[2023-03-16 18:18:12,616] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:18:12,616] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:18:12,616] [INFO] DQC Reference Directory: /var/lib/cwl/stg9e5eb7bc-53a4-4145-ab2a-fc814a99f51a/dqc_reference
[2023-03-16 18:18:13,736] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:18:13,736] [INFO] Task started: Prodigal
[2023-03-16 18:18:13,736] [INFO] Running command: cat /var/lib/cwl/stgb1ca8877-08ad-466b-b86a-f9c19441c570/OceanDNA-b27570.fa | prodigal -d OceanDNA-b27570/cds.fna -a OceanDNA-b27570/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:18:42,777] [INFO] Task succeeded: Prodigal
[2023-03-16 18:18:42,778] [INFO] Task started: HMMsearch
[2023-03-16 18:18:42,778] [INFO] Running command: hmmsearch --tblout OceanDNA-b27570/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9e5eb7bc-53a4-4145-ab2a-fc814a99f51a/dqc_reference/reference_markers.hmm OceanDNA-b27570/protein.faa > /dev/null
[2023-03-16 18:18:43,034] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:18:43,035] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb1ca8877-08ad-466b-b86a-f9c19441c570/OceanDNA-b27570.fa]
[2023-03-16 18:18:43,060] [INFO] Query marker FASTA was written to OceanDNA-b27570/markers.fasta
[2023-03-16 18:18:43,061] [INFO] Task started: Blastn
[2023-03-16 18:18:43,061] [INFO] Running command: blastn -query OceanDNA-b27570/markers.fasta -db /var/lib/cwl/stg9e5eb7bc-53a4-4145-ab2a-fc814a99f51a/dqc_reference/reference_markers.fasta -out OceanDNA-b27570/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:18:43,690] [INFO] Task succeeded: Blastn
[2023-03-16 18:18:43,691] [INFO] Selected 24 target genomes.
[2023-03-16 18:18:43,691] [INFO] Target genome list was writen to OceanDNA-b27570/target_genomes.txt
[2023-03-16 18:18:43,705] [INFO] Task started: fastANI
[2023-03-16 18:18:43,705] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1ca8877-08ad-466b-b86a-f9c19441c570/OceanDNA-b27570.fa --refList OceanDNA-b27570/target_genomes.txt --output OceanDNA-b27570/fastani_result.tsv --threads 1
[2023-03-16 18:19:01,514] [INFO] Task succeeded: fastANI
[2023-03-16 18:19:01,514] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9e5eb7bc-53a4-4145-ab2a-fc814a99f51a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:19:01,515] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9e5eb7bc-53a4-4145-ab2a-fc814a99f51a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:19:01,528] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:19:01,528] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 18:19:01,528] [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
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	78.3189	396	994	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	78.2482	403	994	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.1542	340	994	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	77.8976	290	994	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	77.8862	378	994	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	77.5964	286	994	95	below_threshold
Marivita geojedonensis	strain=DSM 29432	GCA_003002975.1	1123756	1123756	type	True	77.5131	247	994	95	below_threshold
Puniceibacterium sediminis	strain=DSM 29052	GCA_900188035.1	1608407	1608407	type	True	77.5069	240	994	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	77.4976	257	994	95	below_threshold
Marivita geojedonensis	strain=DPG-138	GCA_002115805.1	1123756	1123756	type	True	77.4932	248	994	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	77.3776	291	994	95	below_threshold
Primorskyibacter sedentarius	strain=DSM 104836	GCA_004342065.1	745311	745311	type	True	77.3589	240	994	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	77.3071	228	994	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	77.2872	281	994	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	77.2327	223	994	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.1815	218	994	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.1507	219	994	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.0941	256	994	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	77.0321	225	994	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.0064	222	994	95	below_threshold
Sagittula marina	strain=DSM 102235	GCA_014196795.1	943940	943940	type	True	76.9974	239	994	95	below_threshold
Paracoccus limosus	strain=JCM 17370	GCA_009711185.1	913252	913252	type	True	76.6904	174	994	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.6466	212	994	95	below_threshold
Rhodophyticola porphyridii	strain=MA-7-27	GCA_003688285.1	1852017	1852017	type	True	76.4983	154	994	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 18:19:01,528] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27570/tc_result.tsv
[2023-03-16 18:19:01,528] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:19:01,529] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:19:01,529] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9e5eb7bc-53a4-4145-ab2a-fc814a99f51a/dqc_reference/checkm_data
[2023-03-16 18:19:01,529] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:19:01,538] [INFO] Task started: CheckM
[2023-03-16 18:19:01,538] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27570/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27570/checkm_input OceanDNA-b27570/checkm_result
[2023-03-16 18:19:51,613] [INFO] Task succeeded: CheckM
[2023-03-16 18:19:51,613] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 18:19:51,616] [INFO] ===== Completeness check finished =====
[2023-03-16 18:19:51,616] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:19:51,616] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27570/markers.fasta)
[2023-03-16 18:19:51,616] [INFO] Task started: Blastn
[2023-03-16 18:19:51,616] [INFO] Running command: blastn -query OceanDNA-b27570/markers.fasta -db /var/lib/cwl/stg9e5eb7bc-53a4-4145-ab2a-fc814a99f51a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27570/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:19:52,541] [INFO] Task succeeded: Blastn
[2023-03-16 18:19:52,542] [INFO] Selected 26 target genomes.
[2023-03-16 18:19:52,542] [INFO] Target genome list was writen to OceanDNA-b27570/target_genomes_gtdb.txt
[2023-03-16 18:19:52,672] [INFO] Task started: fastANI
[2023-03-16 18:19:52,672] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1ca8877-08ad-466b-b86a-f9c19441c570/OceanDNA-b27570.fa --refList OceanDNA-b27570/target_genomes_gtdb.txt --output OceanDNA-b27570/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:20:16,623] [INFO] Task succeeded: fastANI
[2023-03-16 18:20:16,638] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 18:20:16,638] [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_019104745.1	s__CAU-1522 sp019104745	78.3936	398	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1522	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184945.1	s__Maliponia aquimaris	78.3384	436	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maliponia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101505.1	s__Mameliella alba	78.3189	396	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mameliella	95.0	98.60	98.14	0.96	0.94	14	-
GCF_018224955.1	s__Aestuariicoccus sp018224955	78.1273	414	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814095.1	s__Sagittula sp002814095	78.0613	342	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016806125.1	s__AWRV01 sp000504185	77.9931	369	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	99.97	99.97	1.00	1.00	2	-
GCA_019218285.1	s__DP3N28-2 sp019218285	77.8955	377	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__DP3N28-2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	77.8874	326	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153725.1	s__Salipiger bermudensis	77.884	292	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.06	97.75	0.87	0.75	4	-
GCF_017311415.1	s__Salipiger abyssi_A	77.773	317	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226775.1	s__Marinovum sp006226775	77.7466	311	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002115805.1	s__Marivita geojedonensis	77.5058	247	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900188035.1	s__Puniceibacterium sediminis	77.5052	241	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314655.1	s__Salibaculum sp001314655	77.4261	254	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102075.1	s__Salipiger thiooxidans	77.4005	288	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
GCF_004342065.1	s__Primorskyibacter sedentarius	77.3625	239	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827095.1	s__Pseudooceanicola sp009827095	77.2676	227	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.98	0.98	2	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	77.2167	236	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	77.1734	218	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_900176485.1	s__Primorskyibacter flagellatus_A	77.0738	204	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689745.1	s__Roseicyclus sp015689745	77.0523	223	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339675.1	s__Rhodovulum steppense	77.0319	225	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335545.1	s__Ascidiaceihabitans sp003335545	76.914	204	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009920775.1	s__Marivivens sp009920775	76.8578	131	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	76.6141	176	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_003688285.1	s__Rhodophyticola porphyridii	76.4851	154	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodophyticola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 18:20:16,638] [INFO] GTDB search result was written to OceanDNA-b27570/result_gtdb.tsv
[2023-03-16 18:20:16,639] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:20:16,641] [INFO] DFAST_QC result json was written to OceanDNA-b27570/dqc_result.json
[2023-03-16 18:20:16,641] [INFO] DFAST_QC completed!
[2023-03-16 18:20:16,641] [INFO] Total running time: 0h2m4s