[2023-03-15 10:21:48,019] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:21:48,019] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:21:48,019] [INFO] DQC Reference Directory: /var/lib/cwl/stgac2539bb-dd8f-410f-b283-917cbef55f9e/dqc_reference
[2023-03-15 10:21:49,126] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:21:49,126] [INFO] Task started: Prodigal
[2023-03-15 10:21:49,126] [INFO] Running command: cat /var/lib/cwl/stgcf146237-125e-4a7a-b88b-53cf35452bb1/OceanDNA-b24120.fa | prodigal -d OceanDNA-b24120/cds.fna -a OceanDNA-b24120/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:22:17,020] [INFO] Task succeeded: Prodigal
[2023-03-15 10:22:17,021] [INFO] Task started: HMMsearch
[2023-03-15 10:22:17,021] [INFO] Running command: hmmsearch --tblout OceanDNA-b24120/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac2539bb-dd8f-410f-b283-917cbef55f9e/dqc_reference/reference_markers.hmm OceanDNA-b24120/protein.faa > /dev/null
[2023-03-15 10:22:17,276] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:22:17,277] [INFO] Found 6/6 markers.
[2023-03-15 10:22:17,306] [INFO] Query marker FASTA was written to OceanDNA-b24120/markers.fasta
[2023-03-15 10:22:17,306] [INFO] Task started: Blastn
[2023-03-15 10:22:17,306] [INFO] Running command: blastn -query OceanDNA-b24120/markers.fasta -db /var/lib/cwl/stgac2539bb-dd8f-410f-b283-917cbef55f9e/dqc_reference/reference_markers.fasta -out OceanDNA-b24120/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:22:18,070] [INFO] Task succeeded: Blastn
[2023-03-15 10:22:18,071] [INFO] Selected 32 target genomes.
[2023-03-15 10:22:18,071] [INFO] Target genome list was writen to OceanDNA-b24120/target_genomes.txt
[2023-03-15 10:22:18,174] [INFO] Task started: fastANI
[2023-03-15 10:22:18,174] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf146237-125e-4a7a-b88b-53cf35452bb1/OceanDNA-b24120.fa --refList OceanDNA-b24120/target_genomes.txt --output OceanDNA-b24120/fastani_result.tsv --threads 1
[2023-03-15 10:22:45,968] [INFO] Task succeeded: fastANI
[2023-03-15 10:22:45,968] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac2539bb-dd8f-410f-b283-917cbef55f9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:22:45,968] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac2539bb-dd8f-410f-b283-917cbef55f9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:22:45,985] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:22:45,985] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 10:22:45,985] [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
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.1829	109	1516	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.0651	138	1516	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.0454	142	1516	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	76.0335	139	1516	95	below_threshold
Dongia mobilis	strain=CGMCC 1.7660	GCA_004363235.1	578943	578943	type	True	76.013	103	1516	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	75.965	132	1516	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	75.8672	124	1516	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	75.8321	90	1516	95	below_threshold
Ensifer sojae	strain=CCBAU 05684	GCA_000261485.1	716925	716925	type	True	75.7943	63	1516	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	75.7858	106	1516	95	below_threshold
Novosphingobium aerophilum	strain=4Y4	GCA_014230305.1	2839843	2839843	type	True	75.7781	61	1516	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	75.6459	171	1516	95	below_threshold
Nisaea denitrificans	strain=DSM 18348	GCA_000426505.1	390877	390877	type	True	75.6321	102	1516	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	75.6161	153	1516	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	75.6106	137	1516	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.592	87	1516	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	75.5918	58	1516	95	below_threshold
Bradyrhizobium lablabi	strain=CCBAU 23086	GCA_001440475.1	722472	722472	suspected-type	True	75.5878	108	1516	95	below_threshold
Aliidongia dinghuensis	strain=CGMCC 1.15725	GCA_014643535.1	1867774	1867774	type	True	75.5628	157	1516	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	75.5206	127	1516	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	75.5171	104	1516	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	75.5148	87	1516	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	75.464	66	1516	95	below_threshold
Bradyrhizobium embrapense	strain=SEMIA 6208	GCA_001189235.2	630921	630921	type	True	75.4565	121	1516	95	below_threshold
Jiella endophytica	strain=CBS5Q-3	GCA_004519335.1	2558362	2558362	type	True	75.4361	102	1516	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	75.4065	70	1516	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.3466	123	1516	95	below_threshold
Sphingomonas jejuensis	strain=DSM 27651	GCA_011927695.1	904715	904715	type	True	75.2847	63	1516	95	below_threshold
Bradyrhizobium guangzhouense	strain=CCBAU 51670	GCA_004114955.1	1325095	1325095	type	True	75.1651	111	1516	95	below_threshold
Microvirga massiliensis	strain=JC119	GCA_001006805.1	1033741	1033741	type	True	75.0565	62	1516	95	below_threshold
Microvirga massiliensis		GCA_001050495.1	1033741	1033741	type	True	75.0555	58	1516	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 10:22:45,986] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24120/tc_result.tsv
[2023-03-15 10:22:45,986] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:22:45,986] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:22:45,986] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac2539bb-dd8f-410f-b283-917cbef55f9e/dqc_reference/checkm_data
[2023-03-15 10:22:45,987] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:22:45,993] [INFO] Task started: CheckM
[2023-03-15 10:22:45,993] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24120/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24120/checkm_input OceanDNA-b24120/checkm_result
[2023-03-15 10:23:52,232] [INFO] Task succeeded: CheckM
[2023-03-15 10:23:52,233] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:23:52,236] [INFO] ===== Completeness check finished =====
[2023-03-15 10:23:52,236] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:23:52,236] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24120/markers.fasta)
[2023-03-15 10:23:52,237] [INFO] Task started: Blastn
[2023-03-15 10:23:52,237] [INFO] Running command: blastn -query OceanDNA-b24120/markers.fasta -db /var/lib/cwl/stgac2539bb-dd8f-410f-b283-917cbef55f9e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24120/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:23:53,633] [INFO] Task succeeded: Blastn
[2023-03-15 10:23:53,634] [INFO] Selected 21 target genomes.
[2023-03-15 10:23:53,634] [INFO] Target genome list was writen to OceanDNA-b24120/target_genomes_gtdb.txt
[2023-03-15 10:23:54,586] [INFO] Task started: fastANI
[2023-03-15 10:23:54,586] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf146237-125e-4a7a-b88b-53cf35452bb1/OceanDNA-b24120.fa --refList OceanDNA-b24120/target_genomes_gtdb.txt --output OceanDNA-b24120/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:24:10,448] [INFO] Task succeeded: fastANI
[2023-03-15 10:24:10,460] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:24:10,460] [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_905181725.1	s__UBA830 sp905181725	82.442	761	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479125.1	s__UBA830 sp905479125	81.552	716	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	98.22	98.19	0.84	0.83	3	-
GCA_002689465.1	s__UBA830 sp002689465	78.4565	172	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002471575.1	s__UBA830 sp002471575	77.5594	342	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	97.90	95.90	0.91	0.84	7	-
GCA_002937455.1	s__UBA830 sp002937455	76.3805	70	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	99.94	99.90	0.94	0.84	5	-
GCA_016869145.1	s__VGEU01 sp016869145	76.3246	190	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__VGEU01;g__VGEU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377375.1	s__WHUE01 sp009377375	76.2959	220	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WHUE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018823745.1	s__Oceanibaculum sp018823745	76.2695	125	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	99.98	99.98	1.00	1.00	4	-
GCA_015232485.1	s__JADFZP01 sp015232485	76.1602	81	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	96.70	95.97	0.70	0.69	3	-
GCA_015232025.1	s__JADFZP01 sp015232025	76.1468	74	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640745.1	s__Nisaea sp017640745	75.9453	127	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576685.1	s__SYSU-D60014 sp003576685	75.8968	123	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903822185.1	s__CAIKMD01 sp903822185	75.8474	92	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__CAIKMD01	95.0	99.70	99.51	0.99	0.98	4	-
GCF_001651875.1	s__Sinorhizobium saheli	75.7073	89	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	99.97	99.97	0.96	0.96	2	-
GCF_001440475.1	s__Bradyrhizobium lablabi	75.5775	111	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001189235.2	s__Bradyrhizobium embrapense	75.4946	121	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859315.1	s__SYSU-D60007 sp007859315	75.4613	148	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__SYSU-D60007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744735.1	s__Caenibius sp017744735	75.4227	78	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius	95.0	99.56	99.56	0.78	0.78	2	-
GCA_003152455.1	s__Pseudolabrys sp003152455	75.3704	75	1516	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 10:24:10,460] [INFO] GTDB search result was written to OceanDNA-b24120/result_gtdb.tsv
[2023-03-15 10:24:10,460] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:24:10,463] [INFO] DFAST_QC result json was written to OceanDNA-b24120/dqc_result.json
[2023-03-15 10:24:10,463] [INFO] DFAST_QC completed!
[2023-03-15 10:24:10,463] [INFO] Total running time: 0h2m22s