[2023-03-15 05:29:10,771] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:29:10,771] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:29:10,771] [INFO] DQC Reference Directory: /var/lib/cwl/stg8121fc68-f531-4b6d-b6b5-228697b6ea20/dqc_reference
[2023-03-15 05:29:12,387] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:29:12,387] [INFO] Task started: Prodigal
[2023-03-15 05:29:12,387] [INFO] Running command: cat /var/lib/cwl/stg9e7171e4-f1c9-4b73-9793-cf0afa705924/OceanDNA-b31950.fa | prodigal -d OceanDNA-b31950/cds.fna -a OceanDNA-b31950/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:29:23,866] [INFO] Task succeeded: Prodigal
[2023-03-15 05:29:23,867] [INFO] Task started: HMMsearch
[2023-03-15 05:29:23,867] [INFO] Running command: hmmsearch --tblout OceanDNA-b31950/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8121fc68-f531-4b6d-b6b5-228697b6ea20/dqc_reference/reference_markers.hmm OceanDNA-b31950/protein.faa > /dev/null
[2023-03-15 05:29:24,056] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:29:24,057] [INFO] Found 6/6 markers.
[2023-03-15 05:29:24,071] [INFO] Query marker FASTA was written to OceanDNA-b31950/markers.fasta
[2023-03-15 05:29:24,071] [INFO] Task started: Blastn
[2023-03-15 05:29:24,071] [INFO] Running command: blastn -query OceanDNA-b31950/markers.fasta -db /var/lib/cwl/stg8121fc68-f531-4b6d-b6b5-228697b6ea20/dqc_reference/reference_markers.fasta -out OceanDNA-b31950/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:29:24,870] [INFO] Task succeeded: Blastn
[2023-03-15 05:29:24,871] [INFO] Selected 30 target genomes.
[2023-03-15 05:29:24,871] [INFO] Target genome list was writen to OceanDNA-b31950/target_genomes.txt
[2023-03-15 05:29:24,884] [INFO] Task started: fastANI
[2023-03-15 05:29:24,884] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e7171e4-f1c9-4b73-9793-cf0afa705924/OceanDNA-b31950.fa --refList OceanDNA-b31950/target_genomes.txt --output OceanDNA-b31950/fastani_result.tsv --threads 1
[2023-03-15 05:29:40,489] [INFO] Task succeeded: fastANI
[2023-03-15 05:29:40,489] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8121fc68-f531-4b6d-b6b5-228697b6ea20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:29:40,489] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8121fc68-f531-4b6d-b6b5-228697b6ea20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:29:40,505] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:29:40,505] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 05:29:40,506] [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 suaedae	strain=GH3-15	GCA_005434915.1	2545755	2545755	type	True	78.5493	250	603	95	below_threshold
Alteraurantiacibacter aestuarii	strain=JCM 16339	GCA_009827405.1	650004	650004	type	True	78.4172	209	603	95	below_threshold
Aurantiacibacter luteus	strain=KA37	GCA_001010945.1	1581420	1581420	type	True	78.2667	266	603	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	78.1643	241	603	95	below_threshold
Aurantiacibacter zhengii	strain=V18	GCA_003584125.1	2307003	2307003	type	True	78.1068	236	603	95	below_threshold
Aurantiacibacter odishensis	strain=KCTC 23981	GCA_003605195.1	1155476	1155476	type	True	78.0363	258	603	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	78.0059	226	603	95	below_threshold
Aurantiacibacter arachoides	strain=RC4-10-4	GCA_009827335.1	1850444	1850444	type	True	78.0028	234	603	95	below_threshold
Croceibacterium atlanticum	strain=26DY36	GCA_001008165.2	1267766	1267766	type	True	77.9851	232	603	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	77.9773	251	603	95	below_threshold
Aurantiacibacter gangjinensis	strain=K7-2	GCA_001010925.1	502682	502682	type	True	77.9497	228	603	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	77.934	230	603	95	below_threshold
Qipengyuania aestuarii	strain=GH1	GCA_019711535.1	2867241	2867241	type	True	77.9331	159	603	95	below_threshold
Aurantiacibacter arachoides	strain=CGMCC 1.15507	GCA_014643415.1	1850444	1850444	type	True	77.9063	230	603	95	below_threshold
Croceibacterium atlanticum	strain=DSM 100738	GCA_014199315.1	1267766	1267766	type	True	77.8988	235	603	95	below_threshold
Tsuneonella amylolytica	strain=NS1	GCA_003626915.1	2338327	2338327	type	True	77.8986	190	603	95	below_threshold
Tsuneonella rigui	strain=KCTC 42620	GCA_003958625.1	1708790	1708790	type	True	77.8968	194	603	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	77.8959	221	603	95	below_threshold
Aurantiacibacter gangjinensis	strain=CGMCC 1.15024	GCA_001886695.1	502682	502682	type	True	77.889	229	603	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	77.8764	206	603	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	77.8534	192	603	95	below_threshold
Croceibacterium ferulae	strain=SX2RGS8	GCA_003660445.1	1854641	1854641	type	True	77.7946	204	603	95	below_threshold
Aurantiacibacter rhizosphaerae	strain=GH3-10	GCA_009807005.1	2691582	2691582	type	True	77.7803	217	603	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	77.7151	217	603	95	below_threshold
Novosphingobium kunmingense	strain=CGMCC 1.12274	GCA_002813245.1	1211806	1211806	type	True	77.6265	183	603	95	below_threshold
Aurantiacibacter marinus	strain=HWDM-33	GCA_001013305.1	874156	874156	type	True	77.4497	175	603	95	below_threshold
Aurantiacibacter marinus	strain=KCTC 23554	GCA_001021555.1	874156	874156	type	True	77.432	176	603	95	below_threshold
Croceibacterium mercuriale	strain=Coronado	GCA_000802385.1	1572751	1572751	type	True	77.4043	203	603	95	below_threshold
Tsuneonella flava	strain=MS1-4	GCA_002870965.1	2055955	2055955	type	True	77.162	157	603	95	below_threshold
Altericroceibacterium spongiae	strain=HN-Y73	GCA_003610805.1	2320269	2320269	type	True	76.8666	117	603	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:29:40,506] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31950/tc_result.tsv
[2023-03-15 05:29:40,506] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:29:40,506] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:29:40,506] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8121fc68-f531-4b6d-b6b5-228697b6ea20/dqc_reference/checkm_data
[2023-03-15 05:29:40,507] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:29:40,510] [INFO] Task started: CheckM
[2023-03-15 05:29:40,511] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31950/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31950/checkm_input OceanDNA-b31950/checkm_result
[2023-03-15 05:30:12,744] [INFO] Task succeeded: CheckM
[2023-03-15 05:30:12,745] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.59%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:30:12,746] [INFO] ===== Completeness check finished =====
[2023-03-15 05:30:12,747] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:30:12,747] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31950/markers.fasta)
[2023-03-15 05:30:12,747] [INFO] Task started: Blastn
[2023-03-15 05:30:12,747] [INFO] Running command: blastn -query OceanDNA-b31950/markers.fasta -db /var/lib/cwl/stg8121fc68-f531-4b6d-b6b5-228697b6ea20/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31950/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:30:14,217] [INFO] Task succeeded: Blastn
[2023-03-15 05:30:14,218] [INFO] Selected 25 target genomes.
[2023-03-15 05:30:14,218] [INFO] Target genome list was writen to OceanDNA-b31950/target_genomes_gtdb.txt
[2023-03-15 05:30:14,258] [INFO] Task started: fastANI
[2023-03-15 05:30:14,258] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e7171e4-f1c9-4b73-9793-cf0afa705924/OceanDNA-b31950.fa --refList OceanDNA-b31950/target_genomes_gtdb.txt --output OceanDNA-b31950/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:30:28,082] [INFO] Task succeeded: fastANI
[2023-03-15 05:30:28,097] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:30:28,097] [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	81.7745	366	603	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	78.9016	300	603	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	78.5656	249	603	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	78.3776	229	603	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744735.1	s__Caenibius sp017744735	78.3097	212	603	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius	95.0	99.56	99.56	0.78	0.78	2	-
GCA_014359685.1	s__Croceibacterium sp014359685	78.3042	172	603	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001635685.1	s__Qipengyuania sp001635685	78.1156	226	603	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.58	97.35	0.92	0.89	12	-
GCF_003584125.1	s__Alteraurantiacibacter zhengii	78.1068	236	603	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	78.0991	239	603	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902498745.1	s__Alteraurantiacibacter sp902498745	78.093	235	603	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	78.0363	258	603	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827295.1	s__Qipengyuania pelagi	78.0042	226	603	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	77.9989	235	603	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900105095.1	s__Erythrobacter sp900105095	77.995	223	603	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001008165.2	s__Croceibacterium atlanticum	77.9894	231	603	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009827515.1	s__Pelagerythrobacter marinus	77.9818	250	603	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815535.1	s__Alteraurantiacibacter spongiae	77.8946	243	603	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	77.889	229	603	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018636735.1	s__Alteriqipengyuania sp018636735	77.8378	224	603	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011054555.1	s__Erythrobacter sp011054555	77.8039	175	603	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003660445.1	s__Croceibacterium ferulae	77.7783	205	603	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009807005.1	s__Alteraurantiacibacter rhizosphaerae	77.7653	218	603	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	77.7639	211	603	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011320115.1	s__Croceibacterium segetis	77.6285	203	603	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002695185.1	s__Qipengyuania sp002695185	77.4334	129	603	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	96.33	96.22	0.77	0.72	4	-
--------------------------------------------------------------------------------
[2023-03-15 05:30:28,097] [INFO] GTDB search result was written to OceanDNA-b31950/result_gtdb.tsv
[2023-03-15 05:30:28,097] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:30:28,100] [INFO] DFAST_QC result json was written to OceanDNA-b31950/dqc_result.json
[2023-03-15 05:30:28,100] [INFO] DFAST_QC completed!
[2023-03-15 05:30:28,100] [INFO] Total running time: 0h1m17s