[2024-01-24 13:09:33,893] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:33,895] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:33,895] [INFO] DQC Reference Directory: /var/lib/cwl/stgbee9177e-1c64-4df8-896e-daf9e2302ca4/dqc_reference
[2024-01-24 13:09:35,185] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:35,186] [INFO] Task started: Prodigal
[2024-01-24 13:09:35,186] [INFO] Running command: gunzip -c /var/lib/cwl/stga7adeb88-ff19-4a58-af30-4d6b01cac643/GCF_003584015.1_ASM358401v1_genomic.fna.gz | prodigal -d GCF_003584015.1_ASM358401v1_genomic.fna/cds.fna -a GCF_003584015.1_ASM358401v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:48,164] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:48,164] [INFO] Task started: HMMsearch
[2024-01-24 13:09:48,164] [INFO] Running command: hmmsearch --tblout GCF_003584015.1_ASM358401v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbee9177e-1c64-4df8-896e-daf9e2302ca4/dqc_reference/reference_markers.hmm GCF_003584015.1_ASM358401v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:48,459] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:48,461] [INFO] Found 6/6 markers.
[2024-01-24 13:09:48,501] [INFO] Query marker FASTA was written to GCF_003584015.1_ASM358401v1_genomic.fna/markers.fasta
[2024-01-24 13:09:48,501] [INFO] Task started: Blastn
[2024-01-24 13:09:48,501] [INFO] Running command: blastn -query GCF_003584015.1_ASM358401v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbee9177e-1c64-4df8-896e-daf9e2302ca4/dqc_reference/reference_markers.fasta -out GCF_003584015.1_ASM358401v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:49,501] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:49,504] [INFO] Selected 20 target genomes.
[2024-01-24 13:09:49,505] [INFO] Target genome list was writen to GCF_003584015.1_ASM358401v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:49,511] [INFO] Task started: fastANI
[2024-01-24 13:09:49,511] [INFO] Running command: fastANI --query /var/lib/cwl/stga7adeb88-ff19-4a58-af30-4d6b01cac643/GCF_003584015.1_ASM358401v1_genomic.fna.gz --refList GCF_003584015.1_ASM358401v1_genomic.fna/target_genomes.txt --output GCF_003584015.1_ASM358401v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:02,062] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:02,063] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbee9177e-1c64-4df8-896e-daf9e2302ca4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:02,063] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbee9177e-1c64-4df8-896e-daf9e2302ca4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:02,078] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:02,078] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:02,078] [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 xanthus	strain=CCTCC AB 2015396	GCA_003584015.1	1784712	1784712	type	True	100.0	1380	1386	95	conclusive
Aurantiacibacter suaedae	strain=GH3-15	GCA_005434915.1	2545755	2545755	type	True	88.1123	788	1386	95	below_threshold
Aurantiacibacter luteus	strain=KA37	GCA_001010945.1	1581420	1581420	type	True	80.2333	498	1386	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	79.796	417	1386	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	79.7847	419	1386	95	below_threshold
Aurantiacibacter odishensis	strain=KCTC 23981	GCA_003605195.1	1155476	1155476	type	True	79.7471	529	1386	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	79.6874	447	1386	95	below_threshold
Aurantiacibacter zhengii	strain=V18	GCA_003584125.1	2307003	2307003	type	True	79.5618	473	1386	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	79.5174	462	1386	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	79.2255	388	1386	95	below_threshold
Alteraurantiacibacter aestuarii	strain=JCM 16339	GCA_009827405.1	650004	650004	type	True	79.1992	343	1386	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	79.1604	398	1386	95	below_threshold
Aurantiacibacter gangjinensis	strain=CGMCC 1.15024	GCA_001886695.1	502682	502682	type	True	79.0113	356	1386	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	78.967	378	1386	95	below_threshold
Novosphingobium flavum	strain=NBRC 111647	GCA_014230315.1	1778672	1778672	type	True	78.9552	396	1386	95	below_threshold
Aurantiacibacter gangjinensis	strain=K7-2	GCA_001010925.1	502682	502682	type	True	78.9108	356	1386	95	below_threshold
Erythrobacter tepidarius	strain=DSM 10594	GCA_002155695.1	60454	60454	type	True	78.9059	399	1386	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	78.8276	349	1386	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	78.7487	371	1386	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	78.7343	431	1386	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:02,080] [INFO] DFAST Taxonomy check result was written to GCF_003584015.1_ASM358401v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:02,080] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:02,081] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:02,081] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbee9177e-1c64-4df8-896e-daf9e2302ca4/dqc_reference/checkm_data
[2024-01-24 13:10:02,082] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:02,121] [INFO] Task started: CheckM
[2024-01-24 13:10:02,122] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003584015.1_ASM358401v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003584015.1_ASM358401v1_genomic.fna/checkm_input GCF_003584015.1_ASM358401v1_genomic.fna/checkm_result
[2024-01-24 13:10:40,802] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:40,804] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:40,820] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:40,820] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:40,821] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003584015.1_ASM358401v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:40,821] [INFO] Task started: Blastn
[2024-01-24 13:10:40,821] [INFO] Running command: blastn -query GCF_003584015.1_ASM358401v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbee9177e-1c64-4df8-896e-daf9e2302ca4/dqc_reference/reference_markers_gtdb.fasta -out GCF_003584015.1_ASM358401v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:42,216] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:42,220] [INFO] Selected 16 target genomes.
[2024-01-24 13:10:42,220] [INFO] Target genome list was writen to GCF_003584015.1_ASM358401v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:42,228] [INFO] Task started: fastANI
[2024-01-24 13:10:42,229] [INFO] Running command: fastANI --query /var/lib/cwl/stga7adeb88-ff19-4a58-af30-4d6b01cac643/GCF_003584015.1_ASM358401v1_genomic.fna.gz --refList GCF_003584015.1_ASM358401v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003584015.1_ASM358401v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:52,644] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:52,657] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:52,657] [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_003584015.1	s__Alteraurantiacibacter xanthus	100.0	1379	1386	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_005434915.1	s__Alteraurantiacibacter suaedae	88.1182	787	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002337385.1	s__Alteraurantiacibacter sp002337385	87.4889	712	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001010945.1	s__Alteraurantiacibacter luteus	80.222	499	1386	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	79.8975	552	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002556635.1	s__Novosphingobium sp002556635	79.8115	460	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605195.1	s__Alteraurantiacibacter odishensis	79.7731	526	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827435.1	s__Croceibacterium salegens	79.7477	509	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125555.1	s__Erythrobacter sp016125555	79.704	434	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584125.1	s__Alteraurantiacibacter zhengii	79.5448	475	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763545.1	s__JACXVD01 sp014763545	79.1952	433	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01	95.0	99.92	99.92	0.96	0.96	2	-
GCA_002279825.1	s__Croceibacterium sp002279825	79.1853	470	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	99.89	99.89	0.97	0.97	2	-
GCF_001886695.1	s__Alteraurantiacibacter gangjinensis	79.0113	356	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002155695.1	s__Erythrobacter tepidarius	78.9065	399	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652615.1	s__Novosphingobium arvoryzae	78.7489	371	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822005.1	s__Novosphingobium sp013822005	78.2677	271	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:52,659] [INFO] GTDB search result was written to GCF_003584015.1_ASM358401v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:52,660] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:52,664] [INFO] DFAST_QC result json was written to GCF_003584015.1_ASM358401v1_genomic.fna/dqc_result.json
[2024-01-24 13:10:52,664] [INFO] DFAST_QC completed!
[2024-01-24 13:10:52,664] [INFO] Total running time: 0h1m19s