[2023-03-14 11:33:35,026] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:33:35,026] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:33:35,026] [INFO] DQC Reference Directory: /var/lib/cwl/stge33ec395-d878-4c46-8254-4aa4bf18bb4c/dqc_reference
[2023-03-14 11:33:36,309] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:33:36,309] [INFO] Task started: Prodigal
[2023-03-14 11:33:36,309] [INFO] Running command: cat /var/lib/cwl/stgba78b5f4-c600-4432-a476-a05dbad6182c/OceanDNA-b31959.fa | prodigal -d OceanDNA-b31959/cds.fna -a OceanDNA-b31959/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:33:53,241] [INFO] Task succeeded: Prodigal
[2023-03-14 11:33:53,241] [INFO] Task started: HMMsearch
[2023-03-14 11:33:53,241] [INFO] Running command: hmmsearch --tblout OceanDNA-b31959/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge33ec395-d878-4c46-8254-4aa4bf18bb4c/dqc_reference/reference_markers.hmm OceanDNA-b31959/protein.faa > /dev/null
[2023-03-14 11:33:53,493] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:33:53,494] [INFO] Found 6/6 markers.
[2023-03-14 11:33:53,511] [INFO] Query marker FASTA was written to OceanDNA-b31959/markers.fasta
[2023-03-14 11:33:53,511] [INFO] Task started: Blastn
[2023-03-14 11:33:53,511] [INFO] Running command: blastn -query OceanDNA-b31959/markers.fasta -db /var/lib/cwl/stge33ec395-d878-4c46-8254-4aa4bf18bb4c/dqc_reference/reference_markers.fasta -out OceanDNA-b31959/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:33:54,322] [INFO] Task succeeded: Blastn
[2023-03-14 11:33:54,323] [INFO] Selected 29 target genomes.
[2023-03-14 11:33:54,323] [INFO] Target genome list was writen to OceanDNA-b31959/target_genomes.txt
[2023-03-14 11:33:54,340] [INFO] Task started: fastANI
[2023-03-14 11:33:54,340] [INFO] Running command: fastANI --query /var/lib/cwl/stgba78b5f4-c600-4432-a476-a05dbad6182c/OceanDNA-b31959.fa --refList OceanDNA-b31959/target_genomes.txt --output OceanDNA-b31959/fastani_result.tsv --threads 1
[2023-03-14 11:34:11,985] [INFO] Task succeeded: fastANI
[2023-03-14 11:34:11,985] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge33ec395-d878-4c46-8254-4aa4bf18bb4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:34:11,985] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge33ec395-d878-4c46-8254-4aa4bf18bb4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:34:12,000] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:34:12,000] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:34:12,001] [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	80.621	463	893	95	below_threshold
Aurantiacibacter luteus	strain=KA37	GCA_001010945.1	1581420	1581420	type	True	79.9724	441	893	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	79.7179	375	893	95	below_threshold
Aurantiacibacter suaedae	strain=GH3-15	GCA_005434915.1	2545755	2545755	type	True	79.698	416	893	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	79.6625	416	893	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	79.5224	416	893	95	below_threshold
Croceibacterium atlanticum	strain=DSM 100738	GCA_014199315.1	1267766	1267766	type	True	79.3523	373	893	95	below_threshold
Croceibacterium atlanticum	strain=26DY36	GCA_001008165.2	1267766	1267766	type	True	79.3347	373	893	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	79.2887	390	893	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	79.2704	373	893	95	below_threshold
Aurantiacibacter arachoides	strain=CGMCC 1.15507	GCA_014643415.1	1850444	1850444	type	True	79.1282	399	893	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	79.1007	370	893	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_001719165.1	39960	39960	type	True	79.084	377	893	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	79.0698	363	893	95	below_threshold
Erythrobacter dokdonensis	strain=DSM 17193	GCA_002155305.1	328225	328225	type	True	79.0627	360	893	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	79.0588	370	893	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	79.0144	326	893	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	78.957	361	893	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	78.9484	342	893	95	below_threshold
Tsuneonella rigui	strain=KCTC 42620	GCA_003958625.1	1708790	1708790	type	True	78.9082	354	893	95	below_threshold
Tsuneonella troitsensis	strain=JCM 17037	GCA_001441535.1	292222	292222	type	True	78.82	312	893	95	below_threshold
Pelagerythrobacter marensis	strain=KCTC 22370	GCA_001028625.1	543877	543877	type	True	78.8088	318	893	95	below_threshold
Qipengyuania vulgaris	strain=DSM 17792	GCA_009827325.1	291985	291985	type	True	78.7648	295	893	95	below_threshold
Tsuneonella troitsensis	strain=KMM 6042	GCA_003730315.1	292222	292222	type	True	78.7615	317	893	95	below_threshold
Croceibacterium mercuriale	strain=Coronado	GCA_000802385.1	1572751	1572751	type	True	78.7398	333	893	95	below_threshold
Pelagerythrobacter marensis	strain=DSM 21428	GCA_001461885.1	543877	543877	type	True	78.7178	330	893	95	below_threshold
Aurantiacibacter rhizosphaerae	strain=GH3-10	GCA_009807005.1	2691582	2691582	type	True	78.6305	382	893	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	78.5879	327	893	95	below_threshold
Aurantiacibacter sediminis	strain=JGD-13	GCA_016019885.1	2793064	2793064	type	True	78.3338	309	893	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:34:12,001] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31959/tc_result.tsv
[2023-03-14 11:34:12,001] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:34:12,001] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:34:12,001] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge33ec395-d878-4c46-8254-4aa4bf18bb4c/dqc_reference/checkm_data
[2023-03-14 11:34:12,002] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:34:12,109] [INFO] Task started: CheckM
[2023-03-14 11:34:12,109] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31959/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31959/checkm_input OceanDNA-b31959/checkm_result
[2023-03-14 11:34:56,024] [INFO] Task succeeded: CheckM
[2023-03-14 11:34:56,024] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:34:56,027] [INFO] ===== Completeness check finished =====
[2023-03-14 11:34:56,027] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:34:56,027] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31959/markers.fasta)
[2023-03-14 11:34:56,027] [INFO] Task started: Blastn
[2023-03-14 11:34:56,027] [INFO] Running command: blastn -query OceanDNA-b31959/markers.fasta -db /var/lib/cwl/stge33ec395-d878-4c46-8254-4aa4bf18bb4c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31959/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:34:57,329] [INFO] Task succeeded: Blastn
[2023-03-14 11:34:57,330] [INFO] Selected 28 target genomes.
[2023-03-14 11:34:57,330] [INFO] Target genome list was writen to OceanDNA-b31959/target_genomes_gtdb.txt
[2023-03-14 11:34:57,379] [INFO] Task started: fastANI
[2023-03-14 11:34:57,379] [INFO] Running command: fastANI --query /var/lib/cwl/stgba78b5f4-c600-4432-a476-a05dbad6182c/OceanDNA-b31959.fa --refList OceanDNA-b31959/target_genomes_gtdb.txt --output OceanDNA-b31959/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:35:14,487] [INFO] Task succeeded: fastANI
[2023-03-14 11:35:14,502] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:35:14,502] [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
GCA_002341345.1	s__Alteraurantiacibacter sp002341345	85.9381	536	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584015.1	s__Alteraurantiacibacter xanthus	80.6128	464	893	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	80.5307	496	893	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	80.4827	399	893	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	80.2818	416	893	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	80.0714	397	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001010945.1	s__Alteraurantiacibacter luteus	79.9729	441	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827515.1	s__Pelagerythrobacter marinus	79.6863	413	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005434915.1	s__Alteraurantiacibacter suaedae	79.6734	418	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018636735.1	s__Alteriqipengyuania sp018636735	79.6572	389	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763545.1	s__JACXVD01 sp014763545	79.6279	404	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01	95.0	99.92	99.92	0.96	0.96	2	-
GCF_003815535.1	s__Alteraurantiacibacter spongiae	79.533	413	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827655.1	s__Alteraurantiacibacter buctensis	79.4611	421	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003569745.1	s__Croceibacterium sp003569745	79.3152	399	893	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	79.2196	404	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011320115.1	s__Croceibacterium segetis	79.1792	366	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605475.1	s__Alteraurantiacibacter aquimixticola_A	79.1767	373	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828065.1	s__Croceibacterium soli	79.1764	378	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135625.1	s__Pelagerythrobacter rhizovicinus	79.1076	369	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902498745.1	s__Alteraurantiacibacter sp902498745	79.0768	409	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015529805.1	s__Qipengyuania soli	78.9362	343	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003958625.1	s__Tsuneonella rigui	78.8588	358	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002712945.1	s__Alteriqipengyuania sp002712945	78.8494	213	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001028625.1	s__Pelagerythrobacter marensis	78.8014	318	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018819685.1	s__Qipengyuania sp018819685	78.4239	236	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.48	99.48	0.85	0.85	2	-
GCF_003958635.1	s__Altericroceibacterium_A xinjiangense	78.3519	289	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altericroceibacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016019885.1	s__Alteraurantiacibacter sp016019885	78.3464	308	893	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	77.8568	274	893	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:35:14,516] [INFO] GTDB search result was written to OceanDNA-b31959/result_gtdb.tsv
[2023-03-14 11:35:14,516] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:35:14,519] [INFO] DFAST_QC result json was written to OceanDNA-b31959/dqc_result.json
[2023-03-14 11:35:14,519] [INFO] DFAST_QC completed!
[2023-03-14 11:35:14,519] [INFO] Total running time: 0h1m39s