[2023-03-15 11:51:17,346] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:51:17,346] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:51:17,347] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c76e2a2-765b-40fa-9538-ab26d8cd4971/dqc_reference
[2023-03-15 11:51:18,950] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:51:18,950] [INFO] Task started: Prodigal
[2023-03-15 11:51:18,951] [INFO] Running command: cat /var/lib/cwl/stg0a7f536c-576c-4044-a80e-1e6bfeae3b2b/OceanDNA-b28166.fa | prodigal -d OceanDNA-b28166/cds.fna -a OceanDNA-b28166/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:51:36,091] [INFO] Task succeeded: Prodigal
[2023-03-15 11:51:36,092] [INFO] Task started: HMMsearch
[2023-03-15 11:51:36,092] [INFO] Running command: hmmsearch --tblout OceanDNA-b28166/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c76e2a2-765b-40fa-9538-ab26d8cd4971/dqc_reference/reference_markers.hmm OceanDNA-b28166/protein.faa > /dev/null
[2023-03-15 11:51:36,289] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:51:36,290] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0a7f536c-576c-4044-a80e-1e6bfeae3b2b/OceanDNA-b28166.fa]
[2023-03-15 11:51:36,313] [INFO] Query marker FASTA was written to OceanDNA-b28166/markers.fasta
[2023-03-15 11:51:36,313] [INFO] Task started: Blastn
[2023-03-15 11:51:36,313] [INFO] Running command: blastn -query OceanDNA-b28166/markers.fasta -db /var/lib/cwl/stg0c76e2a2-765b-40fa-9538-ab26d8cd4971/dqc_reference/reference_markers.fasta -out OceanDNA-b28166/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:51:37,081] [INFO] Task succeeded: Blastn
[2023-03-15 11:51:37,082] [INFO] Selected 29 target genomes.
[2023-03-15 11:51:37,082] [INFO] Target genome list was writen to OceanDNA-b28166/target_genomes.txt
[2023-03-15 11:51:37,102] [INFO] Task started: fastANI
[2023-03-15 11:51:37,102] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a7f536c-576c-4044-a80e-1e6bfeae3b2b/OceanDNA-b28166.fa --refList OceanDNA-b28166/target_genomes.txt --output OceanDNA-b28166/fastani_result.tsv --threads 1
[2023-03-15 11:51:58,107] [INFO] Task succeeded: fastANI
[2023-03-15 11:51:58,108] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c76e2a2-765b-40fa-9538-ab26d8cd4971/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:51:58,108] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c76e2a2-765b-40fa-9538-ab26d8cd4971/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:51:58,124] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:51:58,124] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:51:58,124] [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
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	78.9821	397	884	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.8554	408	884	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	78.4488	333	884	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.4162	390	884	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	78.4139	304	884	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	78.4104	372	884	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.3141	356	884	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	78.2934	324	884	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.1442	311	884	95	below_threshold
Marivita lacus	strain=CGMCC 1.12478	GCA_014637725.1	1323742	1323742	type	True	78.0516	323	884	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	77.9949	340	884	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.9751	322	884	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.9605	321	884	95	below_threshold
Roseovarius faecimaris	strain=MME-070	GCA_009762325.1	2494550	2494550	type	True	77.94	287	884	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	77.8825	306	884	95	below_threshold
Yoonia vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	77.8552	284	884	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	77.8486	307	884	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	77.7787	268	884	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	77.7745	284	884	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	77.7596	288	884	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	77.7529	334	884	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.7407	280	884	95	below_threshold
Puniceibacterium antarcticum	strain=SM1211	GCA_002760615.1	1206336	1206336	type	True	77.7243	288	884	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	77.7218	340	884	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	77.6951	339	884	95	below_threshold
Puniceibacterium confluentis	strain=JSSK-17	GCA_007923445.1	1958944	1958944	type	True	77.5604	292	884	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.3303	260	884	95	below_threshold
Pseudoroseicyclus aestuarii	strain=CECT 9025	GCA_003217255.1	1795041	1795041	type	True	77.2799	217	884	95	below_threshold
Roseovarius litorisediminis	strain=CECT 8287	GCA_900172295.1	1312363	1312363	type	True	77.0226	174	884	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:51:58,124] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28166/tc_result.tsv
[2023-03-15 11:51:58,124] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:51:58,124] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:51:58,124] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c76e2a2-765b-40fa-9538-ab26d8cd4971/dqc_reference/checkm_data
[2023-03-15 11:51:58,125] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:51:58,130] [INFO] Task started: CheckM
[2023-03-15 11:51:58,130] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28166/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28166/checkm_input OceanDNA-b28166/checkm_result
[2023-03-15 11:52:43,605] [INFO] Task succeeded: CheckM
[2023-03-15 11:52:43,605] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.62%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:52:43,608] [INFO] ===== Completeness check finished =====
[2023-03-15 11:52:43,608] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:52:43,608] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28166/markers.fasta)
[2023-03-15 11:52:43,610] [INFO] Task started: Blastn
[2023-03-15 11:52:43,610] [INFO] Running command: blastn -query OceanDNA-b28166/markers.fasta -db /var/lib/cwl/stg0c76e2a2-765b-40fa-9538-ab26d8cd4971/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28166/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:52:44,917] [INFO] Task succeeded: Blastn
[2023-03-15 11:52:44,918] [INFO] Selected 21 target genomes.
[2023-03-15 11:52:44,918] [INFO] Target genome list was writen to OceanDNA-b28166/target_genomes_gtdb.txt
[2023-03-15 11:52:44,940] [INFO] Task started: fastANI
[2023-03-15 11:52:44,941] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a7f536c-576c-4044-a80e-1e6bfeae3b2b/OceanDNA-b28166.fa --refList OceanDNA-b28166/target_genomes_gtdb.txt --output OceanDNA-b28166/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:52:59,759] [INFO] Task succeeded: fastANI
[2023-03-15 11:52:59,771] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:52:59,772] [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_001650895.1	s__EhC02 sp001650895	85.2146	691	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__EhC02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002282555.1	s__EhC02 sp002282555	84.6983	350	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__EhC02	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	79.2966	449	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004799325.1	s__Thalassobius vesicularis	78.9493	366	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002366795.1	s__UBA3069 sp002366795	78.4454	348	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3069	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	78.4272	389	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110775.1	s__Litorimicrobium taeanense	78.406	328	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108275.1	s__Jhaorihella thermophila	78.3116	304	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jhaorihella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	78.3028	346	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792425.1	s__Thalassobius sp017792425	78.2631	324	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339675.1	s__Rhodovulum steppense	78.1837	310	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	78.0854	383	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCF_005887615.1	s__Sulfitobacter_E sabulilitoris	77.9943	340	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	77.9415	322	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCA_018402175.1	s__Yoonia sp018402175	77.8133	246	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	95.02	95.02	0.81	0.81	2	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	77.7856	319	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002786295.1	s__Pseudooceanicola marinus	77.7596	288	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.99	0.99	2	-
GCF_008728195.1	s__Roseovarius indicus	77.6942	339	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
GCA_002166865.1	s__Roseovarius sp002166865	77.6523	265	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142295.1	s__Vannielia litorea	77.2993	245	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Vannielia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217255.1	s__Pseudoroseicyclus aestuarii	77.2928	216	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoroseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:52:59,772] [INFO] GTDB search result was written to OceanDNA-b28166/result_gtdb.tsv
[2023-03-15 11:52:59,772] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:52:59,774] [INFO] DFAST_QC result json was written to OceanDNA-b28166/dqc_result.json
[2023-03-15 11:52:59,775] [INFO] DFAST_QC completed!
[2023-03-15 11:52:59,775] [INFO] Total running time: 0h1m42s