[2024-01-24 13:17:55,271] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:55,274] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:55,274] [INFO] DQC Reference Directory: /var/lib/cwl/stg00e5e2b8-cde6-4873-bad5-be53928a3ca2/dqc_reference
[2024-01-24 13:17:56,462] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:56,463] [INFO] Task started: Prodigal
[2024-01-24 13:17:56,463] [INFO] Running command: gunzip -c /var/lib/cwl/stge0ebcdd7-2918-4d8f-a265-4b0afe46867e/GCF_900101705.1_IMG-taxon_2622736587_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900101705.1_IMG-taxon_2622736587_annotated_assembly_genomic.fna/cds.fna -a GCF_900101705.1_IMG-taxon_2622736587_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:16,515] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:16,515] [INFO] Task started: HMMsearch
[2024-01-24 13:18:16,516] [INFO] Running command: hmmsearch --tblout GCF_900101705.1_IMG-taxon_2622736587_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00e5e2b8-cde6-4873-bad5-be53928a3ca2/dqc_reference/reference_markers.hmm GCF_900101705.1_IMG-taxon_2622736587_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:16,804] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:16,806] [INFO] Found 6/6 markers.
[2024-01-24 13:18:16,848] [INFO] Query marker FASTA was written to GCF_900101705.1_IMG-taxon_2622736587_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:18:16,848] [INFO] Task started: Blastn
[2024-01-24 13:18:16,848] [INFO] Running command: blastn -query GCF_900101705.1_IMG-taxon_2622736587_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg00e5e2b8-cde6-4873-bad5-be53928a3ca2/dqc_reference/reference_markers.fasta -out GCF_900101705.1_IMG-taxon_2622736587_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:17,441] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:17,446] [INFO] Selected 17 target genomes.
[2024-01-24 13:18:17,447] [INFO] Target genome list was writen to GCF_900101705.1_IMG-taxon_2622736587_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:18:17,490] [INFO] Task started: fastANI
[2024-01-24 13:18:17,490] [INFO] Running command: fastANI --query /var/lib/cwl/stge0ebcdd7-2918-4d8f-a265-4b0afe46867e/GCF_900101705.1_IMG-taxon_2622736587_annotated_assembly_genomic.fna.gz --refList GCF_900101705.1_IMG-taxon_2622736587_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900101705.1_IMG-taxon_2622736587_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:31,798] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:31,799] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00e5e2b8-cde6-4873-bad5-be53928a3ca2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:31,799] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00e5e2b8-cde6-4873-bad5-be53928a3ca2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:31,812] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:18:31,812] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:31,812] [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=DSM 23095	GCA_900101705.1	686796	686796	type	True	100.0	1488	1500	95	conclusive
Algoriphagus faecimaris	strain=JCM 16561	GCA_002150585.1	686796	686796	type	True	99.9619	1467	1500	95	conclusive
Algoriphagus hitonicola	strain=DSM 19315	GCA_900113375.1	435880	435880	type	True	80.9894	769	1500	95	below_threshold
Algoriphagus marincola	strain=DSM 16067	GCA_000429405.1	264027	264027	type	True	79.1473	370	1500	95	below_threshold
Algoriphagus algorifonticola	strain=hg1	GCA_007655305.1	2593007	2593007	type	True	78.6365	370	1500	95	below_threshold
Algoriphagus aquimaris	strain=F21	GCA_004358035.1	2547398	2547398	type	True	78.5382	371	1500	95	below_threshold
Algoriphagus formosus	strain=XAY3209	GCA_002807035.1	2007308	2007308	type	True	78.5282	373	1500	95	below_threshold
Algoriphagus ornithinivorans	strain=DSM 15282	GCA_900115305.1	226506	226506	type	True	78.474	347	1500	95	below_threshold
Algoriphagus zhangzhouensis	strain=DSM 25035	GCA_900148515.1	1073327	1073327	type	True	77.7259	296	1500	95	below_threshold
Algoriphagus zhangzhouensis	strain=CGMCC 1.11027	GCA_004366575.1	1073327	1073327	type	True	77.6996	293	1500	95	below_threshold
Algoriphagus boritolerans	strain=DSM 17298	GCA_900108085.1	308111	308111	type	True	77.1184	218	1500	95	below_threshold
Algoriphagus aquimarinus	strain=DSM 23399	GCA_900112005.1	237018	237018	type	True	76.767	201	1500	95	below_threshold
Mongoliitalea daihaiensis	strain=X100-76	GCA_021596945.1	2782006	2782006	type	True	76.5674	108	1500	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:31,815] [INFO] DFAST Taxonomy check result was written to GCF_900101705.1_IMG-taxon_2622736587_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:18:31,815] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:31,815] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:31,816] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00e5e2b8-cde6-4873-bad5-be53928a3ca2/dqc_reference/checkm_data
[2024-01-24 13:18:31,818] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:31,868] [INFO] Task started: CheckM
[2024-01-24 13:18:31,869] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900101705.1_IMG-taxon_2622736587_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900101705.1_IMG-taxon_2622736587_annotated_assembly_genomic.fna/checkm_input GCF_900101705.1_IMG-taxon_2622736587_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:19:32,640] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:32,641] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:32,669] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:32,669] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:32,670] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900101705.1_IMG-taxon_2622736587_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:19:32,670] [INFO] Task started: Blastn
[2024-01-24 13:19:32,670] [INFO] Running command: blastn -query GCF_900101705.1_IMG-taxon_2622736587_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg00e5e2b8-cde6-4873-bad5-be53928a3ca2/dqc_reference/reference_markers_gtdb.fasta -out GCF_900101705.1_IMG-taxon_2622736587_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:33,594] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:33,599] [INFO] Selected 18 target genomes.
[2024-01-24 13:19:33,599] [INFO] Target genome list was writen to GCF_900101705.1_IMG-taxon_2622736587_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:33,619] [INFO] Task started: fastANI
[2024-01-24 13:19:33,620] [INFO] Running command: fastANI --query /var/lib/cwl/stge0ebcdd7-2918-4d8f-a265-4b0afe46867e/GCF_900101705.1_IMG-taxon_2622736587_annotated_assembly_genomic.fna.gz --refList GCF_900101705.1_IMG-taxon_2622736587_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900101705.1_IMG-taxon_2622736587_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:48,047] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:48,064] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:48,065] [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	100.0	1488	1500	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	80.9837	768	1500	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	79.1597	369	1500	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	78.6788	366	1500	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002807035.1	s__Algoriphagus formosus	78.5016	375	1500	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	97.55	97.55	0.93	0.93	2	-
GCF_900115305.1	s__Algoriphagus ornithinivorans	78.4955	345	1500	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	95.91	95.63	0.88	0.85	7	-
GCF_000526355.1	s__Algoriphagus marincola_A	78.2951	384	1500	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900148515.1	s__Algoriphagus zhangzhouensis	77.7259	296	1500	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	77.5275	298	1500	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	77.2594	288	1500	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018336015.1	s__Algoriphagus sp018336015	77.167	216	1500	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	77.1276	217	1500	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.80	99.80	0.99	0.99	2	-
GCF_014324365.1	s__Algoriphagus sp014324365	77.1261	254	1500	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	76.9695	185	1500	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	76.9427	200	1500	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	76.7751	200	1500	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	76.7208	76	1500	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 13:19:48,067] [INFO] GTDB search result was written to GCF_900101705.1_IMG-taxon_2622736587_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:48,068] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:48,073] [INFO] DFAST_QC result json was written to GCF_900101705.1_IMG-taxon_2622736587_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:19:48,074] [INFO] DFAST_QC completed!
[2024-01-24 13:19:48,074] [INFO] Total running time: 0h1m53s