[2023-03-17 01:44:57,314] [INFO] DFAST_QC pipeline started.
[2023-03-17 01:44:57,314] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 01:44:57,314] [INFO] DQC Reference Directory: /var/lib/cwl/stgd5188aa6-1ded-46c4-b650-7ac1e1037841/dqc_reference
[2023-03-17 01:45:00,548] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 01:45:00,548] [INFO] Task started: Prodigal
[2023-03-17 01:45:00,548] [INFO] Running command: cat /var/lib/cwl/stg06b6cdb2-79ad-4ab4-a99e-60ad7bc10f8f/OceanDNA-b31219.fa | prodigal -d OceanDNA-b31219/cds.fna -a OceanDNA-b31219/protein.faa -g 11 -q > /dev/null
[2023-03-17 01:45:18,957] [INFO] Task succeeded: Prodigal
[2023-03-17 01:45:18,957] [INFO] Task started: HMMsearch
[2023-03-17 01:45:18,957] [INFO] Running command: hmmsearch --tblout OceanDNA-b31219/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd5188aa6-1ded-46c4-b650-7ac1e1037841/dqc_reference/reference_markers.hmm OceanDNA-b31219/protein.faa > /dev/null
[2023-03-17 01:45:19,150] [INFO] Task succeeded: HMMsearch
[2023-03-17 01:45:19,150] [INFO] Found 6/6 markers.
[2023-03-17 01:45:19,172] [INFO] Query marker FASTA was written to OceanDNA-b31219/markers.fasta
[2023-03-17 01:45:19,172] [INFO] Task started: Blastn
[2023-03-17 01:45:19,173] [INFO] Running command: blastn -query OceanDNA-b31219/markers.fasta -db /var/lib/cwl/stgd5188aa6-1ded-46c4-b650-7ac1e1037841/dqc_reference/reference_markers.fasta -out OceanDNA-b31219/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:45:19,910] [INFO] Task succeeded: Blastn
[2023-03-17 01:45:19,911] [INFO] Selected 33 target genomes.
[2023-03-17 01:45:19,911] [INFO] Target genome list was writen to OceanDNA-b31219/target_genomes.txt
[2023-03-17 01:45:19,925] [INFO] Task started: fastANI
[2023-03-17 01:45:19,925] [INFO] Running command: fastANI --query /var/lib/cwl/stg06b6cdb2-79ad-4ab4-a99e-60ad7bc10f8f/OceanDNA-b31219.fa --refList OceanDNA-b31219/target_genomes.txt --output OceanDNA-b31219/fastani_result.tsv --threads 1
[2023-03-17 01:45:45,368] [INFO] Task succeeded: fastANI
[2023-03-17 01:45:45,369] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd5188aa6-1ded-46c4-b650-7ac1e1037841/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 01:45:45,369] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd5188aa6-1ded-46c4-b650-7ac1e1037841/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 01:45:45,384] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 01:45:45,384] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 01:45:45,384] [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
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	76.0871	110	1004	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.075	166	1004	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.0551	171	1004	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	75.9183	89	1004	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	75.8932	81	1004	95	below_threshold
Azospirillum formosense	strain=CC-NFb-7	GCA_013340925.1	861533	861533	type	True	75.8785	103	1004	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	75.8542	64	1004	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	75.7978	125	1004	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	75.7927	99	1004	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	75.773	144	1004	95	below_threshold
Skermanella rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	75.769	105	1004	95	below_threshold
Mesorhizobium helmanticense	strain=CSLC115N	GCA_003034915.1	1776423	1776423	type	True	75.7644	73	1004	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	75.7142	81	1004	95	below_threshold
Dongia mobilis	strain=CGMCC 1.7660	GCA_004363235.1	578943	578943	type	True	75.6598	90	1004	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	75.6132	112	1004	95	below_threshold
Bosea caraganae	strain=RCAM 04680	GCA_003351345.1	2763117	2763117	type	True	75.57	88	1004	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	75.5285	83	1004	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	75.5118	85	1004	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	75.5037	63	1004	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	75.5015	108	1004	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.4895	100	1004	95	below_threshold
Paracoccus limosus	strain=JCM 17370	GCA_009711185.1	913252	913252	type	True	75.4605	54	1004	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	75.4385	108	1004	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	75.3231	55	1004	95	below_threshold
Microvirga antarctica	strain=3D7	GCA_017921815.1	2819233	2819233	type	True	75.2703	50	1004	95	below_threshold
Tepidamorphus gemmatus	strain=DSM 19345	GCA_004346195.1	747076	747076	type	True	75.2666	62	1004	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	75.1755	51	1004	95	below_threshold
Brevundimonas bullata	strain=HAMBI_262	GCA_003350205.1	13160	13160	type	True	75.1366	72	1004	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 01:45:45,385] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31219/tc_result.tsv
[2023-03-17 01:45:45,385] [INFO] ===== Taxonomy check completed =====
[2023-03-17 01:45:45,385] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 01:45:45,385] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd5188aa6-1ded-46c4-b650-7ac1e1037841/dqc_reference/checkm_data
[2023-03-17 01:45:45,386] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 01:45:45,391] [INFO] Task started: CheckM
[2023-03-17 01:45:45,391] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31219/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31219/checkm_input OceanDNA-b31219/checkm_result
[2023-03-17 01:46:32,611] [INFO] Task succeeded: CheckM
[2023-03-17 01:46:32,612] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.63%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-17 01:46:32,614] [INFO] ===== Completeness check finished =====
[2023-03-17 01:46:32,614] [INFO] ===== Start GTDB Search =====
[2023-03-17 01:46:32,614] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31219/markers.fasta)
[2023-03-17 01:46:32,616] [INFO] Task started: Blastn
[2023-03-17 01:46:32,616] [INFO] Running command: blastn -query OceanDNA-b31219/markers.fasta -db /var/lib/cwl/stgd5188aa6-1ded-46c4-b650-7ac1e1037841/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31219/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:46:34,054] [INFO] Task succeeded: Blastn
[2023-03-17 01:46:34,055] [INFO] Selected 28 target genomes.
[2023-03-17 01:46:34,055] [INFO] Target genome list was writen to OceanDNA-b31219/target_genomes_gtdb.txt
[2023-03-17 01:46:35,064] [INFO] Task started: fastANI
[2023-03-17 01:46:35,064] [INFO] Running command: fastANI --query /var/lib/cwl/stg06b6cdb2-79ad-4ab4-a99e-60ad7bc10f8f/OceanDNA-b31219.fa --refList OceanDNA-b31219/target_genomes_gtdb.txt --output OceanDNA-b31219/fastani_result_gtdb.tsv --threads 1
[2023-03-17 01:46:52,358] [INFO] Task succeeded: fastANI
[2023-03-17 01:46:52,372] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 01:46:52,373] [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_016763915.1	s__Casp-alpha2 sp016763915	76.9212	93	1004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686255.1	s__Casp-alpha2 sp002686255	76.8391	173	1004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.76	99.74	0.90	0.88	3	-
GCA_002938075.1	s__Casp-alpha2 sp002938075	76.7493	117	1004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	98.70	98.63	0.78	0.77	3	-
GCA_016187325.1	s__JACPJY01 sp016187325	76.5808	162	1004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__JACPJY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013204045.1	s__JABMOQ01 sp013204045	76.5202	98	1004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16_A;g__JABMOQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002325375.1	s__UBA1479 sp002325375	76.3395	156	1004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	99.20	96.43	0.95	0.85	6	-
GCA_018665815.1	s__UBA3470 sp018665815	76.3162	117	1004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA3470	95.0	99.65	99.59	0.93	0.91	9	-
GCA_002696205.1	s__UBA1479 sp002696205	76.2791	153	1004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001510075.1	s__Casp-alpha2 sp001510075	76.2594	95	1004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002781745.1	s__UBA1479 sp002781745	76.2334	139	1004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002433335.1	s__UBA1479 sp002433335	76.1467	124	1004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859895.1	s__JACZKS01 sp014859895	76.098	122	1004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JACZKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706405.1	s__UBA1479 sp002706405	76.0814	128	1004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	99.68	99.68	0.89	0.89	2	-
GCA_016845145.1	s__TMED8 sp016845145	76.0723	160	1004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__TMED8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576685.1	s__SYSU-D60014 sp003576685	76.0504	105	1004	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_002938315.1	s__Casp-alpha2 sp002938315	75.9931	102	1004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.33	99.24	0.87	0.79	4	-
GCF_016653635.2	s__Skermanella sp016653635	75.9239	110	1004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017644185.1	s__UBA4479 sp017644185	75.9063	115	1004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA4479	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765655.1	s__Skermanella mucosa	75.7825	100	1004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006739055.1	s__Stella vacuolata	75.7726	122	1004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898115.1	s__Bosea sp001898115	75.5275	67	1004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.21	98.43	0.96	0.93	3	-
GCA_016869415.1	s__VGEI01 sp016869415	75.517	68	1004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__VGEI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000350085.1	s__Mesorhizobium metallidurans	75.513	85	1004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006738645.1	s__Stella humosa	75.5037	108	1004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014197805.1	s__Rhodospirillum_A centenum	75.4599	62	1004	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_003577315.1	s__Aquamicrobium_A sp003577315	75.3644	77	1004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153305.1	s__Oceanicola granulosus	75.1391	79	1004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 01:46:52,373] [INFO] GTDB search result was written to OceanDNA-b31219/result_gtdb.tsv
[2023-03-17 01:46:52,373] [INFO] ===== GTDB Search completed =====
[2023-03-17 01:46:52,376] [INFO] DFAST_QC result json was written to OceanDNA-b31219/dqc_result.json
[2023-03-17 01:46:52,376] [INFO] DFAST_QC completed!
[2023-03-17 01:46:52,376] [INFO] Total running time: 0h1m55s