[2023-03-18 07:29:32,013] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:29:32,013] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:29:32,013] [INFO] DQC Reference Directory: /var/lib/cwl/stgc893ee1a-02c7-4f7c-b187-e53531d7fec2/dqc_reference
[2023-03-18 07:29:33,123] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:29:33,123] [INFO] Task started: Prodigal
[2023-03-18 07:29:33,123] [INFO] Running command: cat /var/lib/cwl/stgdce6238f-d63a-480f-9667-6c64f7c95448/OceanDNA-b30225.fa | prodigal -d OceanDNA-b30225/cds.fna -a OceanDNA-b30225/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:29:58,637] [INFO] Task succeeded: Prodigal
[2023-03-18 07:29:58,637] [INFO] Task started: HMMsearch
[2023-03-18 07:29:58,637] [INFO] Running command: hmmsearch --tblout OceanDNA-b30225/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc893ee1a-02c7-4f7c-b187-e53531d7fec2/dqc_reference/reference_markers.hmm OceanDNA-b30225/protein.faa > /dev/null
[2023-03-18 07:29:58,860] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:29:58,860] [INFO] Found 6/6 markers.
[2023-03-18 07:29:58,886] [INFO] Query marker FASTA was written to OceanDNA-b30225/markers.fasta
[2023-03-18 07:29:58,886] [INFO] Task started: Blastn
[2023-03-18 07:29:58,886] [INFO] Running command: blastn -query OceanDNA-b30225/markers.fasta -db /var/lib/cwl/stgc893ee1a-02c7-4f7c-b187-e53531d7fec2/dqc_reference/reference_markers.fasta -out OceanDNA-b30225/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:29:59,665] [INFO] Task succeeded: Blastn
[2023-03-18 07:29:59,666] [INFO] Selected 20 target genomes.
[2023-03-18 07:29:59,666] [INFO] Target genome list was writen to OceanDNA-b30225/target_genomes.txt
[2023-03-18 07:29:59,672] [INFO] Task started: fastANI
[2023-03-18 07:29:59,672] [INFO] Running command: fastANI --query /var/lib/cwl/stgdce6238f-d63a-480f-9667-6c64f7c95448/OceanDNA-b30225.fa --refList OceanDNA-b30225/target_genomes.txt --output OceanDNA-b30225/fastani_result.tsv --threads 1
[2023-03-18 07:30:14,065] [INFO] Task succeeded: fastANI
[2023-03-18 07:30:14,065] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc893ee1a-02c7-4f7c-b187-e53531d7fec2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:30:14,065] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc893ee1a-02c7-4f7c-b187-e53531d7fec2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:30:14,076] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:30:14,077] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 07:30:14,077] [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 delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	79.791	614	1304	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	79.5325	599	1304	95	below_threshold
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	79.5085	625	1304	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	79.5049	612	1304	95	below_threshold
Sulfitobacter maritimus	strain=S0837	GCA_013346665.1	2741719	2741719	type	True	79.4847	574	1304	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	78.5787	512	1304	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	78.4945	475	1304	95	below_threshold
Sulfitobacter brevis	strain=DSM 11443	GCA_900112755.1	74348	74348	type	True	78.3432	484	1304	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	78.1188	502	1304	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	78.0968	499	1304	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	78.0634	509	1304	95	below_threshold
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	78.0584	409	1304	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	78.0018	447	1304	95	below_threshold
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	77.9746	453	1304	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	77.8755	398	1304	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	76.8162	248	1304	95	below_threshold
Salinihabitans flavidus	strain=DSM 27842	GCA_900110425.1	569882	569882	type	True	76.7342	225	1304	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.665	177	1304	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	76.4997	187	1304	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	76.4883	188	1304	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:30:14,077] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30225/tc_result.tsv
[2023-03-18 07:30:14,077] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:30:14,077] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:30:14,077] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc893ee1a-02c7-4f7c-b187-e53531d7fec2/dqc_reference/checkm_data
[2023-03-18 07:30:14,078] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:30:14,083] [INFO] Task started: CheckM
[2023-03-18 07:30:14,083] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30225/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30225/checkm_input OceanDNA-b30225/checkm_result
[2023-03-18 07:31:17,048] [INFO] Task succeeded: CheckM
[2023-03-18 07:31:17,048] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.65%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:31:17,051] [INFO] ===== Completeness check finished =====
[2023-03-18 07:31:17,051] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:31:17,051] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30225/markers.fasta)
[2023-03-18 07:31:17,051] [INFO] Task started: Blastn
[2023-03-18 07:31:17,051] [INFO] Running command: blastn -query OceanDNA-b30225/markers.fasta -db /var/lib/cwl/stgc893ee1a-02c7-4f7c-b187-e53531d7fec2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30225/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:31:18,462] [INFO] Task succeeded: Blastn
[2023-03-18 07:31:18,463] [INFO] Selected 20 target genomes.
[2023-03-18 07:31:18,463] [INFO] Target genome list was writen to OceanDNA-b30225/target_genomes_gtdb.txt
[2023-03-18 07:31:18,529] [INFO] Task started: fastANI
[2023-03-18 07:31:18,529] [INFO] Running command: fastANI --query /var/lib/cwl/stgdce6238f-d63a-480f-9667-6c64f7c95448/OceanDNA-b30225.fa --refList OceanDNA-b30225/target_genomes_gtdb.txt --output OceanDNA-b30225/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:31:34,490] [INFO] Task succeeded: fastANI
[2023-03-18 07:31:34,502] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 07:31:34,502] [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_017743885.1	s__Sulfitobacter sp001635605	79.9235	646	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	98.54	95.97	0.90	0.86	4	-
GCF_900102535.1	s__Sulfitobacter delicatus	79.8166	611	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611275.1	s__Sulfitobacter sp001634775	79.785	650	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.83	96.27	0.81	0.78	5	-
GCF_000172095.1	s__Sulfitobacter indolifex	79.5325	599	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002703405.1	s__Sulfitobacter sp002703405	79.5229	524	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.87	96.48	0.79	0.78	3	-
GCF_900113435.1	s__Sulfitobacter dubius	79.5085	625	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.36	97.36	0.82	0.82	2	-
GCF_013346665.1	s__Sulfitobacter maritimus	79.493	573	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650875.1	s__Sulfitobacter sp001650875	78.9464	581	1304	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	78.8649	611	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054325.1	s__Sulfitobacter mediterraneus	78.5787	512	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.52	96.39	0.88	0.86	71	-
GCF_900106935.1	s__Sulfitobacter pontiacus	78.4861	476	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.43	97.01	0.92	0.86	24	-
GCF_016801775.1	s__Sulfitobacter mediterraneus_A	78.4742	530	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	99.99	1.00	1.00	16	-
GCF_013282155.1	s__Sulfitobacter sp013282155	78.3841	487	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.41	99.36	0.93	0.90	3	-
GCF_003352065.1	s__Sulfitobacter sp003352065	78.3683	477	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112755.1	s__Sulfitobacter brevis	78.324	485	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335545.1	s__Ascidiaceihabitans sp003335545	78.2047	459	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139555.1	s__Sulfitobacter sp013139555	78.0602	378	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103185.1	s__Sulfitobacter litoralis	78.0584	409	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.10	98.53	0.92	0.85	6	-
GCF_000622325.1	s__Sulfitobacter geojensis	77.9824	452	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.34	96.22	0.90	0.89	35	-
GCF_001634885.1	s__Sulfitobacter sp001634885	77.8427	409	1304	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.85	95.06	0.84	0.78	4	-
--------------------------------------------------------------------------------
[2023-03-18 07:31:34,502] [INFO] GTDB search result was written to OceanDNA-b30225/result_gtdb.tsv
[2023-03-18 07:31:34,502] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:31:34,504] [INFO] DFAST_QC result json was written to OceanDNA-b30225/dqc_result.json
[2023-03-18 07:31:34,504] [INFO] DFAST_QC completed!
[2023-03-18 07:31:34,504] [INFO] Total running time: 0h2m2s