[2023-03-15 11:24:11,480] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:24:11,481] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:24:11,481] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b76db08-b6a6-4f38-9669-cc9fa01a9f61/dqc_reference
[2023-03-15 11:24:12,547] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:24:12,548] [INFO] Task started: Prodigal
[2023-03-15 11:24:12,548] [INFO] Running command: cat /var/lib/cwl/stgea27017d-8dc9-4d56-a872-ee97afa5fb2b/OceanDNA-b7533.fa | prodigal -d OceanDNA-b7533/cds.fna -a OceanDNA-b7533/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:24:38,875] [INFO] Task succeeded: Prodigal
[2023-03-15 11:24:38,875] [INFO] Task started: HMMsearch
[2023-03-15 11:24:38,875] [INFO] Running command: hmmsearch --tblout OceanDNA-b7533/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b76db08-b6a6-4f38-9669-cc9fa01a9f61/dqc_reference/reference_markers.hmm OceanDNA-b7533/protein.faa > /dev/null
[2023-03-15 11:24:39,099] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:24:39,100] [INFO] Found 6/6 markers.
[2023-03-15 11:24:39,122] [INFO] Query marker FASTA was written to OceanDNA-b7533/markers.fasta
[2023-03-15 11:24:39,123] [INFO] Task started: Blastn
[2023-03-15 11:24:39,123] [INFO] Running command: blastn -query OceanDNA-b7533/markers.fasta -db /var/lib/cwl/stg7b76db08-b6a6-4f38-9669-cc9fa01a9f61/dqc_reference/reference_markers.fasta -out OceanDNA-b7533/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:24:39,717] [INFO] Task succeeded: Blastn
[2023-03-15 11:24:39,717] [INFO] Selected 12 target genomes.
[2023-03-15 11:24:39,718] [INFO] Target genome list was writen to OceanDNA-b7533/target_genomes.txt
[2023-03-15 11:24:39,724] [INFO] Task started: fastANI
[2023-03-15 11:24:39,724] [INFO] Running command: fastANI --query /var/lib/cwl/stgea27017d-8dc9-4d56-a872-ee97afa5fb2b/OceanDNA-b7533.fa --refList OceanDNA-b7533/target_genomes.txt --output OceanDNA-b7533/fastani_result.tsv --threads 1
[2023-03-15 11:24:48,758] [INFO] Task succeeded: fastANI
[2023-03-15 11:24:48,758] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b76db08-b6a6-4f38-9669-cc9fa01a9f61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:24:48,758] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b76db08-b6a6-4f38-9669-cc9fa01a9f61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:24:48,764] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2023-03-15 11:24:48,764] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 11:24:48,765] [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
Leeuwenhoekiella palythoae	strain=LMG 24856	GCA_004104045.1	573501	573501	type	True	96.1066	1139	1263	95	conclusive
Leeuwenhoekiella palythoae	strain=DSM 19859	GCA_900130045.1	573501	573501	type	True	96.0866	1141	1263	95	conclusive
Leeuwenhoekiella blandensis	strain=MED217	GCA_000152985.1	360293	360293	type	True	85.882	934	1263	95	below_threshold
Leeuwenhoekiella marinoflava	strain=DSM 3653	GCA_900129005.1	988	988	type	True	79.6681	699	1263	95	below_threshold
Leeuwenhoekiella marinoflava	strain=LMG 1345	GCA_004104035.1	988	988	type	True	79.6597	693	1263	95	below_threshold
Leeuwenhoekiella aestuarii	strain=R-48165	GCA_004104055.1	2249426	2249426	type	True	79.5876	672	1263	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	76.3755	60	1263	95	below_threshold
Aequorivita iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	75.913	54	1263	95	below_threshold
Cellulophaga tyrosinoxydans	strain=DSM 21164	GCA_900176415.1	504486	504486	type	True	75.3391	60	1263	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:24:48,765] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7533/tc_result.tsv
[2023-03-15 11:24:48,765] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:24:48,765] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:24:48,765] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b76db08-b6a6-4f38-9669-cc9fa01a9f61/dqc_reference/checkm_data
[2023-03-15 11:24:48,766] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:24:48,794] [INFO] Task started: CheckM
[2023-03-15 11:24:48,794] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7533/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7533/checkm_input OceanDNA-b7533/checkm_result
[2023-03-15 11:25:53,194] [INFO] Task succeeded: CheckM
[2023-03-15 11:25:53,195] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:25:53,199] [INFO] ===== Completeness check finished =====
[2023-03-15 11:25:53,199] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:25:53,200] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7533/markers.fasta)
[2023-03-15 11:25:53,201] [INFO] Task started: Blastn
[2023-03-15 11:25:53,201] [INFO] Running command: blastn -query OceanDNA-b7533/markers.fasta -db /var/lib/cwl/stg7b76db08-b6a6-4f38-9669-cc9fa01a9f61/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7533/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:25:54,067] [INFO] Task succeeded: Blastn
[2023-03-15 11:25:54,069] [INFO] Selected 10 target genomes.
[2023-03-15 11:25:54,070] [INFO] Target genome list was writen to OceanDNA-b7533/target_genomes_gtdb.txt
[2023-03-15 11:25:54,079] [INFO] Task started: fastANI
[2023-03-15 11:25:54,079] [INFO] Running command: fastANI --query /var/lib/cwl/stgea27017d-8dc9-4d56-a872-ee97afa5fb2b/OceanDNA-b7533.fa --refList OceanDNA-b7533/target_genomes_gtdb.txt --output OceanDNA-b7533/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:26:02,110] [INFO] Task succeeded: fastANI
[2023-03-15 11:26:02,117] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 11:26:02,118] [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_900130045.1	s__Leeuwenhoekiella palythoae	96.0855	1141	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	96.69	96.09	0.92	0.86	9	conclusive
GCF_000152985.1	s__Leeuwenhoekiella blandensis	85.882	934	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	97.86	97.58	0.89	0.73	11	-
GCF_004104075.1	s__Leeuwenhoekiella polynyae	79.6969	675	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129005.1	s__Leeuwenhoekiella marinoflava	79.6721	698	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004104055.1	s__Leeuwenhoekiella aestuarii	79.5897	674	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.75	99.75	0.97	0.97	2	-
GCF_000687915.1	s__Leeuwenhoekiella sp000687915	78.4892	437	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002744755.1	s__Leeuwenhoekiella nanhaiensis	78.4788	442	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	96.22	96.22	0.78	0.78	2	-
GCF_018861125.1	s__Cellulophaga baltica_A	76.0155	88	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162685.1	s__Psychroserpens sp002162685	75.7788	62	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:26:02,118] [INFO] GTDB search result was written to OceanDNA-b7533/result_gtdb.tsv
[2023-03-15 11:26:02,118] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:26:02,120] [INFO] DFAST_QC result json was written to OceanDNA-b7533/dqc_result.json
[2023-03-15 11:26:02,121] [INFO] DFAST_QC completed!
[2023-03-15 11:26:02,121] [INFO] Total running time: 0h1m51s