[2023-03-15 05:51:32,067] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:51:32,068] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:51:32,068] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d706730-9c62-4f99-87aa-b520ca306632/dqc_reference
[2023-03-15 05:51:33,652] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:51:33,652] [INFO] Task started: Prodigal
[2023-03-15 05:51:33,652] [INFO] Running command: cat /var/lib/cwl/stg0e252b82-82c4-4b63-805c-6d6ffb6351f5/OceanDNA-b24725.fa | prodigal -d OceanDNA-b24725/cds.fna -a OceanDNA-b24725/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:51:49,698] [INFO] Task succeeded: Prodigal
[2023-03-15 05:51:49,698] [INFO] Task started: HMMsearch
[2023-03-15 05:51:49,698] [INFO] Running command: hmmsearch --tblout OceanDNA-b24725/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d706730-9c62-4f99-87aa-b520ca306632/dqc_reference/reference_markers.hmm OceanDNA-b24725/protein.faa > /dev/null
[2023-03-15 05:51:49,928] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:51:49,928] [INFO] Found 6/6 markers.
[2023-03-15 05:51:49,960] [INFO] Query marker FASTA was written to OceanDNA-b24725/markers.fasta
[2023-03-15 05:51:49,960] [INFO] Task started: Blastn
[2023-03-15 05:51:49,960] [INFO] Running command: blastn -query OceanDNA-b24725/markers.fasta -db /var/lib/cwl/stg8d706730-9c62-4f99-87aa-b520ca306632/dqc_reference/reference_markers.fasta -out OceanDNA-b24725/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:51:50,743] [INFO] Task succeeded: Blastn
[2023-03-15 05:51:50,746] [INFO] Selected 34 target genomes.
[2023-03-15 05:51:50,746] [INFO] Target genome list was writen to OceanDNA-b24725/target_genomes.txt
[2023-03-15 05:51:50,774] [INFO] Task started: fastANI
[2023-03-15 05:51:50,774] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e252b82-82c4-4b63-805c-6d6ffb6351f5/OceanDNA-b24725.fa --refList OceanDNA-b24725/target_genomes.txt --output OceanDNA-b24725/fastani_result.tsv --threads 1
[2023-03-15 05:52:19,325] [INFO] Task succeeded: fastANI
[2023-03-15 05:52:19,326] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d706730-9c62-4f99-87aa-b520ca306632/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:52:19,326] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d706730-9c62-4f99-87aa-b520ca306632/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:52:19,343] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:52:19,343] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 05:52:19,343] [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
Minwuia thermotolerans	strain=SY3-15	GCA_002924445.1	2056226	2056226	type	True	78.3347	357	825	95	below_threshold
Ferrovibrio terrae	strain=K5	GCA_007197755.1	2594003	2594003	type	True	76.1872	76	825	95	below_threshold
Roseospira navarrensis	strain=DSM 15114	GCA_009601025.1	140058	140058	type	True	76.0838	98	825	95	below_threshold
Camelimonas lactis	strain=DSM 22958	GCA_004342915.1	659006	659006	type	True	75.9751	61	825	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	75.9308	65	825	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	75.9196	51	825	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	75.8931	52	825	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	75.8585	82	825	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	75.8087	120	825	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	75.7919	77	825	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.7699	100	825	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	75.7618	71	825	95	below_threshold
Tistrella bauzanensis	strain=CGMCC 1.10188	GCA_014636235.1	657419	657419	type	True	75.7581	73	825	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	75.689	69	825	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	75.68	101	825	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	75.6744	55	825	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	75.6715	72	825	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	75.6532	79	825	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	75.6355	99	825	95	below_threshold
Azospirillum melinis	strain=TMCY0552	GCA_013340935.1	328839	328839	type	True	75.591	110	825	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	75.5688	110	825	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	75.5501	76	825	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	75.5499	69	825	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	75.5293	67	825	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	75.5005	73	825	95	below_threshold
Methylobacterium terrae	strain=17Sr1-28	GCA_003173755.1	2202827	2202827	type	True	75.4781	66	825	95	below_threshold
Methylobacterium variabile	strain=DSM 16961	GCA_001043975.1	298794	298794	type	True	75.4408	73	825	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.4288	60	825	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	75.4285	59	825	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.2885	81	825	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	75.2855	62	825	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:52:19,344] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24725/tc_result.tsv
[2023-03-15 05:52:19,347] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:52:19,347] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:52:19,348] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d706730-9c62-4f99-87aa-b520ca306632/dqc_reference/checkm_data
[2023-03-15 05:52:19,348] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:52:19,355] [INFO] Task started: CheckM
[2023-03-15 05:52:19,355] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24725/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24725/checkm_input OceanDNA-b24725/checkm_result
[2023-03-15 05:53:01,991] [INFO] Task succeeded: CheckM
[2023-03-15 05:53:01,991] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:53:02,002] [INFO] ===== Completeness check finished =====
[2023-03-15 05:53:02,003] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:53:02,003] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24725/markers.fasta)
[2023-03-15 05:53:02,004] [INFO] Task started: Blastn
[2023-03-15 05:53:02,004] [INFO] Running command: blastn -query OceanDNA-b24725/markers.fasta -db /var/lib/cwl/stg8d706730-9c62-4f99-87aa-b520ca306632/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24725/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:53:03,508] [INFO] Task succeeded: Blastn
[2023-03-15 05:53:03,514] [INFO] Selected 27 target genomes.
[2023-03-15 05:53:03,514] [INFO] Target genome list was writen to OceanDNA-b24725/target_genomes_gtdb.txt
[2023-03-15 05:53:03,542] [INFO] Task started: fastANI
[2023-03-15 05:53:03,542] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e252b82-82c4-4b63-805c-6d6ffb6351f5/OceanDNA-b24725.fa --refList OceanDNA-b24725/target_genomes_gtdb.txt --output OceanDNA-b24725/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:53:24,812] [INFO] Task succeeded: fastANI
[2023-03-15 05:53:24,825] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:53:24,825] [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_016865035.1	s__Minwuia sp016865035	91.0667	729	825	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Minwuiales;f__Minwuiaceae;g__Minwuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002924445.1	s__Minwuia thermotolerans	78.2917	361	825	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Minwuiales;f__Minwuiaceae;g__Minwuia	95.0	97.67	95.35	0.91	0.86	3	-
GCA_903941105.1	s__CAJANL01 sp903941105	76.2754	58	825	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__CAJANL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197855.1	s__Rhodospira marina	76.267	62	825	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	100.00	99.99	1.00	1.00	3	-
GCA_003576705.1	s__SYSU-D60015 sp003576705	76.2502	139	825	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__SYSU-D60015	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018823745.1	s__Oceanibaculum sp018823745	76.2107	80	825	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	99.98	99.98	1.00	1.00	4	-
GCF_009601025.1	s__Rhodospira navarrensis	76.1013	97	825	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116015.1	s__Azospirillum sp003116015	76.0239	119	825	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307375.1	s__JAFKFH01 sp017307375	76.0238	127	825	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__JAFKFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018336035.1	s__Ferrovibrio sp018336035	76.0046	86	825	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__Ferrovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002195995.1	s__Inquilinus limosus_C	75.9257	122	825	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827815.1	s__Azospirillum brasilense_C	75.8139	118	825	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.36	95.98	0.93	0.90	3	-
GCF_003130795.1	s__Azospirillum thermophilum	75.8087	120	825	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004010155.1	s__Solirhodobacter olei	75.8047	59	825	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Solirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000239815.1	s__Bradyrhizobium sp000239815	75.8006	64	825	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008039615.1	s__SYSU-D60007 sp008039615	75.7699	100	825	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_019239835.1	s__JAFAZJ01 sp019239835	75.7534	57	825	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__JAFAZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827795.1	s__Azospirillum brasilense_E	75.6671	115	825	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	98.90	98.81	0.89	0.86	3	-
GCA_009377445.1	s__WHUA01 sp009377445	75.6604	60	825	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__WHUA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173755.1	s__Methylobacterium terrae	75.4781	66	825	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173775.1	s__Methylobacterium sp003173775	75.3495	78	825	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	95.16	95.16	0.87	0.87	2	-
GCF_000745835.1	s__Belnapia moabensis	75.2082	64	825	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:53:24,828] [INFO] GTDB search result was written to OceanDNA-b24725/result_gtdb.tsv
[2023-03-15 05:53:24,829] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:53:24,833] [INFO] DFAST_QC result json was written to OceanDNA-b24725/dqc_result.json
[2023-03-15 05:53:24,833] [INFO] DFAST_QC completed!
[2023-03-15 05:53:24,833] [INFO] Total running time: 0h1m53s