[2023-03-19 04:46:13,841] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:46:13,841] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:46:13,842] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb83117d-c9f2-4752-8acf-a8c2eac32c2c/dqc_reference
[2023-03-19 04:46:14,955] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:46:14,956] [INFO] Task started: Prodigal
[2023-03-19 04:46:14,956] [INFO] Running command: cat /var/lib/cwl/stgf1d52245-d124-4425-bfec-d13244f8a579/OceanDNA-b1791.fa | prodigal -d OceanDNA-b1791/cds.fna -a OceanDNA-b1791/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:46:30,549] [INFO] Task succeeded: Prodigal
[2023-03-19 04:46:30,549] [INFO] Task started: HMMsearch
[2023-03-19 04:46:30,549] [INFO] Running command: hmmsearch --tblout OceanDNA-b1791/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb83117d-c9f2-4752-8acf-a8c2eac32c2c/dqc_reference/reference_markers.hmm OceanDNA-b1791/protein.faa > /dev/null
[2023-03-19 04:46:30,726] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:46:30,726] [INFO] Found 6/6 markers.
[2023-03-19 04:46:30,743] [INFO] Query marker FASTA was written to OceanDNA-b1791/markers.fasta
[2023-03-19 04:46:30,744] [INFO] Task started: Blastn
[2023-03-19 04:46:30,744] [INFO] Running command: blastn -query OceanDNA-b1791/markers.fasta -db /var/lib/cwl/stgcb83117d-c9f2-4752-8acf-a8c2eac32c2c/dqc_reference/reference_markers.fasta -out OceanDNA-b1791/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:46:31,492] [INFO] Task succeeded: Blastn
[2023-03-19 04:46:31,493] [INFO] Selected 27 target genomes.
[2023-03-19 04:46:31,493] [INFO] Target genome list was writen to OceanDNA-b1791/target_genomes.txt
[2023-03-19 04:46:31,508] [INFO] Task started: fastANI
[2023-03-19 04:46:31,508] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1d52245-d124-4425-bfec-d13244f8a579/OceanDNA-b1791.fa --refList OceanDNA-b1791/target_genomes.txt --output OceanDNA-b1791/fastani_result.tsv --threads 1
[2023-03-19 04:46:52,604] [INFO] Task succeeded: fastANI
[2023-03-19 04:46:52,605] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb83117d-c9f2-4752-8acf-a8c2eac32c2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:46:52,605] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb83117d-c9f2-4752-8acf-a8c2eac32c2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:46:52,616] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:46:52,616] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:46:52,616] [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	76.9634	158	814	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.6764	154	814	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	76.6614	108	814	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.4297	111	814	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	76.3961	146	814	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.384	158	814	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.9789	141	814	95	below_threshold
Gordonia paraffinivorans	strain=NBRC 108238	GCA_000344155.1	175628	175628	type	True	75.7953	67	814	95	below_threshold
Streptomyces angustmyceticus	strain=NRRL B-2347	GCA_002154415.1	285578	285578	type	True	75.4561	78	814	95	below_threshold
Streptomyces angustmyceticus	strain=NBRC 3934	GCA_009176265.1	285578	285578	type	True	75.3851	87	814	95	below_threshold
Saccharopolyspora elongata	strain=7K502	GCA_004348985.1	2530387	2530387	type	True	75.3221	90	814	95	below_threshold
Streptomyces angustmyceticus	strain=JCM 4053	GCA_019933235.1	285578	285578	type	True	75.3101	86	814	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	75.2929	65	814	95	below_threshold
Micromonospora phaseoli	strain=DSM 45730	GCA_003253475.1	1144548	1144548	type	True	75.265	64	814	95	below_threshold
Micromonospora phaseoli	strain=CGMCC 4.7038	GCA_900109115.1	1144548	1144548	type	True	75.2543	65	814	95	below_threshold
Longispora albida	strain=DSM 44784	GCA_000379825.1	203523	203523	type	True	75.1899	58	814	95	below_threshold
Catellatospora vulcania	strain=NEAU-JM1	GCA_009720385.1	1460450	1460450	type	True	75.1741	75	814	95	below_threshold
Fodinicola acaciae	strain=GKU 173	GCA_010993745.1	2681555	2681555	type	True	75.1492	78	814	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:46:52,616] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1791/tc_result.tsv
[2023-03-19 04:46:52,616] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:46:52,617] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:46:52,617] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb83117d-c9f2-4752-8acf-a8c2eac32c2c/dqc_reference/checkm_data
[2023-03-19 04:46:52,617] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:46:52,621] [INFO] Task started: CheckM
[2023-03-19 04:46:52,621] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1791/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1791/checkm_input OceanDNA-b1791/checkm_result
[2023-03-19 04:47:35,526] [INFO] Task succeeded: CheckM
[2023-03-19 04:47:35,526] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:47:35,574] [INFO] ===== Completeness check finished =====
[2023-03-19 04:47:35,575] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:47:35,575] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1791/markers.fasta)
[2023-03-19 04:47:35,576] [INFO] Task started: Blastn
[2023-03-19 04:47:35,576] [INFO] Running command: blastn -query OceanDNA-b1791/markers.fasta -db /var/lib/cwl/stgcb83117d-c9f2-4752-8acf-a8c2eac32c2c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1791/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:47:36,927] [INFO] Task succeeded: Blastn
[2023-03-19 04:47:36,947] [INFO] Selected 10 target genomes.
[2023-03-19 04:47:36,947] [INFO] Target genome list was writen to OceanDNA-b1791/target_genomes_gtdb.txt
[2023-03-19 04:47:36,983] [INFO] Task started: fastANI
[2023-03-19 04:47:36,983] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1d52245-d124-4425-bfec-d13244f8a579/OceanDNA-b1791.fa --refList OceanDNA-b1791/target_genomes_gtdb.txt --output OceanDNA-b1791/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:47:43,123] [INFO] Task succeeded: fastANI
[2023-03-19 04:47:43,130] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:47:43,130] [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_002694825.1	s__UBA11606 sp002694825	96.7471	675	814	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	97.28	96.77	0.84	0.81	7	conclusive
GCA_002699625.1	s__UBA11606 sp002699625	94.3426	587	814	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729125.1	s__UBA11606 sp002729125	91.6836	647	814	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	99.78	99.78	0.92	0.92	2	-
GCA_016845585.1	s__UBA11606 sp016845585	78.6188	314	814	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480195.1	s__UBA11606 sp905480195	78.2591	319	814	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003697065.1	s__J010 sp003697065	77.4138	170	814	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__J010	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003231645.1	s__SZUA-87 sp003231645	77.2835	168	814	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__SZUA-87	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009844405.1	s__VYCW01 sp009844405	76.9435	145	814	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__VYCW01	95.0	99.44	99.17	0.93	0.90	7	-
GCA_009843915.1	s__VYCW01 sp009843915	76.7556	131	814	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__VYCW01	95.0	97.45	96.57	0.82	0.78	5	-
GCA_016185275.1	s__JACPNX01 sp016185275	76.2973	109	814	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JACPNX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:47:43,130] [INFO] GTDB search result was written to OceanDNA-b1791/result_gtdb.tsv
[2023-03-19 04:47:43,130] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:47:43,132] [INFO] DFAST_QC result json was written to OceanDNA-b1791/dqc_result.json
[2023-03-19 04:47:43,132] [INFO] DFAST_QC completed!
[2023-03-19 04:47:43,132] [INFO] Total running time: 0h1m29s