-662317cb03f3/GCF_003664585.1_ASM366458v1_genomic.fna.gz --refList GCF_003664585.1_ASM366458v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003664585.1_ASM366458v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:08,378] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:08,386] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:08,386] [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_003664585.1	s__Paenirhodobacter hankyongi	100.0	1237	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004022265.1	s__Paenirhodobacter ferrireducens	94.664	1056	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	96.45	95.14	0.91	0.87	4	-
GCF_001856665.1	s__LPB0142 sp001856665	83.2187	777	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LPB0142	95.0	98.52	98.52	0.91	0.91	2	-
GCA_003249215.1	s__SZUA-611 sp003249215	82.9946	662	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SZUA-611	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000740785.1	s__Paenirhodobacter enshiensis	82.5821	677	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002452815.1	s__UBA6796 sp002452815	82.1291	695	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA6796	95.0	97.98	97.98	0.95	0.95	2	-
GCF_004022215.1	s__Paenirhodobacter populi	82.032	670	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	97.06	96.55	0.86	0.79	5	-
GCF_005144475.1	s__Rhodobacter capsulatus_C	81.7953	691	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:08,388] [INFO] GTDB search result was written to GCF_003664585.1_ASM366458v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:08,389] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:08,391] [INFO] DFAST_QC result json was written to GCF_003664585.1_ASM366458v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:08,392] [INFO] DFAST_QC completed!
[2024-01-24 13:19:08,392] [INFO] Total running time: 0h1m38s