[2023-03-16 19:45:43,029] [INFO] DFAST_QC pipeline started.
[2023-03-16 19:45:43,029] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 19:45:43,030] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf719916-de94-48cd-a7d8-5409977aebd2/dqc_reference
[2023-03-16 19:45:44,158] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 19:45:44,159] [INFO] Task started: Prodigal
[2023-03-16 19:45:44,159] [INFO] Running command: cat /var/lib/cwl/stgd0ae6f38-fec1-44e4-93c6-318255194484/OceanDNA-b30226.fa | prodigal -d OceanDNA-b30226/cds.fna -a OceanDNA-b30226/protein.faa -g 11 -q > /dev/null
[2023-03-16 19:46:11,155] [INFO] Task succeeded: Prodigal
[2023-03-16 19:46:11,156] [INFO] Task started: HMMsearch
[2023-03-16 19:46:11,156] [INFO] Running command: hmmsearch --tblout OceanDNA-b30226/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf719916-de94-48cd-a7d8-5409977aebd2/dqc_reference/reference_markers.hmm OceanDNA-b30226/protein.faa > /dev/null
[2023-03-16 19:46:11,375] [INFO] Task succeeded: HMMsearch
[2023-03-16 19:46:11,375] [INFO] Found 6/6 markers.
[2023-03-16 19:46:11,402] [INFO] Query marker FASTA was written to OceanDNA-b30226/markers.fasta
[2023-03-16 19:46:11,403] [INFO] Task started: Blastn
[2023-03-16 19:46:11,403] [INFO] Running command: blastn -query OceanDNA-b30226/markers.fasta -db /var/lib/cwl/stgaf719916-de94-48cd-a7d8-5409977aebd2/dqc_reference/reference_markers.fasta -out OceanDNA-b30226/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:46:12,107] [INFO] Task succeeded: Blastn
[2023-03-16 19:46:12,107] [INFO] Selected 22 target genomes.
[2023-03-16 19:46:12,108] [INFO] Target genome list was writen to OceanDNA-b30226/target_genomes.txt
[2023-03-16 19:46:12,118] [INFO] Task started: fastANI
[2023-03-16 19:46:12,118] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0ae6f38-fec1-44e4-93c6-318255194484/OceanDNA-b30226.fa --refList OceanDNA-b30226/target_genomes.txt --output OceanDNA-b30226/fastani_result.tsv --threads 1
[2023-03-16 19:46:31,057] [INFO] Task succeeded: fastANI
[2023-03-16 19:46:31,057] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf719916-de94-48cd-a7d8-5409977aebd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 19:46:31,057] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf719916-de94-48cd-a7d8-5409977aebd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 19:46:31,070] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 19:46:31,070] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 19:46:31,070] [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 mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	78.4477	503	1368	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	77.9557	362	1368	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	77.9327	410	1368	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	77.9238	328	1368	95	below_threshold
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	77.9049	411	1368	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	77.7926	374	1368	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	77.7869	342	1368	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.7716	343	1368	95	below_threshold
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	77.6276	317	1368	95	below_threshold
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	77.6068	351	1368	95	below_threshold
Sulfitobacter noctilucicola	strain=NB-77	GCA_000622385.1	1342301	1342301	type	True	77.5868	318	1368	95	below_threshold
Sulfitobacter maritimus	strain=S0837	GCA_013346665.1	2741719	2741719	type	True	77.5793	333	1368	95	below_threshold
Sulfitobacter noctilucicola	strain=DSM 101015	GCA_014197555.1	1342301	1342301	type	True	77.5717	319	1368	95	below_threshold
Sulfitobacter aestuariivivens	strain=TSTF-M16	GCA_014763045.1	2766981	2766981	type	True	77.4018	363	1368	95	below_threshold
Pseudooceanicola nitratireducens	strain=CGMCC 1.7292	GCA_900109195.1	517719	517719	type	True	76.6191	132	1368	95	below_threshold
Pseudooceanicola nitratireducens	strain=DSM 29619	GCA_900112545.1	517719	517719	type	True	76.6089	135	1368	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.5482	184	1368	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	76.5401	129	1368	95	below_threshold
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	76.3818	200	1368	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.3574	116	1368	95	below_threshold
Donghicola tyrosinivorans	strain=DSM 100212	GCA_003003355.1	1652492	1652492	type	True	76.2209	114	1368	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	75.9614	96	1368	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 19:46:31,070] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30226/tc_result.tsv
[2023-03-16 19:46:31,071] [INFO] ===== Taxonomy check completed =====
[2023-03-16 19:46:31,071] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 19:46:31,071] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf719916-de94-48cd-a7d8-5409977aebd2/dqc_reference/checkm_data
[2023-03-16 19:46:31,072] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 19:46:31,348] [INFO] Task started: CheckM
[2023-03-16 19:46:31,348] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30226/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30226/checkm_input OceanDNA-b30226/checkm_result
[2023-03-16 19:48:02,087] [INFO] Task succeeded: CheckM
[2023-03-16 19:48:02,087] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.91%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 19:48:02,090] [INFO] ===== Completeness check finished =====
[2023-03-16 19:48:02,090] [INFO] ===== Start GTDB Search =====
[2023-03-16 19:48:02,090] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30226/markers.fasta)
[2023-03-16 19:48:02,091] [INFO] Task started: Blastn
[2023-03-16 19:48:02,091] [INFO] Running command: blastn -query OceanDNA-b30226/markers.fasta -db /var/lib/cwl/stgaf719916-de94-48cd-a7d8-5409977aebd2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30226/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:48:04,183] [INFO] Task succeeded: Blastn
[2023-03-16 19:48:04,184] [INFO] Selected 19 target genomes.
[2023-03-16 19:48:04,185] [INFO] Target genome list was writen to OceanDNA-b30226/target_genomes_gtdb.txt
[2023-03-16 19:48:04,231] [INFO] Task started: fastANI
[2023-03-16 19:48:04,231] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0ae6f38-fec1-44e4-93c6-318255194484/OceanDNA-b30226.fa --refList OceanDNA-b30226/target_genomes_gtdb.txt --output OceanDNA-b30226/fastani_result_gtdb.tsv --threads 1
[2023-03-16 19:48:25,972] [INFO] Task succeeded: fastANI
[2023-03-16 19:48:25,983] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 19:48:25,984] [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_003352065.1	s__Sulfitobacter sp003352065	81.6866	816	1368	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	78.4554	502	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.52	96.39	0.88	0.86	71	-
GCF_016801775.1	s__Sulfitobacter mediterraneus_A	78.2165	471	1368	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	78.1279	430	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.41	99.36	0.93	0.90	3	-
GCA_017854855.1	s__Sulfitobacter sp017854855	78.0613	451	1368	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	77.9648	361	1368	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	77.9244	458	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106935.1	s__Sulfitobacter pontiacus	77.9133	329	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.43	97.01	0.92	0.86	24	-
GCF_000622325.1	s__Sulfitobacter geojensis	77.8967	412	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.34	96.22	0.90	0.89	35	-
GCF_000156335.1	s__Sulfitobacter sp000156335	77.7976	387	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622365.1	s__Sulfitobacter noctilucae	77.7836	375	1368	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	77.7541	470	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854675.1	s__Sulfitobacter sp017854675	77.7344	372	1368	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	77.6615	329	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113435.1	s__Sulfitobacter dubius	77.6069	351	1368	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	77.5793	333	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622385.1	s__Sulfitobacter noctilucicola	77.5768	319	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014763045.1	s__Sulfitobacter aestuariivivens	77.4018	363	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	77.2435	316	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-16 19:48:25,984] [INFO] GTDB search result was written to OceanDNA-b30226/result_gtdb.tsv
[2023-03-16 19:48:25,984] [INFO] ===== GTDB Search completed =====
[2023-03-16 19:48:25,986] [INFO] DFAST_QC result json was written to OceanDNA-b30226/dqc_result.json
[2023-03-16 19:48:25,986] [INFO] DFAST_QC completed!
[2023-03-16 19:48:25,986] [INFO] Total running time: 0h2m43s