[2023-03-19 04:55:39,431] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:55:39,433] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:55:39,433] [INFO] DQC Reference Directory: /var/lib/cwl/stg577bd177-e737-476b-ba0d-7474a6db74ab/dqc_reference
[2023-03-19 04:55:40,560] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:55:40,561] [INFO] Task started: Prodigal
[2023-03-19 04:55:40,561] [INFO] Running command: cat /var/lib/cwl/stg6e1c73af-1b8d-4096-842f-d28de425d113/OceanDNA-b31471.fa | prodigal -d OceanDNA-b31471/cds.fna -a OceanDNA-b31471/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:55:55,090] [INFO] Task succeeded: Prodigal
[2023-03-19 04:55:55,091] [INFO] Task started: HMMsearch
[2023-03-19 04:55:55,091] [INFO] Running command: hmmsearch --tblout OceanDNA-b31471/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg577bd177-e737-476b-ba0d-7474a6db74ab/dqc_reference/reference_markers.hmm OceanDNA-b31471/protein.faa > /dev/null
[2023-03-19 04:55:55,258] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:55:55,258] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6e1c73af-1b8d-4096-842f-d28de425d113/OceanDNA-b31471.fa]
[2023-03-19 04:55:55,285] [INFO] Query marker FASTA was written to OceanDNA-b31471/markers.fasta
[2023-03-19 04:55:55,286] [INFO] Task started: Blastn
[2023-03-19 04:55:55,286] [INFO] Running command: blastn -query OceanDNA-b31471/markers.fasta -db /var/lib/cwl/stg577bd177-e737-476b-ba0d-7474a6db74ab/dqc_reference/reference_markers.fasta -out OceanDNA-b31471/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:55:56,138] [INFO] Task succeeded: Blastn
[2023-03-19 04:55:56,140] [INFO] Selected 24 target genomes.
[2023-03-19 04:55:56,140] [INFO] Target genome list was writen to OceanDNA-b31471/target_genomes.txt
[2023-03-19 04:55:56,157] [INFO] Task started: fastANI
[2023-03-19 04:55:56,158] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e1c73af-1b8d-4096-842f-d28de425d113/OceanDNA-b31471.fa --refList OceanDNA-b31471/target_genomes.txt --output OceanDNA-b31471/fastani_result.tsv --threads 1
[2023-03-19 04:56:12,116] [INFO] Task succeeded: fastANI
[2023-03-19 04:56:12,117] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg577bd177-e737-476b-ba0d-7474a6db74ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:56:12,117] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg577bd177-e737-476b-ba0d-7474a6db74ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:56:12,131] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2023-03-19 04:56:12,131] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-19 04:56:12,131] [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
Hankyongella ginsenosidimutans	strain=W1-2-3	GCA_005144965.1	1763828	1763828	type	True	98.3097	727	793	95	conclusive
Pedomonas mirosovicensis	strain=A1X5R2	GCA_022569295.1	2908641	2908641	type	True	77.6936	220	793	95	below_threshold
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	77.4668	160	793	95	below_threshold
Sphingomonas chungangi	strain=CGMCC 1.13654	GCA_013778325.1	2683589	2683589	type	True	77.2481	164	793	95	below_threshold
Sphingomonas sanxanigenens	strain=NX02	GCA_000512205.2	397260	397260	type	True	77.1955	180	793	95	below_threshold
Sphingomonas jejuensis	strain=DSM 27651	GCA_011927695.1	904715	904715	type	True	77.1861	142	793	95	below_threshold
Sphingomonas spermidinifaciens	strain=9NM-10	GCA_002351485.1	1141889	1141889	type	True	77.084	124	793	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	77.0259	186	793	95	below_threshold
Sphingomonas ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	77.0168	144	793	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	76.9811	154	793	95	below_threshold
Sphingomonas jaspsi	strain=DSM 18422	GCA_000585415.1	392409	392409	type	True	76.9674	120	793	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	76.9634	155	793	95	below_threshold
Sphingomonas endophytica	strain=DSM 101535	GCA_014199415.1	869719	869719	type	True	76.9575	161	793	95	below_threshold
Sphingomonas adhaesiva	strain=NBRC 15099	GCA_001592345.1	28212	28212	type	True	76.8811	160	793	95	below_threshold
Sphingomonas adhaesiva	strain=DSM 7418	GCA_002374855.1	28212	28212	type	True	76.7822	176	793	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	76.6521	132	793	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	76.5666	138	793	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	76.5436	134	793	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	76.5282	112	793	95	below_threshold
Cucumibacter marinus	strain=DSM 18995	GCA_000429865.1	1121252	1121252	type	True	76.4716	53	793	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	76.4554	130	793	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.3439	110	793	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	76.2889	121	793	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.1834	94	793	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:56:12,133] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31471/tc_result.tsv
[2023-03-19 04:56:12,135] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:56:12,135] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:56:12,136] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg577bd177-e737-476b-ba0d-7474a6db74ab/dqc_reference/checkm_data
[2023-03-19 04:56:12,136] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:56:12,142] [INFO] Task started: CheckM
[2023-03-19 04:56:12,142] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31471/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31471/checkm_input OceanDNA-b31471/checkm_result
[2023-03-19 04:56:51,155] [INFO] Task succeeded: CheckM
[2023-03-19 04:56:51,155] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:56:51,173] [INFO] ===== Completeness check finished =====
[2023-03-19 04:56:51,173] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:56:51,173] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31471/markers.fasta)
[2023-03-19 04:56:51,175] [INFO] Task started: Blastn
[2023-03-19 04:56:51,175] [INFO] Running command: blastn -query OceanDNA-b31471/markers.fasta -db /var/lib/cwl/stg577bd177-e737-476b-ba0d-7474a6db74ab/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31471/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:56:52,849] [INFO] Task succeeded: Blastn
[2023-03-19 04:56:52,850] [INFO] Selected 26 target genomes.
[2023-03-19 04:56:52,850] [INFO] Target genome list was writen to OceanDNA-b31471/target_genomes_gtdb.txt
[2023-03-19 04:56:52,871] [INFO] Task started: fastANI
[2023-03-19 04:56:52,871] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e1c73af-1b8d-4096-842f-d28de425d113/OceanDNA-b31471.fa --refList OceanDNA-b31471/target_genomes_gtdb.txt --output OceanDNA-b31471/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:57:09,897] [INFO] Task succeeded: fastANI
[2023-03-19 04:57:09,912] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:57:09,912] [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_005144965.1	s__Hankyongella ginsenosidimutans	98.3097	727	793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Hankyongella	95.0	98.05	98.05	0.80	0.80	2	conclusive
GCF_013778325.1	s__Sphingomonas_N chungangi	77.2472	165	793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018006725.1	s__Rhizorhabdus sp018006725	77.2336	152	793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927695.1	s__Sphingomonas_K jejuensis	77.2056	141	793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004681125.1	s__Polymorphobacter_A arshaanensis	77.1618	143	793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793845.1	s__Sphingosinicella sp016793845	77.111	150	793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000419605.1	s__Sphingomonas phyllosphaerae_B	77.0242	114	793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199415.1	s__Sphingomonas endophytica	76.9893	159	793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.00	98.00	0.92	0.92	2	-
GCF_004792695.1	s__Sphingomonas naasensis	76.9811	154	793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016820445.1	s__Sphingomonas sp016820445	76.9674	143	793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.21	97.21	0.90	0.90	2	-
GCF_000585415.1	s__Sphingomicrobium jaspsi	76.9476	121	793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000787715.1	s__Sphingomonas parapaucimobilis	76.8503	149	793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.90	97.90	0.87	0.87	2	-
GCF_014194975.1	s__Sphingomonas sp014194975	76.8248	184	793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002374855.1	s__Sphingomonas adhaesiva	76.7958	175	793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.76	99.56	0.89	0.87	3	-
GCF_000092925.1	s__Starkeya novella	76.6229	134	793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006438735.1	s__Sphingomonas koreensis_A	76.6067	132	793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.05	96.05	0.80	0.80	2	-
GCF_014349105.1	s__17J80-11 sp014349105	76.5744	142	793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__17J80-11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630065.1	s__Blastochloris sulfoviridis	76.5666	138	793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Blastochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421535.1	s__Sphingomonas sp001421535	76.5295	129	793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100155.1	s__Ancylobacter rudongensis	76.5282	112	793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	96.36	96.36	0.88	0.88	2	-
GCF_000429865.1	s__Cucumibacter marinus	76.4716	53	793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Cucumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016629525.1	s__Kaistia sp016629525	76.2812	123	793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016780605.1	s__Reyranella sp016780605	76.1882	73	793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449475.1	s__Angulomicrobium sp018449475	76.163	129	793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Angulomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304475.1	s__Phreatobacter sp017304475	76.151	149	793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002073975.1	s__Rhodovulum sp002073975	76.032	79	793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:57:09,912] [INFO] GTDB search result was written to OceanDNA-b31471/result_gtdb.tsv
[2023-03-19 04:57:09,912] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:57:09,915] [INFO] DFAST_QC result json was written to OceanDNA-b31471/dqc_result.json
[2023-03-19 04:57:09,915] [INFO] DFAST_QC completed!
[2023-03-19 04:57:09,915] [INFO] Total running time: 0h1m30s