[2023-03-17 00:17:04,429] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:17:04,429] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:17:04,429] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b0e25a3-6aa8-46c1-a633-76b6d3925e2b/dqc_reference
[2023-03-17 00:17:05,492] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:17:05,493] [INFO] Task started: Prodigal
[2023-03-17 00:17:05,493] [INFO] Running command: cat /var/lib/cwl/stga9bed93f-21a4-4ba2-9b80-d7f756df390e/OceanDNA-b29492.fa | prodigal -d OceanDNA-b29492/cds.fna -a OceanDNA-b29492/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:17:22,470] [INFO] Task succeeded: Prodigal
[2023-03-17 00:17:22,470] [INFO] Task started: HMMsearch
[2023-03-17 00:17:22,471] [INFO] Running command: hmmsearch --tblout OceanDNA-b29492/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b0e25a3-6aa8-46c1-a633-76b6d3925e2b/dqc_reference/reference_markers.hmm OceanDNA-b29492/protein.faa > /dev/null
[2023-03-17 00:17:22,670] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:17:22,670] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga9bed93f-21a4-4ba2-9b80-d7f756df390e/OceanDNA-b29492.fa]
[2023-03-17 00:17:22,689] [INFO] Query marker FASTA was written to OceanDNA-b29492/markers.fasta
[2023-03-17 00:17:22,689] [INFO] Task started: Blastn
[2023-03-17 00:17:22,689] [INFO] Running command: blastn -query OceanDNA-b29492/markers.fasta -db /var/lib/cwl/stg5b0e25a3-6aa8-46c1-a633-76b6d3925e2b/dqc_reference/reference_markers.fasta -out OceanDNA-b29492/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:17:23,295] [INFO] Task succeeded: Blastn
[2023-03-17 00:17:23,295] [INFO] Selected 20 target genomes.
[2023-03-17 00:17:23,296] [INFO] Target genome list was writen to OceanDNA-b29492/target_genomes.txt
[2023-03-17 00:17:23,309] [INFO] Task started: fastANI
[2023-03-17 00:17:23,309] [INFO] Running command: fastANI --query /var/lib/cwl/stga9bed93f-21a4-4ba2-9b80-d7f756df390e/OceanDNA-b29492.fa --refList OceanDNA-b29492/target_genomes.txt --output OceanDNA-b29492/fastani_result.tsv --threads 1
[2023-03-17 00:17:37,036] [INFO] Task succeeded: fastANI
[2023-03-17 00:17:37,036] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b0e25a3-6aa8-46c1-a633-76b6d3925e2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:17:37,036] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b0e25a3-6aa8-46c1-a633-76b6d3925e2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:17:37,048] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:17:37,048] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 00:17:37,048] [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
Loktanella salsilacus	strain=DSM 16199	GCA_900114485.1	195913	195913	type	True	84.524	742	899	95	below_threshold
Loktanella atrilutea	strain=DSM 29326	GCA_900128995.1	366533	366533	type	True	79.9103	556	899	95	below_threshold
Loktanella fryxellensis	strain=DSM 16213	GCA_900110065.1	245187	245187	type	True	79.4482	461	899	95	below_threshold
Yoonia vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	77.6973	294	899	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	76.9236	182	899	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	76.865	176	899	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	76.7975	148	899	95	below_threshold
Marivita lacus	strain=CGMCC 1.12478	GCA_014637725.1	1323742	1323742	type	True	76.7619	200	899	95	below_threshold
Marivita cryptomonadis	strain=CL-SK44	GCA_002115725.1	505252	505252	type	True	76.663	148	899	95	below_threshold
Yoonia sediminilitoris	strain=DSM 29955	GCA_003058085.1	1286148	1286148	type	True	76.6227	177	899	95	below_threshold
Yoonia sediminilitoris	strain=CECT 8284	GCA_003337495.1	1286148	1286148	type	True	76.6227	177	899	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	76.5173	163	899	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	76.5173	163	899	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	76.5025	182	899	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	76.4933	184	899	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	76.4496	151	899	95	below_threshold
Palleronia marisminoris	strain=CECT 7066	GCA_900172315.1	315423	315423	type	True	76.3862	132	899	95	below_threshold
Jannaschia formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	76.3812	142	899	95	below_threshold
Wenxinia saemankumensis	strain=DSM 100565	GCA_900141735.1	1447782	1447782	type	True	76.3224	166	899	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	76.3002	182	899	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 00:17:37,048] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29492/tc_result.tsv
[2023-03-17 00:17:37,048] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:17:37,048] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:17:37,048] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b0e25a3-6aa8-46c1-a633-76b6d3925e2b/dqc_reference/checkm_data
[2023-03-17 00:17:37,049] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:17:37,061] [INFO] Task started: CheckM
[2023-03-17 00:17:37,061] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29492/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29492/checkm_input OceanDNA-b29492/checkm_result
[2023-03-17 00:18:21,169] [INFO] Task succeeded: CheckM
[2023-03-17 00:18:21,169] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:18:21,200] [INFO] ===== Completeness check finished =====
[2023-03-17 00:18:21,200] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:18:21,200] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29492/markers.fasta)
[2023-03-17 00:18:21,200] [INFO] Task started: Blastn
[2023-03-17 00:18:21,200] [INFO] Running command: blastn -query OceanDNA-b29492/markers.fasta -db /var/lib/cwl/stg5b0e25a3-6aa8-46c1-a633-76b6d3925e2b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29492/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:18:22,087] [INFO] Task succeeded: Blastn
[2023-03-17 00:18:22,087] [INFO] Selected 14 target genomes.
[2023-03-17 00:18:22,088] [INFO] Target genome list was writen to OceanDNA-b29492/target_genomes_gtdb.txt
[2023-03-17 00:18:22,097] [INFO] Task started: fastANI
[2023-03-17 00:18:22,098] [INFO] Running command: fastANI --query /var/lib/cwl/stga9bed93f-21a4-4ba2-9b80-d7f756df390e/OceanDNA-b29492.fa --refList OceanDNA-b29492/target_genomes_gtdb.txt --output OceanDNA-b29492/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:18:30,981] [INFO] Task succeeded: fastANI
[2023-03-17 00:18:30,989] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 00:18:30,989] [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_900114485.1	s__Loktanella salsilacus	84.5185	743	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	97.76	97.75	0.91	0.90	3	-
GCF_900128995.1	s__Loktanella atrilutea	79.901	557	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110065.1	s__Loktanella fryxellensis	79.4482	461	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001420005.1	s__Loktanella sp001420005	78.3882	403	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110705.1	s__Loktanella sp900110705	78.1858	392	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018263905.1	s__Loktanella sp018263905	78.0063	350	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382265.1	s__Yoonia vestfoldensis	77.6906	294	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002158905.1	s__Yoonia vestfoldensis_B	77.5653	279	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004145405.1	s__Loktanella sp004145405	77.546	302	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402175.1	s__Yoonia sp018402175	77.5078	273	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	95.02	95.02	0.81	0.81	2	-
GCF_000152785.1	s__Yoonia vestfoldensis_A	77.4223	255	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001419985.1	s__Yoonia sp001419985	77.0337	201	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763785.1	s__SZUA-611 sp014763785	76.5462	134	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SZUA-611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842855.1	s__Phaeovulum sp002842855	76.4413	111	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeovulum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 00:18:30,990] [INFO] GTDB search result was written to OceanDNA-b29492/result_gtdb.tsv
[2023-03-17 00:18:30,990] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:18:30,992] [INFO] DFAST_QC result json was written to OceanDNA-b29492/dqc_result.json
[2023-03-17 00:18:30,992] [INFO] DFAST_QC completed!
[2023-03-17 00:18:30,992] [INFO] Total running time: 0h1m27s