[2023-03-17 05:16:57,863] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:16:57,863] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:16:57,863] [INFO] DQC Reference Directory: /var/lib/cwl/stg06f6ebed-e5ce-456b-95d9-09b00c906c12/dqc_reference
[2023-03-17 05:16:59,367] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:16:59,367] [INFO] Task started: Prodigal
[2023-03-17 05:16:59,367] [INFO] Running command: cat /var/lib/cwl/stg034a2ed4-fe16-4e81-b7ac-feef32c397fc/OceanDNA-b24591.fa | prodigal -d OceanDNA-b24591/cds.fna -a OceanDNA-b24591/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:17:22,968] [INFO] Task succeeded: Prodigal
[2023-03-17 05:17:22,968] [INFO] Task started: HMMsearch
[2023-03-17 05:17:22,968] [INFO] Running command: hmmsearch --tblout OceanDNA-b24591/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06f6ebed-e5ce-456b-95d9-09b00c906c12/dqc_reference/reference_markers.hmm OceanDNA-b24591/protein.faa > /dev/null
[2023-03-17 05:17:23,177] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:17:23,178] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg034a2ed4-fe16-4e81-b7ac-feef32c397fc/OceanDNA-b24591.fa]
[2023-03-17 05:17:23,200] [INFO] Query marker FASTA was written to OceanDNA-b24591/markers.fasta
[2023-03-17 05:17:23,201] [INFO] Task started: Blastn
[2023-03-17 05:17:23,201] [INFO] Running command: blastn -query OceanDNA-b24591/markers.fasta -db /var/lib/cwl/stg06f6ebed-e5ce-456b-95d9-09b00c906c12/dqc_reference/reference_markers.fasta -out OceanDNA-b24591/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:17:23,820] [INFO] Task succeeded: Blastn
[2023-03-17 05:17:23,821] [INFO] Selected 27 target genomes.
[2023-03-17 05:17:23,821] [INFO] Target genome list was writen to OceanDNA-b24591/target_genomes.txt
[2023-03-17 05:17:23,999] [INFO] Task started: fastANI
[2023-03-17 05:17:24,000] [INFO] Running command: fastANI --query /var/lib/cwl/stg034a2ed4-fe16-4e81-b7ac-feef32c397fc/OceanDNA-b24591.fa --refList OceanDNA-b24591/target_genomes.txt --output OceanDNA-b24591/fastani_result.tsv --threads 1
[2023-03-17 05:17:43,582] [INFO] Task succeeded: fastANI
[2023-03-17 05:17:43,582] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06f6ebed-e5ce-456b-95d9-09b00c906c12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:17:43,582] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06f6ebed-e5ce-456b-95d9-09b00c906c12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:17:43,593] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:17:43,593] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 05:17:43,594] [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
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.5024	251	1246	95	below_threshold
Rhodovibrio salinarum	strain=DSM 9154	GCA_000515255.1	1087	1087	type	True	76.3772	118	1246	95	below_threshold
Rhodovibrio salinarum	strain=DSM 9154	GCA_016583505.1	1087	1087	type	True	76.3491	118	1246	95	below_threshold
Fodinicurvata fenggangensis	strain=DSM 21160	GCA_000686045.1	1121830	1121830	type	True	76.2433	116	1246	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.073	98	1246	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	76.065	138	1246	95	below_threshold
Fodinicurvata sediminis	strain=DSM 21159	GCA_000420625.1	1121832	1121832	type	True	76.0045	102	1246	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	75.6551	153	1246	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	75.6234	81	1246	95	below_threshold
Niveispirillum cyanobacteriorum	strain=CGMCC 1.12958	GCA_014640215.1	1612173	1612173	type	True	75.6045	82	1246	95	below_threshold
Consotaella salsifontis	strain=USBA 369	GCA_900167365.1	1365950	1365950	type	True	75.5539	53	1246	95	below_threshold
Reyranella massiliensis	strain=521	GCA_000312425.1	445220	445220	type	True	75.5114	92	1246	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.474	173	1246	95	below_threshold
Novosphingobium fuchskuhlense	strain=FNE08-7	GCA_001519075.1	1117702	1117702	type	True	75.4681	52	1246	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.4296	134	1246	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	75.415	126	1246	95	below_threshold
Niveispirillum irakense	strain=DSM 11586	GCA_000429645.1	34011	34011	type	True	75.4007	78	1246	95	below_threshold
Xanthobacter agilis	strain=LMG 16336	GCA_021730435.1	47492	47492	type	True	75.3997	104	1246	95	below_threshold
Sphingomonas ginsengisoli An et al. 2013	strain=KACC 16858	GCA_009363895.1	363835	363835	type	True	75.3016	54	1246	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:17:43,594] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24591/tc_result.tsv
[2023-03-17 05:17:43,594] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:17:43,594] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:17:43,594] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06f6ebed-e5ce-456b-95d9-09b00c906c12/dqc_reference/checkm_data
[2023-03-17 05:17:43,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:17:43,604] [INFO] Task started: CheckM
[2023-03-17 05:17:43,604] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24591/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24591/checkm_input OceanDNA-b24591/checkm_result
[2023-03-17 05:18:40,962] [INFO] Task succeeded: CheckM
[2023-03-17 05:18:40,962] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:18:40,967] [INFO] ===== Completeness check finished =====
[2023-03-17 05:18:40,967] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:18:40,967] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24591/markers.fasta)
[2023-03-17 05:18:40,968] [INFO] Task started: Blastn
[2023-03-17 05:18:40,968] [INFO] Running command: blastn -query OceanDNA-b24591/markers.fasta -db /var/lib/cwl/stg06f6ebed-e5ce-456b-95d9-09b00c906c12/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24591/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:18:42,050] [INFO] Task succeeded: Blastn
[2023-03-17 05:18:42,052] [INFO] Selected 29 target genomes.
[2023-03-17 05:18:42,052] [INFO] Target genome list was writen to OceanDNA-b24591/target_genomes_gtdb.txt
[2023-03-17 05:18:42,369] [INFO] Task started: fastANI
[2023-03-17 05:18:42,369] [INFO] Running command: fastANI --query /var/lib/cwl/stg034a2ed4-fe16-4e81-b7ac-feef32c397fc/OceanDNA-b24591.fa --refList OceanDNA-b24591/target_genomes_gtdb.txt --output OceanDNA-b24591/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:19:05,032] [INFO] Task succeeded: fastANI
[2023-03-17 05:19:05,044] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 05:19:05,045] [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_014925385.1	s__WHTV01 sp014925385	76.5136	251	1246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001657395.1	s__Pelagibius sp001657395	76.4017	197	1246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__Pelagibius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006969625.1	s__Algihabitans sp006969625	76.3288	234	1246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Algihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000686045.1	s__Fodinicurvata fenggangensis	76.2433	116	1246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Fodinicurvata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377535.1	s__WHTV01 sp009377535	76.2345	197	1246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007004665.1	s__Denitrobaculum tricleocarpae	76.1738	111	1246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__Denitrobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420625.1	s__Fodinicurvata sediminis	76.0045	102	1246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Fodinicurvata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903941105.1	s__CAJANL01 sp903941105	75.8962	107	1246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__CAJANL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902729435.1	s__Magnetospirillum sp902729435	75.7516	140	1246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418225.1	s__Pannonibacter indicus	75.632	87	1246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter	95.0	96.01	95.55	0.94	0.89	12	-
GCF_000333275.1	s__Nitrospirillum sp000333275	75.5927	118	1246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377525.1	s__Reyranella sp009377525	75.5277	125	1246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000312425.1	s__Reyranella massiliensis	75.5238	91	1246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008039615.1	s__SYSU-D60007 sp008039615	75.4796	172	1246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__SYSU-D60007	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016467395.1	s__Reyranella sp016467395	75.4362	131	1246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017996735.1	s__Niveispirillum sp017996735	75.3928	98	1246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Niveispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156265.1	s__Acidiphilium rubrum	75.3399	60	1246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidiphilium	95.0	97.80	96.68	0.89	0.85	4	-
GCF_014207215.1	s__Caulobacter sp014207215	75.3049	93	1246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174355.1	s__Gluconacetobacter azotocaptans	75.2839	68	1246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.32	99.32	0.91	0.91	2	-
GCF_001014975.1	s__Novosphingobium sp002336885	75.2824	71	1246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.66	97.51	0.82	0.80	4	-
GCF_005145025.1	s__Novosphingobium sp005145025	75.1564	60	1246	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:19:05,046] [INFO] GTDB search result was written to OceanDNA-b24591/result_gtdb.tsv
[2023-03-17 05:19:05,048] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:19:05,052] [INFO] DFAST_QC result json was written to OceanDNA-b24591/dqc_result.json
[2023-03-17 05:19:05,052] [INFO] DFAST_QC completed!
[2023-03-17 05:19:05,052] [INFO] Total running time: 0h2m7s