[2024-01-24 13:09:47,824] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:47,830] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:47,830] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b844c07-2797-4c60-9508-df75d0f31f9d/dqc_reference
[2024-01-24 13:09:49,060] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:49,061] [INFO] Task started: Prodigal
[2024-01-24 13:09:49,061] [INFO] Running command: gunzip -c /var/lib/cwl/stg93514110-8c43-4624-8d35-c4e9eb33ad2b/GCF_002150585.1_ASM215058v1_genomic.fna.gz | prodigal -d GCF_002150585.1_ASM215058v1_genomic.fna/cds.fna -a GCF_002150585.1_ASM215058v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:10,052] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:10,052] [INFO] Task started: HMMsearch
[2024-01-24 13:10:10,052] [INFO] Running command: hmmsearch --tblout GCF_002150585.1_ASM215058v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b844c07-2797-4c60-9508-df75d0f31f9d/dqc_reference/reference_markers.hmm GCF_002150585.1_ASM215058v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:10,368] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:10,369] [INFO] Found 6/6 markers.
[2024-01-24 13:10:10,409] [INFO] Query marker FASTA was written to GCF_002150585.1_ASM215058v1_genomic.fna/markers.fasta
[2024-01-24 13:10:10,410] [INFO] Task started: Blastn
[2024-01-24 13:10:10,410] [INFO] Running command: blastn -query GCF_002150585.1_ASM215058v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b844c07-2797-4c60-9508-df75d0f31f9d/dqc_reference/reference_markers.fasta -out GCF_002150585.1_ASM215058v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:11,027] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:11,030] [INFO] Selected 17 target genomes.
[2024-01-24 13:10:11,030] [INFO] Target genome list was writen to GCF_002150585.1_ASM215058v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:11,036] [INFO] Task started: fastANI
[2024-01-24 13:10:11,037] [INFO] Running command: fastANI --query /var/lib/cwl/stg93514110-8c43-4624-8d35-c4e9eb33ad2b/GCF_002150585.1_ASM215058v1_genomic.fna.gz --refList GCF_002150585.1_ASM215058v1_genomic.fna/target_genomes.txt --output GCF_002150585.1_ASM215058v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:24,993] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:24,993] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b844c07-2797-4c60-9508-df75d0f31f9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:24,994] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b844c07-2797-4c60-9508-df75d0f31f9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:25,006] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:10:25,006] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:25,006] [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 faecimaris	strain=JCM 16561	GCA_002150585.1	686796	686796	type	True	100.0	1486	1494	95	conclusive
Algoriphagus faecimaris	strain=DSM 23095	GCA_900101705.1	686796	686796	type	True	99.986	1468	1494	95	conclusive
Algoriphagus hitonicola	strain=DSM 19315	GCA_900113375.1	435880	435880	type	True	80.9925	785	1494	95	below_threshold
Algoriphagus marincola	strain=DSM 16067	GCA_000429405.1	264027	264027	type	True	79.0569	380	1494	95	below_threshold
Algoriphagus algorifonticola	strain=hg1	GCA_007655305.1	2593007	2593007	type	True	78.922	375	1494	95	below_threshold
Algoriphagus ornithinivorans	strain=DSM 15282	GCA_900115305.1	226506	226506	type	True	78.5824	345	1494	95	below_threshold
Algoriphagus formosus	strain=XAY3209	GCA_002807035.1	2007308	2007308	type	True	78.5622	375	1494	95	below_threshold
Algoriphagus aquimaris	strain=F21	GCA_004358035.1	2547398	2547398	type	True	78.5506	361	1494	95	below_threshold
Algoriphagus zhangzhouensis	strain=DSM 25035	GCA_900148515.1	1073327	1073327	type	True	77.9445	281	1494	95	below_threshold
Algoriphagus zhangzhouensis	strain=CGMCC 1.11027	GCA_004366575.1	1073327	1073327	type	True	77.9138	279	1494	95	below_threshold
Algoriphagus boritolerans	strain=DSM 17298	GCA_900108085.1	308111	308111	type	True	77.2283	220	1494	95	below_threshold
Mongoliitalea daihaiensis	strain=X100-76	GCA_021596945.1	2782006	2782006	type	True	77.0962	105	1494	95	below_threshold
Algoriphagus aquimarinus	strain=DSM 23399	GCA_900112005.1	237018	237018	type	True	76.7877	201	1494	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:25,008] [INFO] DFAST Taxonomy check result was written to GCF_002150585.1_ASM215058v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:25,008] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:25,008] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:25,009] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b844c07-2797-4c60-9508-df75d0f31f9d/dqc_reference/checkm_data
[2024-01-24 13:10:25,010] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:25,055] [INFO] Task started: CheckM
[2024-01-24 13:10:25,056] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002150585.1_ASM215058v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002150585.1_ASM215058v1_genomic.fna/checkm_input GCF_002150585.1_ASM215058v1_genomic.fna/checkm_result
[2024-01-24 13:11:24,891] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:24,893] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:24,918] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:24,919] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:24,919] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002150585.1_ASM215058v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:24,920] [INFO] Task started: Blastn
[2024-01-24 13:11:24,920] [INFO] Running command: blastn -query GCF_002150585.1_ASM215058v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b844c07-2797-4c60-9508-df75d0f31f9d/dqc_reference/reference_markers_gtdb.fasta -out GCF_002150585.1_ASM215058v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:25,694] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:25,699] [INFO] Selected 18 target genomes.
[2024-01-24 13:11:25,699] [INFO] Target genome list was writen to GCF_002150585.1_ASM215058v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:25,711] [INFO] Task started: fastANI
[2024-01-24 13:11:25,711] [INFO] Running command: fastANI --query /var/lib/cwl/stg93514110-8c43-4624-8d35-c4e9eb33ad2b/GCF_002150585.1_ASM215058v1_genomic.fna.gz --refList GCF_002150585.1_ASM215058v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002150585.1_ASM215058v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:39,389] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:39,415] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:39,415] [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_900101705.1	s__Algoriphagus faecimaris	99.986	1468	1494	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.99	99.99	0.98	0.98	2	conclusive
GCF_900113375.1	s__Algoriphagus hitonicola	80.9872	784	1494	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429405.1	s__Algoriphagus marincola	79.0688	379	1494	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	97.35	97.35	0.90	0.90	2	-
GCF_007655305.1	s__Algoriphagus sp007655305	78.9208	375	1494	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526355.1	s__Algoriphagus marincola_A	78.6013	375	1494	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900115305.1	s__Algoriphagus ornithinivorans	78.5932	344	1494	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	95.91	95.63	0.88	0.85	7	-
GCF_002807035.1	s__Algoriphagus formosus	78.5628	375	1494	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	97.55	97.55	0.93	0.93	2	-
GCF_900148515.1	s__Algoriphagus zhangzhouensis	77.9445	281	1494	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000429465.1	s__Algoriphagus vanfongensis	77.7221	284	1494	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373065.1	s__Algoriphagus sp013373065	77.507	273	1494	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	77.2979	240	1494	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108085.1	s__Algoriphagus boritolerans	77.2523	218	1494	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.80	99.80	0.99	0.99	2	-
GCA_018336015.1	s__Algoriphagus sp018336015	77.1916	209	1494	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	77.143	191	1494	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	76.9328	190	1494	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	76.806	199	1494	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005788235.1	s__Algoriphagus sp005788235	76.7253	70	1494	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 13:11:39,416] [INFO] GTDB search result was written to GCF_002150585.1_ASM215058v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:39,417] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:39,420] [INFO] DFAST_QC result json was written to GCF_002150585.1_ASM215058v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:39,421] [INFO] DFAST_QC completed!
[2024-01-24 13:11:39,421] [INFO] Total running time: 0h1m52s