[2024-01-24 11:42:20,314] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:42:20,316] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:42:20,316] [INFO] DQC Reference Directory: /var/lib/cwl/stg402c0dfa-07a3-44e5-a236-e3180e1a4f74/dqc_reference
[2024-01-24 11:42:24,524] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:42:24,525] [INFO] Task started: Prodigal
[2024-01-24 11:42:24,526] [INFO] Running command: gunzip -c /var/lib/cwl/stg84f4662c-f3f0-4591-b0ea-9787fb080ba1/GCF_017254845.1_ASM1725484v1_genomic.fna.gz | prodigal -d GCF_017254845.1_ASM1725484v1_genomic.fna/cds.fna -a GCF_017254845.1_ASM1725484v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:42:47,693] [INFO] Task succeeded: Prodigal
[2024-01-24 11:42:47,693] [INFO] Task started: HMMsearch
[2024-01-24 11:42:47,694] [INFO] Running command: hmmsearch --tblout GCF_017254845.1_ASM1725484v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg402c0dfa-07a3-44e5-a236-e3180e1a4f74/dqc_reference/reference_markers.hmm GCF_017254845.1_ASM1725484v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:42:47,990] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:42:47,991] [INFO] Found 6/6 markers.
[2024-01-24 11:42:48,044] [INFO] Query marker FASTA was written to GCF_017254845.1_ASM1725484v1_genomic.fna/markers.fasta
[2024-01-24 11:42:48,044] [INFO] Task started: Blastn
[2024-01-24 11:42:48,045] [INFO] Running command: blastn -query GCF_017254845.1_ASM1725484v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg402c0dfa-07a3-44e5-a236-e3180e1a4f74/dqc_reference/reference_markers.fasta -out GCF_017254845.1_ASM1725484v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:42:48,648] [INFO] Task succeeded: Blastn
[2024-01-24 11:42:48,652] [INFO] Selected 16 target genomes.
[2024-01-24 11:42:48,653] [INFO] Target genome list was writen to GCF_017254845.1_ASM1725484v1_genomic.fna/target_genomes.txt
[2024-01-24 11:42:48,661] [INFO] Task started: fastANI
[2024-01-24 11:42:48,661] [INFO] Running command: fastANI --query /var/lib/cwl/stg84f4662c-f3f0-4591-b0ea-9787fb080ba1/GCF_017254845.1_ASM1725484v1_genomic.fna.gz --refList GCF_017254845.1_ASM1725484v1_genomic.fna/target_genomes.txt --output GCF_017254845.1_ASM1725484v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:43:03,033] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:03,033] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg402c0dfa-07a3-44e5-a236-e3180e1a4f74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:43:03,034] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg402c0dfa-07a3-44e5-a236-e3180e1a4f74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:43:03,045] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:43:03,046] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:43:03,046] [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 pacificus	strain=YJ13C	GCA_017254845.1	2811234	2811234	type	True	100.0	1748	1750	95	conclusive
Algoriphagus iocasae	strain=DSM 102044	GCA_014206875.1	1836499	1836499	type	True	80.0991	861	1750	95	below_threshold
Algoriphagus halophilus	strain=DSM 15292	GCA_900129785.1	226505	226505	type	True	80.0291	728	1750	95	below_threshold
Algoriphagus lutimaris	strain=KCTC 22630	GCA_017051705.1	613197	613197	type	True	79.8077	659	1750	95	below_threshold
Algoriphagus machipongonensis	strain=PR1	GCA_000166275.1	388413	388413	type	True	78.9478	664	1750	95	below_threshold
Algoriphagus chordae	strain=DSM 19830	GCA_003254055.1	237019	237019	type	True	77.92	349	1750	95	below_threshold
Algoriphagus yeomjeoni	strain=DSM 23446	GCA_003259505.1	291403	291403	type	True	77.83	428	1750	95	below_threshold
Algoriphagus aquimarinus	strain=DSM 23399	GCA_900112005.1	237018	237018	type	True	77.8161	359	1750	95	below_threshold
Algoriphagus zhangzhouensis	strain=DSM 25035	GCA_900148515.1	1073327	1073327	type	True	77.5779	371	1750	95	below_threshold
Algoriphagus zhangzhouensis	strain=CGMCC 1.11027	GCA_004366575.1	1073327	1073327	type	True	77.5692	367	1750	95	below_threshold
Algoriphagus antarcticus	strain=DSM 15986	GCA_002150685.1	238540	238540	type	True	77.4998	346	1750	95	below_threshold
Algoriphagus marinus	strain=am2	GCA_001936475.1	1925762	1925762	type	True	77.2262	324	1750	95	below_threshold
Algoriphagus kandeliae	strain=XY-J91	GCA_004571135.1	2562278	2562278	type	True	77.1423	227	1750	95	below_threshold
Echinicola salinicaeni	strain=P51	GCA_014280965.1	2762757	2762757	type	True	77.0748	112	1750	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:43:03,048] [INFO] DFAST Taxonomy check result was written to GCF_017254845.1_ASM1725484v1_genomic.fna/tc_result.tsv
[2024-01-24 11:43:03,048] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:43:03,048] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:43:03,049] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg402c0dfa-07a3-44e5-a236-e3180e1a4f74/dqc_reference/checkm_data
[2024-01-24 11:43:03,049] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:43:03,101] [INFO] Task started: CheckM
[2024-01-24 11:43:03,101] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017254845.1_ASM1725484v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017254845.1_ASM1725484v1_genomic.fna/checkm_input GCF_017254845.1_ASM1725484v1_genomic.fna/checkm_result
[2024-01-24 11:44:10,801] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:10,802] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:10,824] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:10,825] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:10,825] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017254845.1_ASM1725484v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:10,825] [INFO] Task started: Blastn
[2024-01-24 11:44:10,826] [INFO] Running command: blastn -query GCF_017254845.1_ASM1725484v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg402c0dfa-07a3-44e5-a236-e3180e1a4f74/dqc_reference/reference_markers_gtdb.fasta -out GCF_017254845.1_ASM1725484v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:11,602] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:11,606] [INFO] Selected 14 target genomes.
[2024-01-24 11:44:11,607] [INFO] Target genome list was writen to GCF_017254845.1_ASM1725484v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:11,618] [INFO] Task started: fastANI
[2024-01-24 11:44:11,618] [INFO] Running command: fastANI --query /var/lib/cwl/stg84f4662c-f3f0-4591-b0ea-9787fb080ba1/GCF_017254845.1_ASM1725484v1_genomic.fna.gz --refList GCF_017254845.1_ASM1725484v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017254845.1_ASM1725484v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:25,378] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:25,395] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:25,395] [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_017254845.1	s__Algoriphagus sp017254845	100.0	1748	1750	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_014206875.1	s__Algoriphagus iocasae	80.0991	861	1750	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129785.1	s__Algoriphagus halophilus	80.01	731	1750	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017051705.1	s__Algoriphagus lutimaris	79.8154	658	1750	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000166275.1	s__Algoriphagus machipongonensis	78.961	662	1750	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	77.9516	389	1750	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	77.9494	346	1750	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	77.8249	317	1750	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259505.1	s__Algoriphagus yeomjeoni	77.8217	429	1750	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	77.8145	359	1750	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900148515.1	s__Algoriphagus zhangzhouensis	77.5694	372	1750	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002002735.1	s__Algoriphagus sp002002735	77.3862	225	1750	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009885605.1	s__Algoriphagus sp009885605	77.341	207	1750	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001936475.1	s__Algoriphagus marinus	77.2262	324	1750	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:25,399] [INFO] GTDB search result was written to GCF_017254845.1_ASM1725484v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:25,400] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:25,405] [INFO] DFAST_QC result json was written to GCF_017254845.1_ASM1725484v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:25,406] [INFO] DFAST_QC completed!
[2024-01-24 11:44:25,406] [INFO] Total running time: 0h2m5s