[2023-03-18 04:16:53,214] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:16:53,214] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:16:53,214] [INFO] DQC Reference Directory: /var/lib/cwl/stgd5913e3e-2381-4bf3-815c-dee8d7397e86/dqc_reference
[2023-03-18 04:16:54,343] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:16:54,343] [INFO] Task started: Prodigal
[2023-03-18 04:16:54,344] [INFO] Running command: cat /var/lib/cwl/stg7dfc96ba-514d-49c9-a10a-fc1d8027beaa/OceanDNA-b30346.fa | prodigal -d OceanDNA-b30346/cds.fna -a OceanDNA-b30346/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:17:15,779] [INFO] Task succeeded: Prodigal
[2023-03-18 04:17:15,780] [INFO] Task started: HMMsearch
[2023-03-18 04:17:15,780] [INFO] Running command: hmmsearch --tblout OceanDNA-b30346/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd5913e3e-2381-4bf3-815c-dee8d7397e86/dqc_reference/reference_markers.hmm OceanDNA-b30346/protein.faa > /dev/null
[2023-03-18 04:17:15,982] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:17:15,983] [INFO] Found 6/6 markers.
[2023-03-18 04:17:16,004] [INFO] Query marker FASTA was written to OceanDNA-b30346/markers.fasta
[2023-03-18 04:17:16,004] [INFO] Task started: Blastn
[2023-03-18 04:17:16,004] [INFO] Running command: blastn -query OceanDNA-b30346/markers.fasta -db /var/lib/cwl/stgd5913e3e-2381-4bf3-815c-dee8d7397e86/dqc_reference/reference_markers.fasta -out OceanDNA-b30346/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:17:16,746] [INFO] Task succeeded: Blastn
[2023-03-18 04:17:16,747] [INFO] Selected 18 target genomes.
[2023-03-18 04:17:16,747] [INFO] Target genome list was writen to OceanDNA-b30346/target_genomes.txt
[2023-03-18 04:17:16,782] [INFO] Task started: fastANI
[2023-03-18 04:17:16,782] [INFO] Running command: fastANI --query /var/lib/cwl/stg7dfc96ba-514d-49c9-a10a-fc1d8027beaa/OceanDNA-b30346.fa --refList OceanDNA-b30346/target_genomes.txt --output OceanDNA-b30346/fastani_result.tsv --threads 1
[2023-03-18 04:17:30,317] [INFO] Task succeeded: fastANI
[2023-03-18 04:17:30,318] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd5913e3e-2381-4bf3-815c-dee8d7397e86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:17:30,318] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd5913e3e-2381-4bf3-815c-dee8d7397e86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:17:30,329] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 04:17:30,329] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 04:17:30,329] [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 pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	97.1696	994	1118	95	conclusive
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	88.3833	887	1118	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	80.1662	607	1118	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	79.4991	534	1118	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	79.4936	537	1118	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	79.237	493	1118	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	79.2158	497	1118	95	below_threshold
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	78.8713	497	1118	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	78.4502	501	1118	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	78.3529	455	1118	95	below_threshold
Sulfitobacter noctilucicola	strain=NB-77	GCA_000622385.1	1342301	1342301	type	True	78.1577	359	1118	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	77.8742	429	1118	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	77.6804	309	1118	95	below_threshold
Pseudopuniceibacterium antarcticum	strain=HQ09	GCA_014899185.1	2613965	2613965	type	True	77.319	332	1118	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.2298	275	1118	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.0976	224	1118	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	77.0675	172	1118	95	below_threshold
Celeribacter litoreus	strain=ASW11-22	GCA_020165855.1	2876714	2876714	type	True	76.7015	143	1118	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:17:30,418] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30346/tc_result.tsv
[2023-03-18 04:17:30,418] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:17:30,418] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:17:30,418] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd5913e3e-2381-4bf3-815c-dee8d7397e86/dqc_reference/checkm_data
[2023-03-18 04:17:30,419] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:17:30,459] [INFO] Task started: CheckM
[2023-03-18 04:17:30,459] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30346/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30346/checkm_input OceanDNA-b30346/checkm_result
[2023-03-18 04:18:24,201] [INFO] Task succeeded: CheckM
[2023-03-18 04:18:24,201] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:18:24,204] [INFO] ===== Completeness check finished =====
[2023-03-18 04:18:24,204] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:18:24,204] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30346/markers.fasta)
[2023-03-18 04:18:24,205] [INFO] Task started: Blastn
[2023-03-18 04:18:24,205] [INFO] Running command: blastn -query OceanDNA-b30346/markers.fasta -db /var/lib/cwl/stgd5913e3e-2381-4bf3-815c-dee8d7397e86/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30346/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:18:25,545] [INFO] Task succeeded: Blastn
[2023-03-18 04:18:25,546] [INFO] Selected 10 target genomes.
[2023-03-18 04:18:25,546] [INFO] Target genome list was writen to OceanDNA-b30346/target_genomes_gtdb.txt
[2023-03-18 04:18:25,627] [INFO] Task started: fastANI
[2023-03-18 04:18:25,627] [INFO] Running command: fastANI --query /var/lib/cwl/stg7dfc96ba-514d-49c9-a10a-fc1d8027beaa/OceanDNA-b30346.fa --refList OceanDNA-b30346/target_genomes_gtdb.txt --output OceanDNA-b30346/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:18:33,719] [INFO] Task succeeded: fastANI
[2023-03-18 04:18:33,725] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 04:18:33,725] [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_900106935.1	s__Sulfitobacter pontiacus	97.1848	993	1118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.43	97.01	0.92	0.86	24	conclusive
GCF_900103185.1	s__Sulfitobacter litoralis	88.3833	887	1118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.10	98.53	0.92	0.85	6	-
GCF_006064855.1	s__Sulfitobacter sp006064855	87.2012	846	1118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013282155.1	s__Sulfitobacter sp013282155	81.2928	675	1118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.41	99.36	0.93	0.90	3	-
GCF_000156335.1	s__Sulfitobacter sp000156335	80.8739	691	1118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139555.1	s__Sulfitobacter sp013139555	80.5312	537	1118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116285.1	s__Sulfitobacter marinus	80.1933	604	1118	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	79.6112	535	1118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005887615.1	s__Sulfitobacter_E sabulilitoris	78.4421	502	1118	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_003054325.1	s__Sulfitobacter mediterraneus	78.3446	456	1118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.52	96.39	0.88	0.86	71	-
--------------------------------------------------------------------------------
[2023-03-18 04:18:33,725] [INFO] GTDB search result was written to OceanDNA-b30346/result_gtdb.tsv
[2023-03-18 04:18:33,726] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:18:33,727] [INFO] DFAST_QC result json was written to OceanDNA-b30346/dqc_result.json
[2023-03-18 04:18:33,727] [INFO] DFAST_QC completed!
[2023-03-18 04:18:33,727] [INFO] Total running time: 0h1m41s