[2023-06-08 00:55:00,490] [INFO] DFAST_QC pipeline started.
[2023-06-08 00:55:00,493] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 00:55:00,493] [INFO] DQC Reference Directory: /var/lib/cwl/stge56f6bac-7429-4a0e-8695-10a9ef925162/dqc_reference
[2023-06-08 00:55:01,843] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 00:55:01,845] [INFO] Task started: Prodigal
[2023-06-08 00:55:01,845] [INFO] Running command: gunzip -c /var/lib/cwl/stg336a968f-e074-4a17-9229-de2c2cd0fe87/GCA_902751295.1_P1994_104_bin73_mag_fasta_genomic.fna.gz | prodigal -d GCA_902751295.1_P1994_104_bin73_mag_fasta_genomic.fna/cds.fna -a GCA_902751295.1_P1994_104_bin73_mag_fasta_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 00:55:09,500] [INFO] Task succeeded: Prodigal
[2023-06-08 00:55:09,500] [INFO] Task started: HMMsearch
[2023-06-08 00:55:09,500] [INFO] Running command: hmmsearch --tblout GCA_902751295.1_P1994_104_bin73_mag_fasta_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge56f6bac-7429-4a0e-8695-10a9ef925162/dqc_reference/reference_markers.hmm GCA_902751295.1_P1994_104_bin73_mag_fasta_genomic.fna/protein.faa > /dev/null
[2023-06-08 00:55:09,769] [INFO] Task succeeded: HMMsearch
[2023-06-08 00:55:09,771] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg336a968f-e074-4a17-9229-de2c2cd0fe87/GCA_902751295.1_P1994_104_bin73_mag_fasta_genomic.fna.gz]
[2023-06-08 00:55:09,799] [INFO] Query marker FASTA was written to GCA_902751295.1_P1994_104_bin73_mag_fasta_genomic.fna/markers.fasta
[2023-06-08 00:55:09,800] [INFO] Task started: Blastn
[2023-06-08 00:55:09,800] [INFO] Running command: blastn -query GCA_902751295.1_P1994_104_bin73_mag_fasta_genomic.fna/markers.fasta -db /var/lib/cwl/stge56f6bac-7429-4a0e-8695-10a9ef925162/dqc_reference/reference_markers.fasta -out GCA_902751295.1_P1994_104_bin73_mag_fasta_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:55:10,491] [INFO] Task succeeded: Blastn
[2023-06-08 00:55:10,495] [INFO] Selected 23 target genomes.
[2023-06-08 00:55:10,495] [INFO] Target genome list was writen to GCA_902751295.1_P1994_104_bin73_mag_fasta_genomic.fna/target_genomes.txt
[2023-06-08 00:55:10,500] [INFO] Task started: fastANI
[2023-06-08 00:55:10,500] [INFO] Running command: fastANI --query /var/lib/cwl/stg336a968f-e074-4a17-9229-de2c2cd0fe87/GCA_902751295.1_P1994_104_bin73_mag_fasta_genomic.fna.gz --refList GCA_902751295.1_P1994_104_bin73_mag_fasta_genomic.fna/target_genomes.txt --output GCA_902751295.1_P1994_104_bin73_mag_fasta_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 00:55:25,090] [INFO] Task succeeded: fastANI
[2023-06-08 00:55:25,091] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge56f6bac-7429-4a0e-8695-10a9ef925162/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 00:55:25,092] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge56f6bac-7429-4a0e-8695-10a9ef925162/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 00:55:25,118] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 00:55:25,118] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 00:55:25,119] [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 ponticola	strain=DSM 101064	GCA_014199395.1	1524255	1524255	type	True	77.4715	221	777	95	below_threshold
Yoonia maritima	strain=DSM 101533	GCA_003003285.1	1435347	1435347	type	True	77.3692	172	777	95	below_threshold
Yoonia rosea	strain=DSM 29591	GCA_900156505.1	287098	287098	type	True	77.2418	201	777	95	below_threshold
Yoonia litorea	strain=DSM 29433	GCA_900114675.1	1123755	1123755	type	True	77.0916	142	777	95	below_threshold
Yoonia maricola	strain=DSM 29128	GCA_002797915.1	420999	420999	type	True	77.0128	184	777	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	76.8932	122	777	95	below_threshold
Loktanella salsilacus	strain=DSM 16199	GCA_900114485.1	195913	195913	type	True	76.7981	214	777	95	below_threshold
Cognatiyoonia koreensis	strain=DSM 17925	GCA_900109295.1	364200	364200	type	True	76.6528	143	777	95	below_threshold
Yoonia vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	76.6481	176	777	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.5585	125	777	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	76.4262	98	777	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	76.3709	137	777	95	below_threshold
Flavimaricola marinus	strain=CECT 8899	GCA_900184895.1	1819565	1819565	type	True	76.3363	126	777	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.3233	140	777	95	below_threshold
Limimaricola soesokkakensis	strain=DSM 29956	GCA_003014435.1	1343159	1343159	type	True	76.2758	80	777	95	below_threshold
Loktanella atrilutea	strain=DSM 29326	GCA_900128995.1	366533	366533	type	True	76.2622	126	777	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.2264	121	777	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	76.182	97	777	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	76.1742	78	777	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	75.8752	65	777	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	75.8345	75	777	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	75.8345	75	777	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	75.7329	55	777	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 00:55:25,121] [INFO] DFAST Taxonomy check result was written to GCA_902751295.1_P1994_104_bin73_mag_fasta_genomic.fna/tc_result.tsv
[2023-06-08 00:55:25,122] [INFO] ===== Taxonomy check completed =====
[2023-06-08 00:55:25,122] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 00:55:25,122] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge56f6bac-7429-4a0e-8695-10a9ef925162/dqc_reference/checkm_data
[2023-06-08 00:55:25,124] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 00:55:25,157] [INFO] Task started: CheckM
[2023-06-08 00:55:25,158] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902751295.1_P1994_104_bin73_mag_fasta_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902751295.1_P1994_104_bin73_mag_fasta_genomic.fna/checkm_input GCA_902751295.1_P1994_104_bin73_mag_fasta_genomic.fna/checkm_result
[2023-06-08 00:55:53,682] [INFO] Task succeeded: CheckM
[2023-06-08 00:55:53,684] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.36%
Contamintation: 4.69%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-08 00:55:53,708] [INFO] ===== Completeness check finished =====
[2023-06-08 00:55:53,709] [INFO] ===== Start GTDB Search =====
[2023-06-08 00:55:53,709] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902751295.1_P1994_104_bin73_mag_fasta_genomic.fna/markers.fasta)
[2023-06-08 00:55:53,709] [INFO] Task started: Blastn
[2023-06-08 00:55:53,710] [INFO] Running command: blastn -query GCA_902751295.1_P1994_104_bin73_mag_fasta_genomic.fna/markers.fasta -db /var/lib/cwl/stge56f6bac-7429-4a0e-8695-10a9ef925162/dqc_reference/reference_markers_gtdb.fasta -out GCA_902751295.1_P1994_104_bin73_mag_fasta_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:55:54,760] [INFO] Task succeeded: Blastn
[2023-06-08 00:55:54,764] [INFO] Selected 17 target genomes.
[2023-06-08 00:55:54,764] [INFO] Target genome list was writen to GCA_902751295.1_P1994_104_bin73_mag_fasta_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 00:55:55,058] [INFO] Task started: fastANI
[2023-06-08 00:55:55,059] [INFO] Running command: fastANI --query /var/lib/cwl/stg336a968f-e074-4a17-9229-de2c2cd0fe87/GCA_902751295.1_P1994_104_bin73_mag_fasta_genomic.fna.gz --refList GCA_902751295.1_P1994_104_bin73_mag_fasta_genomic.fna/target_genomes_gtdb.txt --output GCA_902751295.1_P1994_104_bin73_mag_fasta_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 00:56:05,049] [INFO] Task succeeded: fastANI
[2023-06-08 00:56:05,066] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 00:56:05,067] [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_002378665.1	s__Yoonia sp002378665	99.1936	699	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	99.59	99.15	0.91	0.87	4	conclusive
GCA_905182645.1	s__Yoonia sp905182645	78.6266	279	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199395.1	s__Yoonia ponticola	77.4715	221	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967725.1	s__Yoonia sp000967725	77.4128	145	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003285.1	s__Yoonia maritima	77.3692	172	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201935.1	s__Yoonia sp003201935	77.2667	209	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156505.1	s__Yoonia rosea	77.2418	201	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	96.70	96.70	0.95	0.95	2	-
GCF_001419985.1	s__Yoonia sp001419985	77.1313	211	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002933395.1	s__Yoonia maritima_A	77.1101	167	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854565.1	s__Yoonia sp017854565	77.095	189	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000169435.1	s__Yoonia sp000169435	77.0646	191	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797915.1	s__Yoonia maricola	77.0263	183	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143545.1	s__Yoonia sp900143545	76.9602	206	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859355.1	s__Yoonia sp014859355	76.8816	155	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114485.1	s__Loktanella salsilacus	76.7973	214	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	97.76	97.75	0.91	0.90	3	-
GCA_001650895.1	s__EhC02 sp001650895	76.191	94	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__EhC02	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153305.1	s__Oceanicola granulosus	75.6949	67	777	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 00:56:05,069] [INFO] GTDB search result was written to GCA_902751295.1_P1994_104_bin73_mag_fasta_genomic.fna/result_gtdb.tsv
[2023-06-08 00:56:05,070] [INFO] ===== GTDB Search completed =====
[2023-06-08 00:56:05,077] [INFO] DFAST_QC result json was written to GCA_902751295.1_P1994_104_bin73_mag_fasta_genomic.fna/dqc_result.json
[2023-06-08 00:56:05,078] [INFO] DFAST_QC completed!
[2023-06-08 00:56:05,078] [INFO] Total running time: 0h1m5s