[2024-01-24 12:13:28,925] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:28,927] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:28,927] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1f42677-9f2e-4861-9c44-c390546065d7/dqc_reference
[2024-01-24 12:13:30,471] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:30,471] [INFO] Task started: Prodigal
[2024-01-24 12:13:30,472] [INFO] Running command: gunzip -c /var/lib/cwl/stg08b4a732-9edb-4db3-8e7a-9c42e87b73c6/GCF_004362805.1_ASM436280v1_genomic.fna.gz | prodigal -d GCF_004362805.1_ASM436280v1_genomic.fna/cds.fna -a GCF_004362805.1_ASM436280v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:50,686] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:50,686] [INFO] Task started: HMMsearch
[2024-01-24 12:13:50,686] [INFO] Running command: hmmsearch --tblout GCF_004362805.1_ASM436280v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1f42677-9f2e-4861-9c44-c390546065d7/dqc_reference/reference_markers.hmm GCF_004362805.1_ASM436280v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:51,016] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:51,017] [INFO] Found 6/6 markers.
[2024-01-24 12:13:51,056] [INFO] Query marker FASTA was written to GCF_004362805.1_ASM436280v1_genomic.fna/markers.fasta
[2024-01-24 12:13:51,057] [INFO] Task started: Blastn
[2024-01-24 12:13:51,057] [INFO] Running command: blastn -query GCF_004362805.1_ASM436280v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1f42677-9f2e-4861-9c44-c390546065d7/dqc_reference/reference_markers.fasta -out GCF_004362805.1_ASM436280v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:51,716] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:51,730] [INFO] Selected 14 target genomes.
[2024-01-24 12:13:51,731] [INFO] Target genome list was writen to GCF_004362805.1_ASM436280v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:51,821] [INFO] Task started: fastANI
[2024-01-24 12:13:51,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg08b4a732-9edb-4db3-8e7a-9c42e87b73c6/GCF_004362805.1_ASM436280v1_genomic.fna.gz --refList GCF_004362805.1_ASM436280v1_genomic.fna/target_genomes.txt --output GCF_004362805.1_ASM436280v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:04,333] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:04,334] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1f42677-9f2e-4861-9c44-c390546065d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:04,334] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1f42677-9f2e-4861-9c44-c390546065d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:04,347] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:04,348] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:04,348] [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 boseongensis	strain=CECT 8446	GCA_004362805.1	1442587	1442587	type	True	100.0	1385	1385	95	conclusive
Algoriphagus mannitolivorans	strain=DSM 15301	GCA_000429425.1	226504	226504	type	True	80.0675	659	1385	95	below_threshold
Algoriphagus sanaruensis	strain=M8-2	GCA_001593605.1	1727163	1727163	type	True	78.376	422	1385	95	below_threshold
Algoriphagus aquaeductus	strain=T4	GCA_003253485.1	475299	475299	type	True	78.2148	425	1385	95	below_threshold
Algoriphagus lacus	strain=N3	GCA_003583985.1	2056311	2056311	type	True	78.1412	449	1385	95	below_threshold
Algoriphagus terrigena	strain=DSM 22685	GCA_000429445.1	344884	344884	type	True	77.638	275	1385	95	below_threshold
Algoriphagus ornithinivorans	strain=DSM 15282	GCA_900115305.1	226506	226506	type	True	77.6141	301	1385	95	below_threshold
Algoriphagus boritolerans	strain=DSM 17298	GCA_900108085.1	308111	308111	type	True	77.5613	340	1385	95	below_threshold
Algoriphagus pacificus	strain=YJ13C	GCA_017254845.1	2811234	2811234	type	True	77.3516	282	1385	95	below_threshold
Algoriphagus zhangzhouensis	strain=CGMCC 1.11027	GCA_004366575.1	1073327	1073327	type	True	77.2889	317	1385	95	below_threshold
Algoriphagus zhangzhouensis	strain=DSM 25035	GCA_900148515.1	1073327	1073327	type	True	77.1866	318	1385	95	below_threshold
Algoriphagus marinus	strain=am2	GCA_001936475.1	1925762	1925762	type	True	77.0037	262	1385	95	below_threshold
Mongoliitalea lutea	strain=KCTC 23224	GCA_014652135.1	849756	849756	type	True	76.7039	119	1385	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:04,349] [INFO] DFAST Taxonomy check result was written to GCF_004362805.1_ASM436280v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:04,350] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:04,350] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:04,350] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1f42677-9f2e-4861-9c44-c390546065d7/dqc_reference/checkm_data
[2024-01-24 12:14:04,352] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:04,392] [INFO] Task started: CheckM
[2024-01-24 12:14:04,392] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004362805.1_ASM436280v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004362805.1_ASM436280v1_genomic.fna/checkm_input GCF_004362805.1_ASM436280v1_genomic.fna/checkm_result
[2024-01-24 12:15:02,321] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:02,322] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:02,342] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:02,342] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:02,343] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004362805.1_ASM436280v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:02,343] [INFO] Task started: Blastn
[2024-01-24 12:15:02,343] [INFO] Running command: blastn -query GCF_004362805.1_ASM436280v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1f42677-9f2e-4861-9c44-c390546065d7/dqc_reference/reference_markers_gtdb.fasta -out GCF_004362805.1_ASM436280v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:03,201] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:03,213] [INFO] Selected 17 target genomes.
[2024-01-24 12:15:03,213] [INFO] Target genome list was writen to GCF_004362805.1_ASM436280v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:03,248] [INFO] Task started: fastANI
[2024-01-24 12:15:03,249] [INFO] Running command: fastANI --query /var/lib/cwl/stg08b4a732-9edb-4db3-8e7a-9c42e87b73c6/GCF_004362805.1_ASM436280v1_genomic.fna.gz --refList GCF_004362805.1_ASM436280v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004362805.1_ASM436280v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:17,057] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:17,073] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:17,073] [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_004362805.1	s__Algoriphagus boseongensis	100.0	1385	1385	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_000429425.1	s__Algoriphagus mannitolivorans	80.0701	658	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001593605.1	s__Algoriphagus sanaruensis	78.3851	420	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014324365.1	s__Algoriphagus sp014324365	78.2708	448	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253485.1	s__Algoriphagus aquaeductus	78.2015	426	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583985.1	s__Algoriphagus lacus	78.1357	451	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002002735.1	s__Algoriphagus sp002002735	77.696	404	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115305.1	s__Algoriphagus ornithinivorans	77.6235	300	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	95.91	95.63	0.88	0.85	7	-
GCF_017254845.1	s__Algoriphagus sp017254845	77.3709	280	1385	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	77.3678	188	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903952135.1	s__Algoriphagus sp903952135	77.3232	172	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.47	99.47	0.91	0.91	2	-
GCF_007997215.1	s__Algoriphagus aquimarinus_A	77.2557	213	1385	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	77.2542	214	1385	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	77.2036	315	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001936475.1	s__Algoriphagus marinus	77.0037	262	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113375.1	s__Algoriphagus hitonicola	76.9587	243	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652135.1	s__Mongoliitalea lutea	76.704	120	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliitalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:17,075] [INFO] GTDB search result was written to GCF_004362805.1_ASM436280v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:17,076] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:17,080] [INFO] DFAST_QC result json was written to GCF_004362805.1_ASM436280v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:17,080] [INFO] DFAST_QC completed!
[2024-01-24 12:15:17,080] [INFO] Total running time: 0h1m48s