[2023-03-18 01:43:48,320] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:43:48,320] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:43:48,320] [INFO] DQC Reference Directory: /var/lib/cwl/stg46299fc8-a93a-49d7-afa0-fb6c2f885001/dqc_reference
[2023-03-18 01:43:49,430] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:43:49,430] [INFO] Task started: Prodigal
[2023-03-18 01:43:49,431] [INFO] Running command: cat /var/lib/cwl/stg328564f5-6e9b-4aa9-8641-dcd6c33e9785/OceanDNA-b31944.fa | prodigal -d OceanDNA-b31944/cds.fna -a OceanDNA-b31944/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:44:02,074] [INFO] Task succeeded: Prodigal
[2023-03-18 01:44:02,075] [INFO] Task started: HMMsearch
[2023-03-18 01:44:02,075] [INFO] Running command: hmmsearch --tblout OceanDNA-b31944/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46299fc8-a93a-49d7-afa0-fb6c2f885001/dqc_reference/reference_markers.hmm OceanDNA-b31944/protein.faa > /dev/null
[2023-03-18 01:44:02,245] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:44:02,246] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg328564f5-6e9b-4aa9-8641-dcd6c33e9785/OceanDNA-b31944.fa]
[2023-03-18 01:44:02,259] [INFO] Query marker FASTA was written to OceanDNA-b31944/markers.fasta
[2023-03-18 01:44:02,259] [INFO] Task started: Blastn
[2023-03-18 01:44:02,259] [INFO] Running command: blastn -query OceanDNA-b31944/markers.fasta -db /var/lib/cwl/stg46299fc8-a93a-49d7-afa0-fb6c2f885001/dqc_reference/reference_markers.fasta -out OceanDNA-b31944/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:44:03,059] [INFO] Task succeeded: Blastn
[2023-03-18 01:44:03,101] [INFO] Selected 25 target genomes.
[2023-03-18 01:44:03,102] [INFO] Target genome list was writen to OceanDNA-b31944/target_genomes.txt
[2023-03-18 01:44:03,114] [INFO] Task started: fastANI
[2023-03-18 01:44:03,114] [INFO] Running command: fastANI --query /var/lib/cwl/stg328564f5-6e9b-4aa9-8641-dcd6c33e9785/OceanDNA-b31944.fa --refList OceanDNA-b31944/target_genomes.txt --output OceanDNA-b31944/fastani_result.tsv --threads 1
[2023-03-18 01:44:16,055] [INFO] Task succeeded: fastANI
[2023-03-18 01:44:16,055] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46299fc8-a93a-49d7-afa0-fb6c2f885001/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:44:16,055] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46299fc8-a93a-49d7-afa0-fb6c2f885001/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:44:16,069] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:44:16,069] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:44:16,069] [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	78.3454	300	657	95	below_threshold
Aurantiacibacter gangjinensis	strain=CGMCC 1.15024	GCA_001886695.1	502682	502682	type	True	78.3392	285	657	95	below_threshold
Aurantiacibacter gangjinensis	strain=K7-2	GCA_001010925.1	502682	502682	type	True	78.3285	285	657	95	below_threshold
Alteraurantiacibacter aestuarii	strain=JCM 16339	GCA_009827405.1	650004	650004	type	True	78.0921	181	657	95	below_threshold
Aurantiacibacter suaedae	strain=GH3-15	GCA_005434915.1	2545755	2545755	type	True	78.09	277	657	95	below_threshold
Aurantiacibacter rhizosphaerae	strain=GH3-10	GCA_009807005.1	2691582	2691582	type	True	77.9208	285	657	95	below_threshold
Croceibacterium atlanticum	strain=26DY36	GCA_001008165.2	1267766	1267766	type	True	77.8916	213	657	95	below_threshold
Croceibacterium atlanticum	strain=DSM 100738	GCA_014199315.1	1267766	1267766	type	True	77.869	213	657	95	below_threshold
Aurantiacibacter odishensis	strain=KCTC 23981	GCA_003605195.1	1155476	1155476	type	True	77.8209	301	657	95	below_threshold
Aurantiacibacter zhengii	strain=V18	GCA_003584125.1	2307003	2307003	type	True	77.7492	266	657	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	77.7471	208	657	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	77.667	216	657	95	below_threshold
Aurantiacibacter luteus	strain=KA37	GCA_001010945.1	1581420	1581420	type	True	77.6366	276	657	95	below_threshold
Qipengyuania aquimaris	strain=JCM 12189	GCA_009827445.1	255984	255984	suspected-type	True	77.4797	182	657	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	77.455	198	657	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	77.4465	215	657	95	below_threshold
Croceibacterium xixiisoli	strain=S36	GCA_009827305.1	1476466	1476466	type	True	77.4413	204	657	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	77.4196	186	657	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	77.3142	170	657	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	77.2854	168	657	95	below_threshold
Croceicoccus naphthovorans	strain=DSM 102796	GCA_014196855.1	1348774	1348774	type	True	77.2815	158	657	95	below_threshold
Croceicoccus naphthovorans	strain=PQ-2	GCA_001028705.1	1348774	1348774	type	True	77.2124	160	657	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	77.1686	185	657	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	76.7742	158	657	95	below_threshold
Pontixanthobacter aquaemixtae	strain=KCTC 52763	GCA_009827395.1	1958940	1958940	type	True	76.6068	147	657	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:44:16,069] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31944/tc_result.tsv
[2023-03-18 01:44:16,069] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:44:16,069] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:44:16,070] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46299fc8-a93a-49d7-afa0-fb6c2f885001/dqc_reference/checkm_data
[2023-03-18 01:44:16,070] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:44:16,074] [INFO] Task started: CheckM
[2023-03-18 01:44:16,074] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31944/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31944/checkm_input OceanDNA-b31944/checkm_result
[2023-03-18 01:44:50,440] [INFO] Task succeeded: CheckM
[2023-03-18 01:44:50,440] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.42%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:44:50,442] [INFO] ===== Completeness check finished =====
[2023-03-18 01:44:50,442] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:44:50,442] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31944/markers.fasta)
[2023-03-18 01:44:50,443] [INFO] Task started: Blastn
[2023-03-18 01:44:50,443] [INFO] Running command: blastn -query OceanDNA-b31944/markers.fasta -db /var/lib/cwl/stg46299fc8-a93a-49d7-afa0-fb6c2f885001/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31944/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:44:51,662] [INFO] Task succeeded: Blastn
[2023-03-18 01:44:51,663] [INFO] Selected 24 target genomes.
[2023-03-18 01:44:51,663] [INFO] Target genome list was writen to OceanDNA-b31944/target_genomes_gtdb.txt
[2023-03-18 01:44:51,761] [INFO] Task started: fastANI
[2023-03-18 01:44:51,761] [INFO] Running command: fastANI --query /var/lib/cwl/stg328564f5-6e9b-4aa9-8641-dcd6c33e9785/OceanDNA-b31944.fa --refList OceanDNA-b31944/target_genomes_gtdb.txt --output OceanDNA-b31944/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:45:04,583] [INFO] Task succeeded: fastANI
[2023-03-18 01:45:04,596] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:45:04,596] [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_902498745.1	s__Alteraurantiacibacter sp902498745	78.5989	312	657	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	78.3353	287	657	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003584015.1	s__Alteraurantiacibacter xanthus	78.3322	301	657	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	78.2095	319	657	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005434915.1	s__Alteraurantiacibacter suaedae	78.0903	277	657	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	78.0568	252	657	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	77.9933	247	657	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01	95.0	99.92	99.92	0.96	0.96	2	-
GCF_003605475.1	s__Alteraurantiacibacter aquimixticola_A	77.8535	279	657	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	77.8467	300	657	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	77.7534	267	657	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002367375.1	s__Alteraurantiacibacter sp002367375	77.6702	218	657	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	77.6481	275	657	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006542605.1	s__Erythrobacter sp006542605	77.6457	231	657	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001678665.1	s__Qipengyuania sp001678665	77.6325	200	657	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018828205.1	s__Qipengyuania sp018828205	77.6321	171	657	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827435.1	s__Croceibacterium salegens	77.544	200	657	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005884405.1	s__Qipengyuania marisflavi	77.4597	202	657	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803135.1	s__Pelagerythrobacter sp016803135	77.4381	175	657	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114695.1	s__Parerythrobacter sp004114695	77.3299	206	657	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002377695.1	s__Alteriqipengyuania sp002377695	77.3082	182	657	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.97	99.97	1.00	1.00	2	-
GCA_017308255.1	s__Croceibacterium sp001897135	77.2816	213	657	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	99.96	99.96	0.98	0.98	2	-
GCA_018819685.1	s__Qipengyuania sp018819685	76.9728	143	657	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.48	99.48	0.85	0.85	2	-
GCF_002556635.1	s__Novosphingobium sp002556635	76.9184	175	657	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827395.1	s__Pontixanthobacter aquaemixtae	76.6068	147	657	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:45:04,597] [INFO] GTDB search result was written to OceanDNA-b31944/result_gtdb.tsv
[2023-03-18 01:45:04,597] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:45:04,599] [INFO] DFAST_QC result json was written to OceanDNA-b31944/dqc_result.json
[2023-03-18 01:45:04,599] [INFO] DFAST_QC completed!
[2023-03-18 01:45:04,599] [INFO] Total running time: 0h1m16s