[2023-03-15 16:02:07,986] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:02:07,986] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:02:07,986] [INFO] DQC Reference Directory: /var/lib/cwl/stg330fa584-20e2-4953-863e-88989af59bf8/dqc_reference
[2023-03-15 16:02:09,125] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:02:09,125] [INFO] Task started: Prodigal
[2023-03-15 16:02:09,126] [INFO] Running command: cat /var/lib/cwl/stg489179ad-9ac4-4093-b3b7-52aabe8bbcf8/OceanDNA-b30408.fa | prodigal -d OceanDNA-b30408/cds.fna -a OceanDNA-b30408/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:02:21,464] [INFO] Task succeeded: Prodigal
[2023-03-15 16:02:21,464] [INFO] Task started: HMMsearch
[2023-03-15 16:02:21,464] [INFO] Running command: hmmsearch --tblout OceanDNA-b30408/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg330fa584-20e2-4953-863e-88989af59bf8/dqc_reference/reference_markers.hmm OceanDNA-b30408/protein.faa > /dev/null
[2023-03-15 16:02:21,643] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:02:21,644] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg489179ad-9ac4-4093-b3b7-52aabe8bbcf8/OceanDNA-b30408.fa]
[2023-03-15 16:02:21,663] [INFO] Query marker FASTA was written to OceanDNA-b30408/markers.fasta
[2023-03-15 16:02:21,664] [INFO] Task started: Blastn
[2023-03-15 16:02:21,665] [INFO] Running command: blastn -query OceanDNA-b30408/markers.fasta -db /var/lib/cwl/stg330fa584-20e2-4953-863e-88989af59bf8/dqc_reference/reference_markers.fasta -out OceanDNA-b30408/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:02:22,376] [INFO] Task succeeded: Blastn
[2023-03-15 16:02:22,377] [INFO] Selected 23 target genomes.
[2023-03-15 16:02:22,377] [INFO] Target genome list was writen to OceanDNA-b30408/target_genomes.txt
[2023-03-15 16:02:22,394] [INFO] Task started: fastANI
[2023-03-15 16:02:22,394] [INFO] Running command: fastANI --query /var/lib/cwl/stg489179ad-9ac4-4093-b3b7-52aabe8bbcf8/OceanDNA-b30408.fa --refList OceanDNA-b30408/target_genomes.txt --output OceanDNA-b30408/fastani_result.tsv --threads 1
[2023-03-15 16:02:37,139] [INFO] Task succeeded: fastANI
[2023-03-15 16:02:37,139] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg330fa584-20e2-4953-863e-88989af59bf8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:02:37,140] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg330fa584-20e2-4953-863e-88989af59bf8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:02:37,152] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:02:37,153] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 16:02:37,153] [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
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	78.8593	297	596	95	below_threshold
Sulfitobacter maritimus	strain=S0837	GCA_013346665.1	2741719	2741719	type	True	78.3556	230	596	95	below_threshold
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	78.3517	259	596	95	below_threshold
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	78.3374	271	596	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	78.1565	230	596	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	78.0977	239	596	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	78.0055	253	596	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.9885	256	596	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	77.7215	183	596	95	below_threshold
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	77.6977	185	596	95	below_threshold
Roseobacter cerasinus	strain=AI77	GCA_009811755.1	2602289	2602289	type	True	77.6894	212	596	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	77.5366	193	596	95	below_threshold
Sulfitobacter brevis	strain=DSM 11443	GCA_900112755.1	74348	74348	type	True	77.5245	222	596	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	77.4727	204	596	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.4597	157	596	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.4527	160	596	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.3821	155	596	95	below_threshold
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_008124775.1	404236	404236	type	True	77.2666	162	596	95	below_threshold
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_000152805.1	404236	404236	type	True	77.2587	164	596	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	77.2181	192	596	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.9047	153	596	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	76.8432	143	596	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.774	105	596	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 16:02:37,153] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30408/tc_result.tsv
[2023-03-15 16:02:37,153] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:02:37,153] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:02:37,153] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg330fa584-20e2-4953-863e-88989af59bf8/dqc_reference/checkm_data
[2023-03-15 16:02:37,154] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:02:37,170] [INFO] Task started: CheckM
[2023-03-15 16:02:37,170] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30408/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30408/checkm_input OceanDNA-b30408/checkm_result
[2023-03-15 16:03:10,779] [INFO] Task succeeded: CheckM
[2023-03-15 16:03:10,779] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.84%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 16:03:10,782] [INFO] ===== Completeness check finished =====
[2023-03-15 16:03:10,782] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:03:10,782] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30408/markers.fasta)
[2023-03-15 16:03:10,783] [INFO] Task started: Blastn
[2023-03-15 16:03:10,783] [INFO] Running command: blastn -query OceanDNA-b30408/markers.fasta -db /var/lib/cwl/stg330fa584-20e2-4953-863e-88989af59bf8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30408/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:03:12,049] [INFO] Task succeeded: Blastn
[2023-03-15 16:03:12,050] [INFO] Selected 19 target genomes.
[2023-03-15 16:03:12,050] [INFO] Target genome list was writen to OceanDNA-b30408/target_genomes_gtdb.txt
[2023-03-15 16:03:12,060] [INFO] Task started: fastANI
[2023-03-15 16:03:12,060] [INFO] Running command: fastANI --query /var/lib/cwl/stg489179ad-9ac4-4093-b3b7-52aabe8bbcf8/OceanDNA-b30408.fa --refList OceanDNA-b30408/target_genomes_gtdb.txt --output OceanDNA-b30408/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:03:27,736] [INFO] Task succeeded: fastANI
[2023-03-15 16:03:27,747] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 16:03:27,747] [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_001634885.1	s__Sulfitobacter sp001634885	95.8477	547	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.85	95.06	0.84	0.78	4	conclusive
GCF_017743885.1	s__Sulfitobacter sp001635605	79.0934	310	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	98.54	95.97	0.90	0.86	4	-
GCF_001650875.1	s__Sulfitobacter sp001650875	79.0114	317	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363555.1	s__Sulfitobacter sp009363555	78.9976	312	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335585.1	s__Sulfitobacter sp003335585	78.9354	338	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886735.1	s__Sulfitobacter alexandrii	78.933	327	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005887615.1	s__Sulfitobacter_E sabulilitoris	78.8593	297	596	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_003611275.1	s__Sulfitobacter sp001634775	78.5942	284	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.83	96.27	0.81	0.78	5	-
GCF_013346665.1	s__Sulfitobacter maritimus	78.3556	230	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102535.1	s__Sulfitobacter delicatus	78.3374	271	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	77.9885	256	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_018139985.1	s__JAGSOU01 sp018139985	77.8133	208	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003651245.1	s__Roseovarius spongiae	77.7569	210	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016801775.1	s__Sulfitobacter mediterraneus_A	77.6277	224	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	99.99	1.00	1.00	16	-
GCA_003217735.2	s__Marinibacterium sp003217735	77.6269	234	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCA_016521575.1	s__Sedimentitalea sp016521575	77.5723	169	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442255.1	s__Salipiger mucosus	77.5154	191	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216475.1	s__GCA-004216475 sp004216475	77.2832	182	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GCA-004216475	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	77.2624	211	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-15 16:03:27,748] [INFO] GTDB search result was written to OceanDNA-b30408/result_gtdb.tsv
[2023-03-15 16:03:27,748] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:03:27,750] [INFO] DFAST_QC result json was written to OceanDNA-b30408/dqc_result.json
[2023-03-15 16:03:27,750] [INFO] DFAST_QC completed!
[2023-03-15 16:03:27,750] [INFO] Total running time: 0h1m20s