[2024-01-25 18:28:50,560] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:28:50,561] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:28:50,561] [INFO] DQC Reference Directory: /var/lib/cwl/stg269e6b1a-282f-4207-a1c0-2a2eb4ed3ea8/dqc_reference
[2024-01-25 18:28:51,708] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:28:51,708] [INFO] Task started: Prodigal
[2024-01-25 18:28:51,709] [INFO] Running command: gunzip -c /var/lib/cwl/stg08169a82-7513-48b5-86ec-c99ea2c4ba11/GCF_016019885.1_ASM1601988v1_genomic.fna.gz | prodigal -d GCF_016019885.1_ASM1601988v1_genomic.fna/cds.fna -a GCF_016019885.1_ASM1601988v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:28:59,210] [INFO] Task succeeded: Prodigal
[2024-01-25 18:28:59,210] [INFO] Task started: HMMsearch
[2024-01-25 18:28:59,210] [INFO] Running command: hmmsearch --tblout GCF_016019885.1_ASM1601988v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg269e6b1a-282f-4207-a1c0-2a2eb4ed3ea8/dqc_reference/reference_markers.hmm GCF_016019885.1_ASM1601988v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:28:59,382] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:28:59,383] [INFO] Found 6/6 markers.
[2024-01-25 18:28:59,405] [INFO] Query marker FASTA was written to GCF_016019885.1_ASM1601988v1_genomic.fna/markers.fasta
[2024-01-25 18:28:59,405] [INFO] Task started: Blastn
[2024-01-25 18:28:59,405] [INFO] Running command: blastn -query GCF_016019885.1_ASM1601988v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg269e6b1a-282f-4207-a1c0-2a2eb4ed3ea8/dqc_reference/reference_markers.fasta -out GCF_016019885.1_ASM1601988v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:29:00,081] [INFO] Task succeeded: Blastn
[2024-01-25 18:29:00,084] [INFO] Selected 18 target genomes.
[2024-01-25 18:29:00,084] [INFO] Target genome list was writen to GCF_016019885.1_ASM1601988v1_genomic.fna/target_genomes.txt
[2024-01-25 18:29:00,092] [INFO] Task started: fastANI
[2024-01-25 18:29:00,092] [INFO] Running command: fastANI --query /var/lib/cwl/stg08169a82-7513-48b5-86ec-c99ea2c4ba11/GCF_016019885.1_ASM1601988v1_genomic.fna.gz --refList GCF_016019885.1_ASM1601988v1_genomic.fna/target_genomes.txt --output GCF_016019885.1_ASM1601988v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:29:10,124] [INFO] Task succeeded: fastANI
[2024-01-25 18:29:10,125] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg269e6b1a-282f-4207-a1c0-2a2eb4ed3ea8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:29:10,125] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg269e6b1a-282f-4207-a1c0-2a2eb4ed3ea8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:29:10,135] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:29:10,135] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:29:10,136] [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
Aurantiacibacter sediminis	strain=JGD-13	GCA_016019885.1	2793064	2793064	type	True	100.0	886	886	95	conclusive
Aurantiacibacter gangjinensis	strain=K7-2	GCA_001010925.1	502682	502682	type	True	79.3867	484	886	95	below_threshold
Aurantiacibacter gangjinensis	strain=CGMCC 1.15024	GCA_001886695.1	502682	502682	type	True	79.3363	491	886	95	below_threshold
Aurantiacibacter odishensis	strain=KCTC 23981	GCA_003605195.1	1155476	1155476	type	True	79.1113	457	886	95	below_threshold
Aurantiacibacter rhizosphaerae	strain=GH3-10	GCA_009807005.1	2691582	2691582	type	True	78.7277	432	886	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	78.6464	301	886	95	below_threshold
Aurantiacibacter zhengii	strain=V18	GCA_003584125.1	2307003	2307003	type	True	78.6378	452	886	95	below_threshold
Qipengyuania seohaensis	strain=SW-135	GCA_002795865.1	266951	266951	type	True	78.4955	250	886	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	78.465	283	886	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	78.4644	282	886	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	78.3848	297	886	95	below_threshold
Aurantiacibacter atlanticus	strain=s21-N3	GCA_001077815.2	1648404	1648404	type	True	78.2831	345	886	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	78.2581	295	886	95	below_threshold
Aurantiacibacter arachoides	strain=CGMCC 1.15507	GCA_014643415.1	1850444	1850444	type	True	78.1976	380	886	95	below_threshold
Aurantiacibacter arachoides	strain=RC4-10-4	GCA_009827335.1	1850444	1850444	type	True	78.1939	378	886	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	78.1162	252	886	95	below_threshold
Pontixanthobacter aquaemixtae	strain=KCTC 52763	GCA_009827395.1	1958940	1958940	type	True	78.0671	222	886	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	78.0663	249	886	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:29:10,137] [INFO] DFAST Taxonomy check result was written to GCF_016019885.1_ASM1601988v1_genomic.fna/tc_result.tsv
[2024-01-25 18:29:10,138] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:29:10,138] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:29:10,138] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg269e6b1a-282f-4207-a1c0-2a2eb4ed3ea8/dqc_reference/checkm_data
[2024-01-25 18:29:10,139] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:29:10,167] [INFO] Task started: CheckM
[2024-01-25 18:29:10,168] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016019885.1_ASM1601988v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016019885.1_ASM1601988v1_genomic.fna/checkm_input GCF_016019885.1_ASM1601988v1_genomic.fna/checkm_result
[2024-01-25 18:29:35,567] [INFO] Task succeeded: CheckM
[2024-01-25 18:29:35,568] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:29:35,587] [INFO] ===== Completeness check finished =====
[2024-01-25 18:29:35,587] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:29:35,588] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016019885.1_ASM1601988v1_genomic.fna/markers.fasta)
[2024-01-25 18:29:35,588] [INFO] Task started: Blastn
[2024-01-25 18:29:35,588] [INFO] Running command: blastn -query GCF_016019885.1_ASM1601988v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg269e6b1a-282f-4207-a1c0-2a2eb4ed3ea8/dqc_reference/reference_markers_gtdb.fasta -out GCF_016019885.1_ASM1601988v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:29:36,712] [INFO] Task succeeded: Blastn
[2024-01-25 18:29:36,715] [INFO] Selected 15 target genomes.
[2024-01-25 18:29:36,715] [INFO] Target genome list was writen to GCF_016019885.1_ASM1601988v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:29:36,732] [INFO] Task started: fastANI
[2024-01-25 18:29:36,732] [INFO] Running command: fastANI --query /var/lib/cwl/stg08169a82-7513-48b5-86ec-c99ea2c4ba11/GCF_016019885.1_ASM1601988v1_genomic.fna.gz --refList GCF_016019885.1_ASM1601988v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016019885.1_ASM1601988v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:29:45,438] [INFO] Task succeeded: fastANI
[2024-01-25 18:29:45,447] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:29:45,448] [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_016019885.1	s__Alteraurantiacibacter sp016019885	100.0	886	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_902498745.1	s__Alteraurantiacibacter sp902498745	79.7997	548	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605475.1	s__Alteraurantiacibacter aquimixticola_A	79.4811	484	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886695.1	s__Alteraurantiacibacter gangjinensis	79.3363	491	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002367375.1	s__Alteraurantiacibacter sp002367375	79.1357	373	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605195.1	s__Alteraurantiacibacter odishensis	79.1229	455	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004965515.1	s__Alteraurantiacibacter aquimixticola	78.8607	400	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687545.1	s__Paraurantiacibacter namhicola	78.7535	345	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Paraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009807005.1	s__Alteraurantiacibacter rhizosphaerae	78.7379	431	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584125.1	s__Alteraurantiacibacter zhengii	78.657	450	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000756795.1	s__Qipengyuania vulgaris_A	78.399	289	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827335.1	s__Alteraurantiacibacter arachoides	78.1939	378	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009827395.1	s__Pontixanthobacter aquaemixtae	78.0671	222	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763545.1	s__JACXVD01 sp014763545	78.0024	289	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01	95.0	99.92	99.92	0.96	0.96	2	-
GCF_009827655.1	s__Alteraurantiacibacter buctensis	77.8205	268	886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:29:45,449] [INFO] GTDB search result was written to GCF_016019885.1_ASM1601988v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:29:45,449] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:29:45,452] [INFO] DFAST_QC result json was written to GCF_016019885.1_ASM1601988v1_genomic.fna/dqc_result.json
[2024-01-25 18:29:45,452] [INFO] DFAST_QC completed!
[2024-01-25 18:29:45,452] [INFO] Total running time: 0h0m55s