[2023-03-18 04:16:53,219] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:16:53,219] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:16:53,219] [INFO] DQC Reference Directory: /var/lib/cwl/stge0c68f43-41ae-49f4-a0df-fade9afadee5/dqc_reference
[2023-03-18 04:16:54,324] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:16:54,325] [INFO] Task started: Prodigal
[2023-03-18 04:16:54,325] [INFO] Running command: cat /var/lib/cwl/stg60c755dc-4021-4ea7-b4b4-71b8bacdd05e/OceanDNA-b24239.fa | prodigal -d OceanDNA-b24239/cds.fna -a OceanDNA-b24239/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:17:26,833] [INFO] Task succeeded: Prodigal
[2023-03-18 04:17:26,834] [INFO] Task started: HMMsearch
[2023-03-18 04:17:26,834] [INFO] Running command: hmmsearch --tblout OceanDNA-b24239/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0c68f43-41ae-49f4-a0df-fade9afadee5/dqc_reference/reference_markers.hmm OceanDNA-b24239/protein.faa > /dev/null
[2023-03-18 04:17:27,072] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:17:27,072] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg60c755dc-4021-4ea7-b4b4-71b8bacdd05e/OceanDNA-b24239.fa]
[2023-03-18 04:17:27,105] [INFO] Query marker FASTA was written to OceanDNA-b24239/markers.fasta
[2023-03-18 04:17:27,106] [INFO] Task started: Blastn
[2023-03-18 04:17:27,106] [INFO] Running command: blastn -query OceanDNA-b24239/markers.fasta -db /var/lib/cwl/stge0c68f43-41ae-49f4-a0df-fade9afadee5/dqc_reference/reference_markers.fasta -out OceanDNA-b24239/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:17:27,885] [INFO] Task succeeded: Blastn
[2023-03-18 04:17:27,886] [INFO] Selected 28 target genomes.
[2023-03-18 04:17:27,886] [INFO] Target genome list was writen to OceanDNA-b24239/target_genomes.txt
[2023-03-18 04:17:27,923] [INFO] Task started: fastANI
[2023-03-18 04:17:27,924] [INFO] Running command: fastANI --query /var/lib/cwl/stg60c755dc-4021-4ea7-b4b4-71b8bacdd05e/OceanDNA-b24239.fa --refList OceanDNA-b24239/target_genomes.txt --output OceanDNA-b24239/fastani_result.tsv --threads 1
[2023-03-18 04:17:48,807] [INFO] Task succeeded: fastANI
[2023-03-18 04:17:48,808] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0c68f43-41ae-49f4-a0df-fade9afadee5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:17:48,808] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0c68f43-41ae-49f4-a0df-fade9afadee5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:17:48,823] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:17:48,823] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 04:17:48,823] [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	76.7623	335	1759	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.6978	268	1759	95	below_threshold
Ferrovibrio terrae	strain=K5	GCA_007197755.1	2594003	2594003	type	True	76.6189	228	1759	95	below_threshold
Oceanibacterium hippocampi	strain=CECT 7691	GCA_900172325.1	745714	745714	type	True	76.5965	324	1759	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.5499	232	1759	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.5147	310	1759	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.4063	209	1759	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.2898	270	1759	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.2883	206	1759	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.1934	419	1759	95	below_threshold
Rhodothalassium salexigens	strain=DSM 2132	GCA_004341375.1	1086	1086	type	True	76.1742	169	1759	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.1698	363	1759	95	below_threshold
Rhodothalassium salexigens	strain=DSM 2132	GCA_014197775.1	1086	1086	type	True	76.1481	174	1759	95	below_threshold
Rhodothalassium salexigens	strain=DSM 2132	GCA_016583875.1	1086	1086	type	True	76.1418	165	1759	95	below_threshold
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	76.141	219	1759	95	below_threshold
Roseospira navarrensis	strain=DSM 15114	GCA_009601025.1	140058	140058	type	True	76.1233	195	1759	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.1069	407	1759	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	76.0487	393	1759	95	below_threshold
Kaustia mangrovi	strain=R1DC25	GCA_015482775.1	2593653	2593653	type	True	75.9554	210	1759	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_014201415.1	1743235	1743235	type	True	75.8663	151	1759	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	75.8618	149	1759	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	75.8225	226	1759	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	75.7412	218	1759	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	75.604	181	1759	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.5539	209	1759	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	75.5232	233	1759	95	below_threshold
Cereibacter sphaeroides	strain=2.4.1	GCA_000273405.1	1063	1063	type	True	75.2782	167	1759	95	below_threshold
Cereibacter sphaeroides	strain=NBRC 12203	GCA_007991035.1	1063	1063	type	True	75.2519	163	1759	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:17:48,824] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24239/tc_result.tsv
[2023-03-18 04:17:48,824] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:17:48,824] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:17:48,824] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0c68f43-41ae-49f4-a0df-fade9afadee5/dqc_reference/checkm_data
[2023-03-18 04:17:48,825] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:17:48,953] [INFO] Task started: CheckM
[2023-03-18 04:17:48,953] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24239/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24239/checkm_input OceanDNA-b24239/checkm_result
[2023-03-18 04:19:05,907] [INFO] Task succeeded: CheckM
[2023-03-18 04:19:05,907] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:19:05,910] [INFO] ===== Completeness check finished =====
[2023-03-18 04:19:05,910] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:19:05,911] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24239/markers.fasta)
[2023-03-18 04:19:05,911] [INFO] Task started: Blastn
[2023-03-18 04:19:05,911] [INFO] Running command: blastn -query OceanDNA-b24239/markers.fasta -db /var/lib/cwl/stge0c68f43-41ae-49f4-a0df-fade9afadee5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24239/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:19:07,424] [INFO] Task succeeded: Blastn
[2023-03-18 04:19:07,425] [INFO] Selected 29 target genomes.
[2023-03-18 04:19:07,425] [INFO] Target genome list was writen to OceanDNA-b24239/target_genomes_gtdb.txt
[2023-03-18 04:19:07,602] [INFO] Task started: fastANI
[2023-03-18 04:19:07,602] [INFO] Running command: fastANI --query /var/lib/cwl/stg60c755dc-4021-4ea7-b4b4-71b8bacdd05e/OceanDNA-b24239.fa --refList OceanDNA-b24239/target_genomes_gtdb.txt --output OceanDNA-b24239/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:19:31,059] [INFO] Task succeeded: fastANI
[2023-03-18 04:19:31,075] [INFO] Found 29 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 04:19:31,075] [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_003576705.1	s__SYSU-D60015 sp003576705	76.8269	402	1759	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_002924445.1	s__Minwuia thermotolerans	76.7624	336	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Minwuiales;f__Minwuiaceae;g__Minwuia	95.0	97.67	95.35	0.91	0.86	3	-
GCF_007197755.1	s__Ferrovibrio terrae	76.6181	227	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__Ferrovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172325.1	s__Oceanibacterium hippocampi	76.5899	325	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Oceanibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904705.1	s__Nisaea sp014904705	76.5409	233	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869175.1	s__VGEV01 sp016869175	76.5372	324	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__VGEV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014925385.1	s__WHTV01 sp014925385	76.5214	309	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002796975.1	s__Ferrovibrio sp002796975	76.5091	242	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__Ferrovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728835.1	s__Hypericibacter adhaerens	76.2816	270	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Hypericibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	76.2131	415	1759	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_004341375.1	s__Rhodothalassium salexigens	76.1837	168	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Rhodothalassiaceae;g__Rhodothalassium	95.0	97.98	95.92	0.96	0.92	5	-
GCA_006739055.1	s__Stella vacuolata	76.1823	386	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004923295.1	s__Azospirillum sp003115975	76.1817	295	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	99.99	99.99	0.99	0.99	2	-
GCA_015232025.1	s__JADFZP01 sp015232025	76.1739	177	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006738645.1	s__Stella humosa	76.1652	358	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017307375.1	s__JAFKFH01 sp017307375	76.1493	378	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__JAFKFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100455.1	s__Roseospirillum parvum	76.146	217	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Roseospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018667855.1	s__GCA-2731375 sp018667855	76.1132	266	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.62	99.58	0.85	0.84	3	-
GCF_902729435.1	s__Magnetospirillum sp902729435	76.1066	245	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002731375.1	s__GCA-2731375 sp002731375	76.0895	213	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.58	99.58	0.91	0.91	2	-
GCA_010032545.1	s__Reyranella sp010032545	76.0554	194	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992495.1	s__Reyranella soli	76.0415	381	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003336875.1	s__Oleisolibacter albus	75.9866	230	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Oleisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018135625.1	s__BOG-935 sp018135625	75.9575	213	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__BOG-935	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124315.1	s__RI-34 sp016124315	75.9567	193	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SMXS01;f__SMXS01;g__RI-34	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009885795.1	s__VFKA01 sp009885795	75.8708	173	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__VFKA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013112485.1	s__Paracraurococcus sp013112485	75.8142	315	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124525.1	s__Oceanicella actignis	75.7419	218	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicella	95.0	98.87	98.87	0.96	0.96	3	-
GCA_018660265.1	s__GCA-2731375 sp018660265	75.6804	139	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.92	99.87	0.96	0.94	11	-
--------------------------------------------------------------------------------
[2023-03-18 04:19:31,075] [INFO] GTDB search result was written to OceanDNA-b24239/result_gtdb.tsv
[2023-03-18 04:19:31,075] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:19:31,078] [INFO] DFAST_QC result json was written to OceanDNA-b24239/dqc_result.json
[2023-03-18 04:19:31,078] [INFO] DFAST_QC completed!
[2023-03-18 04:19:31,078] [INFO] Total running time: 0h2m38s