[2024-01-25 18:09:20,307] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:09:20,308] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:09:20,308] [INFO] DQC Reference Directory: /var/lib/cwl/stg238a0060-6cc6-4299-ae18-4ed6b93f84ba/dqc_reference
[2024-01-25 18:09:21,422] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:09:21,423] [INFO] Task started: Prodigal
[2024-01-25 18:09:21,423] [INFO] Running command: gunzip -c /var/lib/cwl/stg1742166d-1ed6-4db6-82d6-e6f2b006497e/GCF_001659685.2_ASM165968v2_genomic.fna.gz | prodigal -d GCF_001659685.2_ASM165968v2_genomic.fna/cds.fna -a GCF_001659685.2_ASM165968v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:09:38,696] [INFO] Task succeeded: Prodigal
[2024-01-25 18:09:38,697] [INFO] Task started: HMMsearch
[2024-01-25 18:09:38,697] [INFO] Running command: hmmsearch --tblout GCF_001659685.2_ASM165968v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg238a0060-6cc6-4299-ae18-4ed6b93f84ba/dqc_reference/reference_markers.hmm GCF_001659685.2_ASM165968v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:09:38,978] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:09:38,979] [INFO] Found 6/6 markers.
[2024-01-25 18:09:39,023] [INFO] Query marker FASTA was written to GCF_001659685.2_ASM165968v2_genomic.fna/markers.fasta
[2024-01-25 18:09:39,024] [INFO] Task started: Blastn
[2024-01-25 18:09:39,024] [INFO] Running command: blastn -query GCF_001659685.2_ASM165968v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg238a0060-6cc6-4299-ae18-4ed6b93f84ba/dqc_reference/reference_markers.fasta -out GCF_001659685.2_ASM165968v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:39,588] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:39,590] [INFO] Selected 15 target genomes.
[2024-01-25 18:09:39,591] [INFO] Target genome list was writen to GCF_001659685.2_ASM165968v2_genomic.fna/target_genomes.txt
[2024-01-25 18:09:39,601] [INFO] Task started: fastANI
[2024-01-25 18:09:39,602] [INFO] Running command: fastANI --query /var/lib/cwl/stg1742166d-1ed6-4db6-82d6-e6f2b006497e/GCF_001659685.2_ASM165968v2_genomic.fna.gz --refList GCF_001659685.2_ASM165968v2_genomic.fna/target_genomes.txt --output GCF_001659685.2_ASM165968v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:09:50,269] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:50,269] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg238a0060-6cc6-4299-ae18-4ed6b93f84ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:09:50,269] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg238a0060-6cc6-4299-ae18-4ed6b93f84ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:09:50,275] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:09:50,275] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:09:50,275] [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
Labilibacter marinus	strain=Y11	GCA_001659685.2	1477105	1477105	type	True	100.0	1966	1970	95	conclusive
Labilibacter sediminis	strain=CG51	GCA_005877885.1	2570926	2570926	type	True	78.3976	369	1970	95	below_threshold
Saccharicrinis fermentans	strain=DSM 9555	GCA_000517085.1	982	982	type	True	78.0961	359	1970	95	below_threshold
Saccharicrinis fermentans	strain=JCM 21142	GCA_000583675.1	982	982	type	True	78.0841	349	1970	95	below_threshold
Saccharicrinis aurantiacus	strain=HQYD1	GCA_001660705.2	1849719	1849719	type	True	78.001	301	1970	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:09:50,279] [INFO] DFAST Taxonomy check result was written to GCF_001659685.2_ASM165968v2_genomic.fna/tc_result.tsv
[2024-01-25 18:09:50,279] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:09:50,279] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:09:50,280] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg238a0060-6cc6-4299-ae18-4ed6b93f84ba/dqc_reference/checkm_data
[2024-01-25 18:09:50,280] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:09:50,340] [INFO] Task started: CheckM
[2024-01-25 18:09:50,340] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001659685.2_ASM165968v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001659685.2_ASM165968v2_genomic.fna/checkm_input GCF_001659685.2_ASM165968v2_genomic.fna/checkm_result
[2024-01-25 18:10:39,863] [INFO] Task succeeded: CheckM
[2024-01-25 18:10:39,864] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:10:39,885] [INFO] ===== Completeness check finished =====
[2024-01-25 18:10:39,885] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:10:39,886] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001659685.2_ASM165968v2_genomic.fna/markers.fasta)
[2024-01-25 18:10:39,886] [INFO] Task started: Blastn
[2024-01-25 18:10:39,887] [INFO] Running command: blastn -query GCF_001659685.2_ASM165968v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg238a0060-6cc6-4299-ae18-4ed6b93f84ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_001659685.2_ASM165968v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:40,676] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:40,679] [INFO] Selected 19 target genomes.
[2024-01-25 18:10:40,679] [INFO] Target genome list was writen to GCF_001659685.2_ASM165968v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:10:40,715] [INFO] Task started: fastANI
[2024-01-25 18:10:40,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg1742166d-1ed6-4db6-82d6-e6f2b006497e/GCF_001659685.2_ASM165968v2_genomic.fna.gz --refList GCF_001659685.2_ASM165968v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001659685.2_ASM165968v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:10:56,545] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:56,551] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:10:56,552] [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_001659685.2	s__Saccharicrinis marinus	100.0	1966	1970	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Saccharicrinis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005877885.1	s__Saccharicrinis sediminis	78.391	369	1970	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Saccharicrinis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000517085.1	s__Saccharicrinis fermentans	78.0961	359	1970	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Saccharicrinis	95.0	99.97	99.97	1.00	1.00	2	-
GCF_001660705.2	s__Saccharicrinis aurantiacus	78.0015	301	1970	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Saccharicrinis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182605.1	s__Saccharicrinis carchari	76.8176	170	1970	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Saccharicrinis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018271995.1	s__Carboxylicivirga linearis	76.7751	110	1970	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Carboxylicivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003249255.1	s__SZUA-582 sp003249255	76.4687	114	1970	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__SZUA-582	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009669305.1	s__Ancylomarina sp009669305	76.1493	78	1970	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Ancylomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016406085.1	s__Aureibaculum sp016406085	74.9911	50	1970	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:10:56,553] [INFO] GTDB search result was written to GCF_001659685.2_ASM165968v2_genomic.fna/result_gtdb.tsv
[2024-01-25 18:10:56,554] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:10:56,556] [INFO] DFAST_QC result json was written to GCF_001659685.2_ASM165968v2_genomic.fna/dqc_result.json
[2024-01-25 18:10:56,556] [INFO] DFAST_QC completed!
[2024-01-25 18:10:56,556] [INFO] Total running time: 0h1m36s