[2024-01-24 14:05:16,111] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:16,113] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:16,114] [INFO] DQC Reference Directory: /var/lib/cwl/stg62303fa0-86cd-4cdf-a672-188b14715ae9/dqc_reference
[2024-01-24 14:05:17,395] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:17,396] [INFO] Task started: Prodigal
[2024-01-24 14:05:17,396] [INFO] Running command: gunzip -c /var/lib/cwl/stg01848c8d-f442-444d-843b-7bb5cc0a8556/GCF_003259505.1_ASM325950v1_genomic.fna.gz | prodigal -d GCF_003259505.1_ASM325950v1_genomic.fna/cds.fna -a GCF_003259505.1_ASM325950v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:38,683] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:38,684] [INFO] Task started: HMMsearch
[2024-01-24 14:05:38,684] [INFO] Running command: hmmsearch --tblout GCF_003259505.1_ASM325950v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62303fa0-86cd-4cdf-a672-188b14715ae9/dqc_reference/reference_markers.hmm GCF_003259505.1_ASM325950v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:39,003] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:39,004] [INFO] Found 6/6 markers.
[2024-01-24 14:05:39,053] [INFO] Query marker FASTA was written to GCF_003259505.1_ASM325950v1_genomic.fna/markers.fasta
[2024-01-24 14:05:39,054] [INFO] Task started: Blastn
[2024-01-24 14:05:39,054] [INFO] Running command: blastn -query GCF_003259505.1_ASM325950v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62303fa0-86cd-4cdf-a672-188b14715ae9/dqc_reference/reference_markers.fasta -out GCF_003259505.1_ASM325950v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:39,665] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:39,669] [INFO] Selected 13 target genomes.
[2024-01-24 14:05:39,670] [INFO] Target genome list was writen to GCF_003259505.1_ASM325950v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:39,746] [INFO] Task started: fastANI
[2024-01-24 14:05:39,746] [INFO] Running command: fastANI --query /var/lib/cwl/stg01848c8d-f442-444d-843b-7bb5cc0a8556/GCF_003259505.1_ASM325950v1_genomic.fna.gz --refList GCF_003259505.1_ASM325950v1_genomic.fna/target_genomes.txt --output GCF_003259505.1_ASM325950v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:51,316] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:51,316] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62303fa0-86cd-4cdf-a672-188b14715ae9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:51,317] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62303fa0-86cd-4cdf-a672-188b14715ae9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:51,332] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:05:51,332] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:05:51,332] [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
Algoriphagus yeomjeoni	strain=DSM 23446	GCA_003259505.1	291403	291403	type	True	100.0	1640	1641	95	conclusive
Algoriphagus locisalis	strain=DSM 23445	GCA_900116615.1	305507	305507	type	True	81.9466	999	1641	95	below_threshold
Algoriphagus aquimarinus	strain=DSM 23399	GCA_900112005.1	237018	237018	type	True	80.8076	870	1641	95	below_threshold
Algoriphagus chordae	strain=DSM 19830	GCA_003254055.1	237019	237019	type	True	80.6995	806	1641	95	below_threshold
Algoriphagus antarcticus	strain=DSM 15986	GCA_003387655.1	238540	238540	type	True	80.3671	843	1641	95	below_threshold
Algoriphagus antarcticus	strain=DSM 15986	GCA_002150685.1	238540	238540	type	True	80.3441	831	1641	95	below_threshold
Algoriphagus ratkowskyi	strain=DSM 22686	GCA_002150505.1	57028	57028	type	True	79.8413	754	1641	95	below_threshold
Algoriphagus ratkowskyi	strain=DSM 22686	GCA_003254355.1	57028	57028	type	True	79.8362	755	1641	95	below_threshold
Belliella aquatica	strain=JCM 19468	GCA_022549755.1	1323734	1323734	type	True	76.9283	100	1641	95	below_threshold
Echinicola marina	strain=SCS 3-6	GCA_020463795.1	2859768	2859768	type	True	76.3848	103	1641	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:51,334] [INFO] DFAST Taxonomy check result was written to GCF_003259505.1_ASM325950v1_genomic.fna/tc_result.tsv
[2024-01-24 14:05:51,335] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:51,335] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:51,336] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62303fa0-86cd-4cdf-a672-188b14715ae9/dqc_reference/checkm_data
[2024-01-24 14:05:51,338] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:51,390] [INFO] Task started: CheckM
[2024-01-24 14:05:51,390] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003259505.1_ASM325950v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003259505.1_ASM325950v1_genomic.fna/checkm_input GCF_003259505.1_ASM325950v1_genomic.fna/checkm_result
[2024-01-24 14:06:54,243] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:54,245] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:54,267] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:54,267] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:54,268] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003259505.1_ASM325950v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:54,268] [INFO] Task started: Blastn
[2024-01-24 14:06:54,268] [INFO] Running command: blastn -query GCF_003259505.1_ASM325950v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62303fa0-86cd-4cdf-a672-188b14715ae9/dqc_reference/reference_markers_gtdb.fasta -out GCF_003259505.1_ASM325950v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:55,048] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:55,051] [INFO] Selected 8 target genomes.
[2024-01-24 14:06:55,051] [INFO] Target genome list was writen to GCF_003259505.1_ASM325950v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:55,057] [INFO] Task started: fastANI
[2024-01-24 14:06:55,057] [INFO] Running command: fastANI --query /var/lib/cwl/stg01848c8d-f442-444d-843b-7bb5cc0a8556/GCF_003259505.1_ASM325950v1_genomic.fna.gz --refList GCF_003259505.1_ASM325950v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003259505.1_ASM325950v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:04,133] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:04,148] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:04,148] [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_003259505.1	s__Algoriphagus yeomjeoni	100.0	1640	1641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900116615.1	s__Algoriphagus locisalis	81.9612	997	1641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112005.1	s__Algoriphagus aquimarinus	80.822	869	1641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997215.1	s__Algoriphagus aquimarinus_A	80.7955	921	1641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254055.1	s__Algoriphagus chordae	80.7185	804	1641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014838715.1	s__Algoriphagus sp014838715	80.4578	747	1641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002150685.1	s__Algoriphagus antarcticus	80.3443	831	1641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002150505.1	s__Algoriphagus ratkowskyi	79.8378	754	1641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	99.99	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:04,150] [INFO] GTDB search result was written to GCF_003259505.1_ASM325950v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:04,150] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:04,153] [INFO] DFAST_QC result json was written to GCF_003259505.1_ASM325950v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:04,153] [INFO] DFAST_QC completed!
[2024-01-24 14:07:04,153] [INFO] Total running time: 0h1m48s