[2023-03-19 03:22:59,815] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:22:59,823] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:22:59,823] [INFO] DQC Reference Directory: /var/lib/cwl/stg694af588-f424-4f62-9b15-b5dc7b11ecd7/dqc_reference
[2023-03-19 03:23:00,904] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:23:00,905] [INFO] Task started: Prodigal
[2023-03-19 03:23:00,905] [INFO] Running command: cat /var/lib/cwl/stg9d88b301-0a32-4447-ad59-6bddbe0043fa/OceanDNA-b26776.fa | prodigal -d OceanDNA-b26776/cds.fna -a OceanDNA-b26776/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:23:12,218] [INFO] Task succeeded: Prodigal
[2023-03-19 03:23:12,218] [INFO] Task started: HMMsearch
[2023-03-19 03:23:12,218] [INFO] Running command: hmmsearch --tblout OceanDNA-b26776/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg694af588-f424-4f62-9b15-b5dc7b11ecd7/dqc_reference/reference_markers.hmm OceanDNA-b26776/protein.faa > /dev/null
[2023-03-19 03:23:12,428] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:23:12,429] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9d88b301-0a32-4447-ad59-6bddbe0043fa/OceanDNA-b26776.fa]
[2023-03-19 03:23:12,509] [INFO] Query marker FASTA was written to OceanDNA-b26776/markers.fasta
[2023-03-19 03:23:12,510] [INFO] Task started: Blastn
[2023-03-19 03:23:12,510] [INFO] Running command: blastn -query OceanDNA-b26776/markers.fasta -db /var/lib/cwl/stg694af588-f424-4f62-9b15-b5dc7b11ecd7/dqc_reference/reference_markers.fasta -out OceanDNA-b26776/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:23:13,212] [INFO] Task succeeded: Blastn
[2023-03-19 03:23:13,235] [INFO] Selected 35 target genomes.
[2023-03-19 03:23:13,236] [INFO] Target genome list was writen to OceanDNA-b26776/target_genomes.txt
[2023-03-19 03:23:13,255] [INFO] Task started: fastANI
[2023-03-19 03:23:13,255] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d88b301-0a32-4447-ad59-6bddbe0043fa/OceanDNA-b26776.fa --refList OceanDNA-b26776/target_genomes.txt --output OceanDNA-b26776/fastani_result.tsv --threads 1
[2023-03-19 03:23:41,126] [INFO] Task succeeded: fastANI
[2023-03-19 03:23:41,126] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg694af588-f424-4f62-9b15-b5dc7b11ecd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:23:41,126] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg694af588-f424-4f62-9b15-b5dc7b11ecd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:23:41,144] [INFO] Found 34 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:23:41,144] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 03:23:41,144] [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
Aurantimonas manganoxydans	strain=SI85-9A1	GCA_000153465.1	651183	651183	type	True	76.6768	139	581	95	below_threshold
Aurantimonas manganoxydans	strain=DSM 21871	GCA_001463865.1	651183	651183	type	True	76.6757	138	581	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	76.6305	137	581	95	below_threshold
Aureimonas leprariae	strain=YIM 132180	GCA_008802405.1	2615207	2615207	type	True	76.6179	137	581	95	below_threshold
Aureimonas pseudogalii	strain=DSM 102238	GCA_014196835.1	1744844	1744844	type	True	76.521	141	581	95	below_threshold
Chelativorans alearense	strain=UJN715	GCA_010993735.1	2681495	2681495	type	True	76.5171	110	581	95	below_threshold
Mesorhizobium intechi	strain=BD68	GCA_002879535.2	537601	537601	type	True	76.4555	103	581	95	below_threshold
Aureimonas populi	strain=KCTC 42087	GCA_017815515.1	1701758	1701758	type	True	76.421	121	581	95	below_threshold
Aurantimonas aggregata	strain=KCTC 52919	GCA_010500835.1	2047720	2047720	type	True	76.42	118	581	95	below_threshold
Jiella pacifica	strain=40Bstr34	GCA_010500815.1	2696469	2696469	type	True	76.3228	120	581	95	below_threshold
Chelativorans xinjiangense	strain=lm93	GCA_009812055.1	2681485	2681485	type	True	76.3211	123	581	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	76.2668	123	581	95	below_threshold
Rhizobium rhizolycopersici	strain=DBTS2	GCA_013378445.1	2746702	2746702	type	True	76.2411	100	581	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_014201415.1	1743235	1743235	type	True	76.2398	98	581	95	below_threshold
Lutibaculum baratangense	strain=AMV1	GCA_000496075.1	1358440	1358440	type	True	76.2379	97	581	95	below_threshold
Chelatococcus composti	strain=CGMCC 1.15283	GCA_014641535.1	1743235	1743235	type	True	76.2218	99	581	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	76.2216	100	581	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	76.1049	118	581	95	below_threshold
Methylobacterium radiotolerans	strain=NBRC 15690	GCA_007991055.1	31998	31998	type	True	75.954	114	581	95	below_threshold
Methylobacterium radiotolerans	strain=JCM 2831	GCA_000019725.1	31998	31998	type	True	75.9347	117	581	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	75.9213	131	581	95	below_threshold
Methylobacterium symbioticum	strain=SB0023/3	GCA_902141845.1	2584084	2584084	type	True	75.8992	116	581	95	below_threshold
Methylorubrum aminovorans	strain=NBRC 15686	GCA_022179725.1	269069	269069	type	True	75.8959	102	581	95	below_threshold
Methylobacterium longum	strain=DSM 23933	GCA_022179385.1	767694	767694	type	True	75.8394	90	581	95	below_threshold
Sinorhizobium medicae	strain=A321	GCA_009599935.1	110321	110321	type	True	75.7719	59	581	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	75.7488	101	581	95	below_threshold
Sinorhizobium medicae	strain=USDA1037	GCA_007827695.1	110321	110321	type	True	75.7471	60	581	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	75.7054	102	581	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	75.6237	100	581	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	75.6116	103	581	95	below_threshold
Parvularcula oceani	strain=JLT2013	GCA_000733125.1	1247963	1247963	type	True	75.521	57	581	95	below_threshold
Parvularcula dongshanensis	strain=DSM 102850	GCA_014199615.1	1173995	1173995	type	True	75.5109	61	581	95	below_threshold
Amphiplicatus metriothermophilus	strain=CGMCC 1.12710	GCA_900199215.1	1519374	1519374	type	True	75.177	55	581	95	below_threshold
Amphiplicatus metriothermophilus	strain=DSM 105738	GCA_014199495.1	1519374	1519374	type	True	75.177	55	581	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 03:23:41,155] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26776/tc_result.tsv
[2023-03-19 03:23:41,177] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:23:41,177] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:23:41,177] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg694af588-f424-4f62-9b15-b5dc7b11ecd7/dqc_reference/checkm_data
[2023-03-19 03:23:41,178] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:23:41,183] [INFO] Task started: CheckM
[2023-03-19 03:23:41,184] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26776/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26776/checkm_input OceanDNA-b26776/checkm_result
[2023-03-19 03:24:13,173] [INFO] Task succeeded: CheckM
[2023-03-19 03:24:13,173] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:24:13,287] [INFO] ===== Completeness check finished =====
[2023-03-19 03:24:13,287] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:24:13,287] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26776/markers.fasta)
[2023-03-19 03:24:13,288] [INFO] Task started: Blastn
[2023-03-19 03:24:13,289] [INFO] Running command: blastn -query OceanDNA-b26776/markers.fasta -db /var/lib/cwl/stg694af588-f424-4f62-9b15-b5dc7b11ecd7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26776/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:24:14,516] [INFO] Task succeeded: Blastn
[2023-03-19 03:24:14,523] [INFO] Selected 35 target genomes.
[2023-03-19 03:24:14,523] [INFO] Target genome list was writen to OceanDNA-b26776/target_genomes_gtdb.txt
[2023-03-19 03:24:14,693] [INFO] Task started: fastANI
[2023-03-19 03:24:14,693] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d88b301-0a32-4447-ad59-6bddbe0043fa/OceanDNA-b26776.fa --refList OceanDNA-b26776/target_genomes_gtdb.txt --output OceanDNA-b26776/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:24:48,274] [INFO] Task succeeded: fastANI
[2023-03-19 03:24:48,292] [INFO] Found 33 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 03:24:48,292] [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
GCF_000497755.1	s__Aliihoeflea sp000497755	76.9161	129	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aliihoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153465.1	s__Aurantimonas manganoxydans	76.6925	138	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.4342	99.99	99.99	1.00	1.00	2	-
GCF_001463765.1	s__Aureimonas sp001463765	76.6598	130	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993735.1	s__Chelativorans alearense	76.534	109	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Chelativorans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425575.1	s__Leaf443 sp001425575	76.528	171	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Leaf443	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196835.1	s__Aureimonas pseudogalii	76.521	140	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016467435.1	s__Mesorhizobium sp016467435	76.4456	117	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.58	98.58	0.95	0.95	2	-
GCF_002879535.1	s__Mesorhizobium intechi	76.4419	105	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500835.1	s__Aurantimonas aggregata	76.4202	118	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002893625.1	s__Mangrovicella endophytica	76.3717	112	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mangrovicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898995.1	s__63-22 sp001898995	76.3533	100	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__63-22	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014191375.1	s__Paramesorhizobium sp014191375	76.3407	98	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paramesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009812055.1	s__Chelativorans xinjiangense	76.3359	122	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Chelativorans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177325.1	s__Mesorhizobium_A australicum_A	76.324	141	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104035.1	s__Aureimonas jatrophae	76.3176	116	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	99.97	99.97	0.99	0.99	2	-
GCF_001463705.1	s__Aureimonas sp001463705	76.2603	133	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000496075.1	s__Lutibaculum baratangense	76.2564	96	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Tepidamorphaceae;g__Lutibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008039875.1	s__Methylobacterium sp008039875	76.241	109	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.26	97.89	0.94	0.87	4	-
GCF_002295115.1	s__Mesorhizobium sp002295115	76.2247	129	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.79	96.42	0.94	0.85	9	-
GCF_006442965.1	s__Mesorhizobium sp006442965	76.1966	127	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_005503535.1	s__Mesorhizobium sp005503535	76.1295	116	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830515.1	s__Mesorhizobium tianshanense	76.0921	110	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199915.1	s__Prosthecomicrobium pneumaticum	76.0901	127	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Prosthecomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902141845.1	s__Methylobacterium symbioticum	75.9096	118	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827695.1	s__Sinorhizobium medicae	75.7264	61	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	99.40	99.02	0.92	0.89	63	-
GCF_004114535.1	s__Bradyrhizobium nanningense	75.6922	90	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.21	99.11	0.94	0.93	3	-
GCF_016031635.1	s__Bradyrhizobium diversitatis	75.6071	110	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.2113	96.64	96.14	0.84	0.83	6	-
GCF_014198245.1	s__Bradyrhizobium sp014198245	75.5927	100	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000733125.1	s__Parvularcula oceani	75.521	57	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199615.1	s__Parvularcula dongshanensis	75.5109	61	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000296215.2	s__Bradyrhizobium sp000296215	75.4947	102	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.76	97.76	0.87	0.87	2	-
GCA_003576705.1	s__SYSU-D60015 sp003576705	75.4482	90	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__SYSU-D60015	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900199215.1	s__Amphiplicatus metriothermophilus	75.177	55	581	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Amphiplicatus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-19 03:24:48,295] [INFO] GTDB search result was written to OceanDNA-b26776/result_gtdb.tsv
[2023-03-19 03:24:48,298] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:24:48,304] [INFO] DFAST_QC result json was written to OceanDNA-b26776/dqc_result.json
[2023-03-19 03:24:48,304] [INFO] DFAST_QC completed!
[2023-03-19 03:24:48,304] [INFO] Total running time: 0h1m48s