[2023-03-18 09:19:07,002] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:19:07,002] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:19:07,003] [INFO] DQC Reference Directory: /var/lib/cwl/stgc59568e4-8ad1-40e4-93bd-14272738f039/dqc_reference
[2023-03-18 09:19:08,109] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:19:08,109] [INFO] Task started: Prodigal
[2023-03-18 09:19:08,109] [INFO] Running command: cat /var/lib/cwl/stgc173dcc1-eee0-4582-8c4e-1def0ab812cd/OceanDNA-b9659.fa | prodigal -d OceanDNA-b9659/cds.fna -a OceanDNA-b9659/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:19:23,993] [INFO] Task succeeded: Prodigal
[2023-03-18 09:19:23,993] [INFO] Task started: HMMsearch
[2023-03-18 09:19:23,993] [INFO] Running command: hmmsearch --tblout OceanDNA-b9659/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc59568e4-8ad1-40e4-93bd-14272738f039/dqc_reference/reference_markers.hmm OceanDNA-b9659/protein.faa > /dev/null
[2023-03-18 09:19:24,182] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:19:24,183] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc173dcc1-eee0-4582-8c4e-1def0ab812cd/OceanDNA-b9659.fa]
[2023-03-18 09:19:24,213] [INFO] Query marker FASTA was written to OceanDNA-b9659/markers.fasta
[2023-03-18 09:19:24,214] [INFO] Task started: Blastn
[2023-03-18 09:19:24,214] [INFO] Running command: blastn -query OceanDNA-b9659/markers.fasta -db /var/lib/cwl/stgc59568e4-8ad1-40e4-93bd-14272738f039/dqc_reference/reference_markers.fasta -out OceanDNA-b9659/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:19:24,784] [INFO] Task succeeded: Blastn
[2023-03-18 09:19:24,794] [INFO] Selected 16 target genomes.
[2023-03-18 09:19:24,795] [INFO] Target genome list was writen to OceanDNA-b9659/target_genomes.txt
[2023-03-18 09:19:24,839] [INFO] Task started: fastANI
[2023-03-18 09:19:24,839] [INFO] Running command: fastANI --query /var/lib/cwl/stgc173dcc1-eee0-4582-8c4e-1def0ab812cd/OceanDNA-b9659.fa --refList OceanDNA-b9659/target_genomes.txt --output OceanDNA-b9659/fastani_result.tsv --threads 1
[2023-03-18 09:19:35,868] [INFO] Task succeeded: fastANI
[2023-03-18 09:19:35,868] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc59568e4-8ad1-40e4-93bd-14272738f039/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:19:35,868] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc59568e4-8ad1-40e4-93bd-14272738f039/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:19:35,876] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 09:19:35,876] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 09:19:35,876] [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
Maribacter arcticus	strain=DSM 23546	GCA_900167935.1	561365	561365	type	True	99.1536	792	808	95	conclusive
Maribacter orientalis	strain=DSM 16471	GCA_900109345.1	228957	228957	type	True	90.4005	753	808	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001913155.1	1836467	1836467	type	True	80.6454	566	808	95	below_threshold
Maribacter stanieri	strain=DSM 19891	GCA_900112245.1	440514	440514	type	True	80.5915	559	808	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001673755.1	1836467	1836467	type	True	80.5737	565	808	95	below_threshold
Maribacter aquivivus	strain=DSM 16478	GCA_900142175.1	228958	228958	type	True	80.4929	534	808	95	below_threshold
Maribacter spongiicola	strain=DSM 25233	GCA_004364165.1	1206753	1206753	type	True	80.4545	532	808	95	below_threshold
Maribacter caenipelagi	strain=CECT 8455	GCA_004364175.1	1447781	1447781	type	True	80.1601	536	808	95	below_threshold
Maribacter forsetii	strain=DSM 18668	GCA_000744105.1	444515	444515	type	True	79.9618	502	808	95	below_threshold
Maribacter algarum	strain=RZ26	GCA_005885635.1	2578118	2578118	type	True	76.5351	135	808	95	below_threshold
Maribacter polysiphoniae	strain=DSM 23514	GCA_003148665.1	429344	429344	type	True	76.407	94	808	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 09:19:35,878] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9659/tc_result.tsv
[2023-03-18 09:19:35,882] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:19:35,882] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:19:35,882] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc59568e4-8ad1-40e4-93bd-14272738f039/dqc_reference/checkm_data
[2023-03-18 09:19:35,883] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:19:35,889] [INFO] Task started: CheckM
[2023-03-18 09:19:35,889] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9659/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9659/checkm_input OceanDNA-b9659/checkm_result
[2023-03-18 09:20:17,925] [INFO] Task succeeded: CheckM
[2023-03-18 09:20:17,926] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.63%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:20:17,960] [INFO] ===== Completeness check finished =====
[2023-03-18 09:20:17,960] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:20:17,960] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9659/markers.fasta)
[2023-03-18 09:20:17,961] [INFO] Task started: Blastn
[2023-03-18 09:20:17,961] [INFO] Running command: blastn -query OceanDNA-b9659/markers.fasta -db /var/lib/cwl/stgc59568e4-8ad1-40e4-93bd-14272738f039/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9659/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:20:18,743] [INFO] Task succeeded: Blastn
[2023-03-18 09:20:18,752] [INFO] Selected 11 target genomes.
[2023-03-18 09:20:18,752] [INFO] Target genome list was writen to OceanDNA-b9659/target_genomes_gtdb.txt
[2023-03-18 09:20:18,930] [INFO] Task started: fastANI
[2023-03-18 09:20:18,930] [INFO] Running command: fastANI --query /var/lib/cwl/stgc173dcc1-eee0-4582-8c4e-1def0ab812cd/OceanDNA-b9659.fa --refList OceanDNA-b9659/target_genomes_gtdb.txt --output OceanDNA-b9659/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:20:27,733] [INFO] Task succeeded: fastANI
[2023-03-18 09:20:27,740] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 09:20:27,740] [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_900167935.1	s__Maribacter arcticus	99.1536	792	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900109345.1	s__Maribacter orientalis	90.4005	753	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005771495.1	s__Maribacter sp005771495	80.8184	594	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050675.1	s__Maribacter sp011050675	80.6913	562	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001913155.1	s__Maribacter hydrothermalis	80.6454	566	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900112245.1	s__Maribacter stanieri	80.5915	559	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	98.09	98.09	0.92	0.92	2	-
GCF_900142175.1	s__Maribacter aquivivus	80.4929	534	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364165.1	s__Maribacter spongiicola	80.4545	532	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744105.1	s__Maribacter forsetii	79.9618	502	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005885635.1	s__RZ26 sp005885635	76.5351	135	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__RZ26	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001401755.1	s__Aquimarina longa	75.6359	62	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:20:27,742] [INFO] GTDB search result was written to OceanDNA-b9659/result_gtdb.tsv
[2023-03-18 09:20:27,742] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:20:27,744] [INFO] DFAST_QC result json was written to OceanDNA-b9659/dqc_result.json
[2023-03-18 09:20:27,744] [INFO] DFAST_QC completed!
[2023-03-18 09:20:27,744] [INFO] Total running time: 0h1m21s