[2023-03-16 17:47:08,947] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:47:08,947] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:47:08,947] [INFO] DQC Reference Directory: /var/lib/cwl/stg23ef22b0-af6f-488e-a982-77a0a2fb1eb3/dqc_reference
[2023-03-16 17:47:10,994] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:47:10,995] [INFO] Task started: Prodigal
[2023-03-16 17:47:10,996] [INFO] Running command: cat /var/lib/cwl/stg051d98ce-8091-43fc-9839-5f7ee55fb22c/OceanDNA-b31967.fa | prodigal -d OceanDNA-b31967/cds.fna -a OceanDNA-b31967/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:47:30,709] [INFO] Task succeeded: Prodigal
[2023-03-16 17:47:30,710] [INFO] Task started: HMMsearch
[2023-03-16 17:47:30,710] [INFO] Running command: hmmsearch --tblout OceanDNA-b31967/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23ef22b0-af6f-488e-a982-77a0a2fb1eb3/dqc_reference/reference_markers.hmm OceanDNA-b31967/protein.faa > /dev/null
[2023-03-16 17:47:30,907] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:47:30,907] [INFO] Found 6/6 markers.
[2023-03-16 17:47:30,930] [INFO] Query marker FASTA was written to OceanDNA-b31967/markers.fasta
[2023-03-16 17:47:30,931] [INFO] Task started: Blastn
[2023-03-16 17:47:30,931] [INFO] Running command: blastn -query OceanDNA-b31967/markers.fasta -db /var/lib/cwl/stg23ef22b0-af6f-488e-a982-77a0a2fb1eb3/dqc_reference/reference_markers.fasta -out OceanDNA-b31967/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:47:31,853] [INFO] Task succeeded: Blastn
[2023-03-16 17:47:31,855] [INFO] Selected 22 target genomes.
[2023-03-16 17:47:31,856] [INFO] Target genome list was writen to OceanDNA-b31967/target_genomes.txt
[2023-03-16 17:47:31,870] [INFO] Task started: fastANI
[2023-03-16 17:47:31,870] [INFO] Running command: fastANI --query /var/lib/cwl/stg051d98ce-8091-43fc-9839-5f7ee55fb22c/OceanDNA-b31967.fa --refList OceanDNA-b31967/target_genomes.txt --output OceanDNA-b31967/fastani_result.tsv --threads 1
[2023-03-16 17:47:44,478] [INFO] Task succeeded: fastANI
[2023-03-16 17:47:44,478] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23ef22b0-af6f-488e-a982-77a0a2fb1eb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:47:44,478] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23ef22b0-af6f-488e-a982-77a0a2fb1eb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:47:44,491] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:47:44,491] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 17:47:44,491] [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	87.3946	766	1035	95	below_threshold
Aurantiacibacter suaedae	strain=GH3-15	GCA_005434915.1	2545755	2545755	type	True	86.4494	735	1035	95	below_threshold
Aurantiacibacter luteus	strain=KA37	GCA_001010945.1	1581420	1581420	type	True	79.5577	435	1035	95	below_threshold
Aurantiacibacter odishensis	strain=KCTC 23981	GCA_003605195.1	1155476	1155476	type	True	79.4924	466	1035	95	below_threshold
Aurantiacibacter arachoides	strain=RC4-10-4	GCA_009827335.1	1850444	1850444	type	True	79.2313	404	1035	95	below_threshold
Alteraurantiacibacter aestuarii	strain=JCM 16339	GCA_009827405.1	650004	650004	type	True	79.211	295	1035	95	below_threshold
Aurantiacibacter arachoides	strain=CGMCC 1.15507	GCA_014643415.1	1850444	1850444	type	True	79.1661	409	1035	95	below_threshold
Aurantiacibacter zhengii	strain=V18	GCA_003584125.1	2307003	2307003	type	True	79.1633	415	1035	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	79.1541	331	1035	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	78.8629	386	1035	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.8115	340	1035	95	below_threshold
Tsuneonella amylolytica	strain=NS1	GCA_003626915.1	2338327	2338327	type	True	78.729	304	1035	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	78.7136	343	1035	95	below_threshold
Novosphingobium piscinae	strain=KCTC 42194	GCA_014230355.1	1507448	1507448	type	True	78.6347	320	1035	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	78.6136	321	1035	95	below_threshold
Tsuneonella rigui	strain=KCTC 42620	GCA_003958625.1	1708790	1708790	type	True	78.6092	326	1035	95	below_threshold
Aurantiacibacter rhizosphaerae	strain=GH3-10	GCA_009807005.1	2691582	2691582	type	True	78.6075	425	1035	95	below_threshold
Aurantiacibacter gangjinensis	strain=CGMCC 1.15024	GCA_001886695.1	502682	502682	type	True	78.6033	337	1035	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	78.5505	303	1035	95	below_threshold
Aurantiacibacter gangjinensis	strain=K7-2	GCA_001010925.1	502682	502682	type	True	78.5272	340	1035	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	78.4906	346	1035	95	below_threshold
Erythrobacter tepidarius	strain=DSM 10594	GCA_002155695.1	60454	60454	type	True	78.4322	344	1035	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 17:47:44,492] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31967/tc_result.tsv
[2023-03-16 17:47:44,493] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:47:44,493] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:47:44,493] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23ef22b0-af6f-488e-a982-77a0a2fb1eb3/dqc_reference/checkm_data
[2023-03-16 17:47:44,493] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:47:44,499] [INFO] Task started: CheckM
[2023-03-16 17:47:44,499] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31967/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31967/checkm_input OceanDNA-b31967/checkm_result
[2023-03-16 17:48:44,452] [INFO] Task succeeded: CheckM
[2023-03-16 17:48:44,453] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 17:48:44,465] [INFO] ===== Completeness check finished =====
[2023-03-16 17:48:44,465] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:48:44,465] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31967/markers.fasta)
[2023-03-16 17:48:44,467] [INFO] Task started: Blastn
[2023-03-16 17:48:44,467] [INFO] Running command: blastn -query OceanDNA-b31967/markers.fasta -db /var/lib/cwl/stg23ef22b0-af6f-488e-a982-77a0a2fb1eb3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31967/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:48:46,407] [INFO] Task succeeded: Blastn
[2023-03-16 17:48:46,411] [INFO] Selected 15 target genomes.
[2023-03-16 17:48:46,411] [INFO] Target genome list was writen to OceanDNA-b31967/target_genomes_gtdb.txt
[2023-03-16 17:48:46,489] [INFO] Task started: fastANI
[2023-03-16 17:48:46,489] [INFO] Running command: fastANI --query /var/lib/cwl/stg051d98ce-8091-43fc-9839-5f7ee55fb22c/OceanDNA-b31967.fa --refList OceanDNA-b31967/target_genomes_gtdb.txt --output OceanDNA-b31967/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:49:00,165] [INFO] Task succeeded: fastANI
[2023-03-16 17:49:00,174] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 17:49:00,175] [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_002337385.1	s__Alteraurantiacibacter sp002337385	99.9824	832	1035	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_003584015.1	s__Alteraurantiacibacter xanthus	87.4063	765	1035	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	86.4494	735	1035	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	79.6723	505	1035	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	79.4924	466	1035	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	79.386	482	1035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827405.1	s__Alteraurantiacibacter aestuarii	79.1946	296	1035	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	79.1746	414	1035	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	79.1676	435	1035	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	79.1353	376	1035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744735.1	s__Caenibius sp017744735	78.8828	394	1035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius	95.0	99.56	99.56	0.78	0.78	2	-
GCF_902498745.1	s__Alteraurantiacibacter sp902498745	78.7535	381	1035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626915.1	s__Tsuneonella amylolytica	78.7148	305	1035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815535.1	s__Alteraurantiacibacter spongiae	78.6884	362	1035	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	78.6155	336	1035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-16 17:49:00,177] [INFO] GTDB search result was written to OceanDNA-b31967/result_gtdb.tsv
[2023-03-16 17:49:00,179] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:49:00,182] [INFO] DFAST_QC result json was written to OceanDNA-b31967/dqc_result.json
[2023-03-16 17:49:00,183] [INFO] DFAST_QC completed!
[2023-03-16 17:49:00,183] [INFO] Total running time: 0h1m51s