[2023-03-14 13:30:36,827] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:30:36,828] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:30:36,828] [INFO] DQC Reference Directory: /var/lib/cwl/stg2459a1e3-6774-4be2-8ede-70562cd7b316/dqc_reference
[2023-03-14 13:30:38,294] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:30:38,295] [INFO] Task started: Prodigal
[2023-03-14 13:30:38,295] [INFO] Running command: cat /var/lib/cwl/stg3d45b2ec-afb5-4543-93e8-29211d4cfd2e/OceanDNA-b937.fa | prodigal -d OceanDNA-b937/cds.fna -a OceanDNA-b937/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:30:54,851] [INFO] Task succeeded: Prodigal
[2023-03-14 13:30:54,851] [INFO] Task started: HMMsearch
[2023-03-14 13:30:54,852] [INFO] Running command: hmmsearch --tblout OceanDNA-b937/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2459a1e3-6774-4be2-8ede-70562cd7b316/dqc_reference/reference_markers.hmm OceanDNA-b937/protein.faa > /dev/null
[2023-03-14 13:30:55,305] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:30:55,306] [INFO] Found 6/6 markers.
[2023-03-14 13:30:55,338] [INFO] Query marker FASTA was written to OceanDNA-b937/markers.fasta
[2023-03-14 13:30:55,346] [INFO] Task started: Blastn
[2023-03-14 13:30:55,346] [INFO] Running command: blastn -query OceanDNA-b937/markers.fasta -db /var/lib/cwl/stg2459a1e3-6774-4be2-8ede-70562cd7b316/dqc_reference/reference_markers.fasta -out OceanDNA-b937/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:30:57,259] [INFO] Task succeeded: Blastn
[2023-03-14 13:30:57,261] [INFO] Selected 26 target genomes.
[2023-03-14 13:30:57,262] [INFO] Target genome list was writen to OceanDNA-b937/target_genomes.txt
[2023-03-14 13:30:57,280] [INFO] Task started: fastANI
[2023-03-14 13:30:57,281] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d45b2ec-afb5-4543-93e8-29211d4cfd2e/OceanDNA-b937.fa --refList OceanDNA-b937/target_genomes.txt --output OceanDNA-b937/fastani_result.tsv --threads 1
[2023-03-14 13:31:26,603] [INFO] Task succeeded: fastANI
[2023-03-14 13:31:26,603] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2459a1e3-6774-4be2-8ede-70562cd7b316/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:31:26,603] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2459a1e3-6774-4be2-8ede-70562cd7b316/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:31:26,616] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:31:26,617] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 13:31:26,617] [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
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	77.4987	232	794	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	77.1157	219	794	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	77.0965	142	794	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.486	175	794	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.4327	192	794	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	76.3922	112	794	95	below_threshold
Motilibacter rhizosphaerae	strain=DSM 45622	GCA_004216915.1	598652	598652	type	True	75.8173	87	794	95	below_threshold
Streptomyces termitum	strain=JCM 4518	GCA_014650175.1	67368	67368	type	True	75.784	130	794	95	below_threshold
Propioniciclava coleopterorum	strain=HDW11	GCA_011393335.1	2714937	2714937	type	True	75.554	77	794	95	below_threshold
Streptomyces californicus	strain=NRRL B-2098	GCA_000717645.1	67351	67351	type	True	75.5425	108	794	95	below_threshold
Streptomyces californicus	strain=FDAARGOS_1209	GCA_016906185.1	67351	67351	type	True	75.5341	109	794	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	75.5158	122	794	95	below_threshold
Actinomadura formosensis	strain=NBRC 14204	GCA_001552155.1	60706	60706	type	True	75.5047	93	794	95	below_threshold
Streptosporangium becharense	strain=CECT 8961	GCA_014191075.1	1816182	1816182	type	True	75.4507	122	794	95	below_threshold
Streptosporangium becharense	strain=DSM 46887	GCA_014204985.1	1816182	1816182	type	True	75.4367	124	794	95	below_threshold
Streptomyces cacaoi	strain=NRRL B-1220	GCA_002154495.1	1898	1898	type	True	75.4119	92	794	95	below_threshold
Streptomyces cacaoi	strain=DSM 40057	GCA_013004455.1	1898	1898	type	True	75.3737	95	794	95	below_threshold
Kocuria turfanensis	strain=HO-9042	GCA_001580365.1	388357	388357	type	True	75.3658	78	794	95	below_threshold
Streptomyces cacaoi	strain=NBRC 12748	GCA_006539165.1	1898	1898	type	True	75.2746	108	794	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	75.2056	162	794	95	below_threshold
Kocuria sediminis	strain=JCM 17929	GCA_009735315.1	1038857	1038857	type	True	75.1807	77	794	95	below_threshold
Kutzneria kofuensis	strain=DSM 43851	GCA_014203355.1	103725	103725	type	True	75.1192	167	794	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	75.0906	74	794	95	below_threshold
Cellulosimicrobium funkei	strain=JCM 14302	GCA_004519295.1	264251	264251	suspected-type	True	75.0604	78	794	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 13:31:26,617] [INFO] DFAST Taxonomy check result was written to OceanDNA-b937/tc_result.tsv
[2023-03-14 13:31:26,618] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:31:26,618] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:31:26,618] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2459a1e3-6774-4be2-8ede-70562cd7b316/dqc_reference/checkm_data
[2023-03-14 13:31:26,619] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:31:26,623] [INFO] Task started: CheckM
[2023-03-14 13:31:26,623] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b937/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b937/checkm_input OceanDNA-b937/checkm_result
[2023-03-14 13:32:17,196] [INFO] Task succeeded: CheckM
[2023-03-14 13:32:17,197] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.74%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:32:17,202] [INFO] ===== Completeness check finished =====
[2023-03-14 13:32:17,202] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:32:17,203] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b937/markers.fasta)
[2023-03-14 13:32:17,204] [INFO] Task started: Blastn
[2023-03-14 13:32:17,204] [INFO] Running command: blastn -query OceanDNA-b937/markers.fasta -db /var/lib/cwl/stg2459a1e3-6774-4be2-8ede-70562cd7b316/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b937/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:32:19,095] [INFO] Task succeeded: Blastn
[2023-03-14 13:32:19,097] [INFO] Selected 8 target genomes.
[2023-03-14 13:32:19,097] [INFO] Target genome list was writen to OceanDNA-b937/target_genomes_gtdb.txt
[2023-03-14 13:32:19,106] [INFO] Task started: fastANI
[2023-03-14 13:32:19,106] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d45b2ec-afb5-4543-93e8-29211d4cfd2e/OceanDNA-b937.fa --refList OceanDNA-b937/target_genomes_gtdb.txt --output OceanDNA-b937/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:32:23,365] [INFO] Task succeeded: fastANI
[2023-03-14 13:32:23,370] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 13:32:23,370] [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_002699725.1	s__S20-B6 sp002699725	87.1874	572	794	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	98.58	98.41	0.87	0.86	3	-
GCA_002329075.1	s__S20-B6 sp002329075	86.2993	600	794	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	98.53	97.43	0.90	0.85	7	-
GCA_014381945.1	s__S20-B6 sp014381945	86.2068	651	794	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002346745.1	s__S20-B6 sp002346745	83.2271	520	794	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	97.72	96.97	0.85	0.81	8	-
GCA_016845305.1	s__UBA9410 sp016845305	80.1307	442	794	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015658775.1	s__UBA3125 sp015658775	79.6315	329	794	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA3125	95.0	98.89	98.89	0.81	0.81	2	-
GCA_014239855.1	s__UBA9410 sp014239855	79.389	365	794	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014240365.1	s__UBA9410 sp014240365	78.6343	305	794	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	98.11	98.07	0.86	0.84	5	-
--------------------------------------------------------------------------------
[2023-03-14 13:32:23,371] [INFO] GTDB search result was written to OceanDNA-b937/result_gtdb.tsv
[2023-03-14 13:32:23,372] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:32:23,375] [INFO] DFAST_QC result json was written to OceanDNA-b937/dqc_result.json
[2023-03-14 13:32:23,376] [INFO] DFAST_QC completed!
[2023-03-14 13:32:23,376] [INFO] Total running time: 0h1m47s