[2023-03-18 01:06:53,675] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:06:53,676] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:06:53,676] [INFO] DQC Reference Directory: /var/lib/cwl/stge1735188-3a78-4b04-81f3-4d09187c4113/dqc_reference
[2023-03-18 01:06:54,773] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:06:54,774] [INFO] Task started: Prodigal
[2023-03-18 01:06:54,774] [INFO] Running command: cat /var/lib/cwl/stg1f12d9de-f28a-4925-bef4-c93c954850e5/OceanDNA-b23287.fa | prodigal -d OceanDNA-b23287/cds.fna -a OceanDNA-b23287/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:07:08,163] [INFO] Task succeeded: Prodigal
[2023-03-18 01:07:08,164] [INFO] Task started: HMMsearch
[2023-03-18 01:07:08,164] [INFO] Running command: hmmsearch --tblout OceanDNA-b23287/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1735188-3a78-4b04-81f3-4d09187c4113/dqc_reference/reference_markers.hmm OceanDNA-b23287/protein.faa > /dev/null
[2023-03-18 01:07:08,356] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:07:08,357] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1f12d9de-f28a-4925-bef4-c93c954850e5/OceanDNA-b23287.fa]
[2023-03-18 01:07:08,375] [INFO] Query marker FASTA was written to OceanDNA-b23287/markers.fasta
[2023-03-18 01:07:08,376] [INFO] Task started: Blastn
[2023-03-18 01:07:08,376] [INFO] Running command: blastn -query OceanDNA-b23287/markers.fasta -db /var/lib/cwl/stge1735188-3a78-4b04-81f3-4d09187c4113/dqc_reference/reference_markers.fasta -out OceanDNA-b23287/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:07:09,079] [INFO] Task succeeded: Blastn
[2023-03-18 01:07:09,080] [INFO] Selected 28 target genomes.
[2023-03-18 01:07:09,080] [INFO] Target genome list was writen to OceanDNA-b23287/target_genomes.txt
[2023-03-18 01:07:09,098] [INFO] Task started: fastANI
[2023-03-18 01:07:09,098] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f12d9de-f28a-4925-bef4-c93c954850e5/OceanDNA-b23287.fa --refList OceanDNA-b23287/target_genomes.txt --output OceanDNA-b23287/fastani_result.tsv --threads 1
[2023-03-18 01:07:30,269] [INFO] Task succeeded: fastANI
[2023-03-18 01:07:30,269] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1735188-3a78-4b04-81f3-4d09187c4113/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:07:30,270] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1735188-3a78-4b04-81f3-4d09187c4113/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:07:30,284] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:07:30,284] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:07:30,284] [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
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.8926	124	730	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.781	162	730	95	below_threshold
Dongia mobilis	strain=CGMCC 1.7660	GCA_004363235.1	578943	578943	type	True	76.6917	115	730	95	below_threshold
Hypericibacter terrae	strain=R5913	GCA_008728855.1	2602015	2602015	type	True	76.6767	163	730	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.5766	143	730	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.5499	148	730	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.4611	204	730	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.4313	103	730	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.4182	207	730	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	76.3932	136	730	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	76.3592	146	730	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	76.2764	110	730	95	below_threshold
Marivibrio halodurans	strain=CGMCC 1.15697	GCA_017963645.1	2039722	2039722	type	True	76.2251	119	730	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.1351	114	730	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	76.0778	96	730	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	75.9858	130	730	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	75.9365	50	730	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.8807	154	730	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.8294	93	730	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	75.7949	146	730	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_014201415.1	1743235	1743235	type	True	75.6895	60	730	95	below_threshold
Chelatococcus composti	strain=CGMCC 1.15283	GCA_014641535.1	1743235	1743235	type	True	75.6895	60	730	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	75.6849	98	730	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	75.669	61	730	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.5977	95	730	95	below_threshold
Rubellimicrobium aerolatum	strain=DSM 19297	GCA_017872975.1	490979	490979	type	True	75.2104	51	730	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:07:30,285] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23287/tc_result.tsv
[2023-03-18 01:07:30,285] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:07:30,285] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:07:30,285] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1735188-3a78-4b04-81f3-4d09187c4113/dqc_reference/checkm_data
[2023-03-18 01:07:30,286] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:07:30,319] [INFO] Task started: CheckM
[2023-03-18 01:07:30,319] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23287/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23287/checkm_input OceanDNA-b23287/checkm_result
[2023-03-18 01:08:06,519] [INFO] Task succeeded: CheckM
[2023-03-18 01:08:06,520] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:08:06,537] [INFO] ===== Completeness check finished =====
[2023-03-18 01:08:06,537] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:08:06,538] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23287/markers.fasta)
[2023-03-18 01:08:06,539] [INFO] Task started: Blastn
[2023-03-18 01:08:06,539] [INFO] Running command: blastn -query OceanDNA-b23287/markers.fasta -db /var/lib/cwl/stge1735188-3a78-4b04-81f3-4d09187c4113/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23287/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:08:07,803] [INFO] Task succeeded: Blastn
[2023-03-18 01:08:07,813] [INFO] Selected 23 target genomes.
[2023-03-18 01:08:07,813] [INFO] Target genome list was writen to OceanDNA-b23287/target_genomes_gtdb.txt
[2023-03-18 01:08:07,837] [INFO] Task started: fastANI
[2023-03-18 01:08:07,837] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f12d9de-f28a-4925-bef4-c93c954850e5/OceanDNA-b23287.fa --refList OceanDNA-b23287/target_genomes_gtdb.txt --output OceanDNA-b23287/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:08:24,607] [INFO] Task succeeded: fastANI
[2023-03-18 01:08:24,620] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:08:24,620] [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_018699755.1	s__JABIRQ01 sp018699755	84.383	524	730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CADEGL01;f__CADEGL01;g__JABIRQ01	95.0	98.91	98.91	0.81	0.81	2	-
GCA_018823745.1	s__Oceanibaculum sp018823745	76.9425	139	730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	99.98	99.98	1.00	1.00	4	-
GCA_003576685.1	s__SYSU-D60014 sp003576685	76.7593	122	730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60014	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728855.1	s__Hypericibacter terrae	76.6889	162	730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Hypericibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826885.1	s__CADEGL01 sp902826885	76.6459	155	730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CADEGL01;f__CADEGL01;g__CADEGL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006738865.1	s__Stella sp006738865	76.5237	141	730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006739055.1	s__Stella vacuolata	76.4814	138	730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344765.1	s__Ferruginivarius sediminum	76.4704	105	730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__Ferruginivarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	76.4134	209	730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014197805.1	s__Rhodospirillum_A centenum	76.3969	108	730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Rhodospirillum_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902826565.1	s__CADEFF01 sp902826565	76.3855	129	730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__CADEFF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523655.1	s__Bin65 sp011523655	76.3795	133	730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Bin65;f__Bin65;g__Bin65	95.0	95.25	95.16	0.87	0.83	5	-
GCA_016195085.1	s__JACQAG01 sp016195085	76.3747	118	730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVZ01;f__SHVZ01;g__JACQAG01	95.0	99.88	99.88	0.96	0.96	2	-
GCA_005884705.1	s__Reyranella sp005884705	76.2087	98	730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002281855.1	s__Reyranella sp002281855	76.1576	117	730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	99.99	99.99	0.99	0.99	3	-
GCA_016869975.1	s__JAFAZJ01 sp016869975	76.1511	119	730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__JAFAZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240745.1	s__Reyranella sp018240745	76.1432	129	730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016699855.1	s__GCA-016699855 sp016699855	76.1305	124	730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__GCA-016699855	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793165.1	s__CAIOSQ01 sp016793165	76.0642	125	730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__CAIOSQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000164635.1	s__Roseomonas cervicalis	76.0213	91	730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011087645.1	s__JABDJY01 sp011087645	75.8605	74	730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABDJY01	95.0	99.97	99.97	0.97	0.97	2	-
GCA_016872535.1	s__2-12-FULL-67-15 sp016872535	75.7212	82	730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-12-FULL-67-15;g__2-12-FULL-67-15	95.0	95.80	95.80	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-03-18 01:08:24,620] [INFO] GTDB search result was written to OceanDNA-b23287/result_gtdb.tsv
[2023-03-18 01:08:24,620] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:08:24,623] [INFO] DFAST_QC result json was written to OceanDNA-b23287/dqc_result.json
[2023-03-18 01:08:24,623] [INFO] DFAST_QC completed!
[2023-03-18 01:08:24,623] [INFO] Total running time: 0h1m31s