[2023-03-15 12:33:51,736] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:33:51,736] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:33:51,736] [INFO] DQC Reference Directory: /var/lib/cwl/stge495eca4-090d-43de-880f-f124910528fb/dqc_reference
[2023-03-15 12:33:52,866] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:33:52,867] [INFO] Task started: Prodigal
[2023-03-15 12:33:52,867] [INFO] Running command: cat /var/lib/cwl/stg958e87b3-8cd5-481a-add7-3cf62a75933d/OceanDNA-b7473.fa | prodigal -d OceanDNA-b7473/cds.fna -a OceanDNA-b7473/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:34:11,625] [INFO] Task succeeded: Prodigal
[2023-03-15 12:34:11,625] [INFO] Task started: HMMsearch
[2023-03-15 12:34:11,625] [INFO] Running command: hmmsearch --tblout OceanDNA-b7473/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge495eca4-090d-43de-880f-f124910528fb/dqc_reference/reference_markers.hmm OceanDNA-b7473/protein.faa > /dev/null
[2023-03-15 12:34:11,840] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:34:11,841] [INFO] Found 6/6 markers.
[2023-03-15 12:34:11,865] [INFO] Query marker FASTA was written to OceanDNA-b7473/markers.fasta
[2023-03-15 12:34:11,866] [INFO] Task started: Blastn
[2023-03-15 12:34:11,866] [INFO] Running command: blastn -query OceanDNA-b7473/markers.fasta -db /var/lib/cwl/stge495eca4-090d-43de-880f-f124910528fb/dqc_reference/reference_markers.fasta -out OceanDNA-b7473/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:34:12,485] [INFO] Task succeeded: Blastn
[2023-03-15 12:34:12,486] [INFO] Selected 25 target genomes.
[2023-03-15 12:34:12,487] [INFO] Target genome list was writen to OceanDNA-b7473/target_genomes.txt
[2023-03-15 12:34:12,500] [INFO] Task started: fastANI
[2023-03-15 12:34:12,500] [INFO] Running command: fastANI --query /var/lib/cwl/stg958e87b3-8cd5-481a-add7-3cf62a75933d/OceanDNA-b7473.fa --refList OceanDNA-b7473/target_genomes.txt --output OceanDNA-b7473/fastani_result.tsv --threads 1
[2023-03-15 12:34:27,902] [INFO] Task succeeded: fastANI
[2023-03-15 12:34:27,902] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge495eca4-090d-43de-880f-f124910528fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:34:27,903] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge495eca4-090d-43de-880f-f124910528fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:34:27,913] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:34:27,913] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 12:34:27,913] [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 marinoflava	strain=LMG 1345	GCA_004104035.1	988	988	type	True	77.4511	177	926	95	below_threshold
Leeuwenhoekiella marinoflava	strain=DSM 3653	GCA_900129005.1	988	988	type	True	77.4343	177	926	95	below_threshold
Leeuwenhoekiella aequorea	strain=LMG 22550	GCA_004104375.1	283736	283736	type	True	77.2956	152	926	95	below_threshold
Leeuwenhoekiella blandensis	strain=MED217	GCA_000152985.1	360293	360293	type	True	77.0939	165	926	95	below_threshold
Leeuwenhoekiella aestuarii	strain=R-48165	GCA_004104055.1	2249426	2249426	type	True	77.0249	188	926	95	below_threshold
Leeuwenhoekiella palythoae	strain=LMG 24856	GCA_004104045.1	573501	573501	type	True	76.9385	180	926	95	below_threshold
Joostella marina	strain=DSM 19592	GCA_000260115.1	453852	453852	type	True	76.2656	58	926	95	below_threshold
Salegentibacter holothuriorum	strain=DSM 23405	GCA_900168045.1	241145	241145	type	True	76.0739	77	926	95	below_threshold
Aquimarina macrocephali	strain=JAMB N27	GCA_000520995.1	666563	666563	type	True	75.9278	62	926	95	below_threshold
Salegentibacter salegens	strain=ACAM 48	GCA_900142975.1	143223	143223	type	True	75.9097	82	926	95	below_threshold
Salegentibacter maritimus	strain=F63223	GCA_016236915.1	2794347	2794347	type	True	75.8969	53	926	95	below_threshold
Salegentibacter salegens	strain=DSM 5424	GCA_003001895.1	143223	143223	type	True	75.8585	82	926	95	below_threshold
Aquimarina latercula	strain=DSM 2041	GCA_000430645.1	987	987	type	True	75.7628	63	926	95	below_threshold
Aquimarina amphilecti	strain=DSM 25232	GCA_900109375.1	1038014	1038014	type	True	75.5463	63	926	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 12:34:27,914] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7473/tc_result.tsv
[2023-03-15 12:34:27,914] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:34:27,914] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:34:27,915] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge495eca4-090d-43de-880f-f124910528fb/dqc_reference/checkm_data
[2023-03-15 12:34:27,915] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:34:27,921] [INFO] Task started: CheckM
[2023-03-15 12:34:27,921] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7473/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7473/checkm_input OceanDNA-b7473/checkm_result
[2023-03-15 12:35:16,591] [INFO] Task succeeded: CheckM
[2023-03-15 12:35:16,591] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 12:35:16,617] [INFO] ===== Completeness check finished =====
[2023-03-15 12:35:16,617] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:35:16,618] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7473/markers.fasta)
[2023-03-15 12:35:16,618] [INFO] Task started: Blastn
[2023-03-15 12:35:16,618] [INFO] Running command: blastn -query OceanDNA-b7473/markers.fasta -db /var/lib/cwl/stge495eca4-090d-43de-880f-f124910528fb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7473/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:35:17,609] [INFO] Task succeeded: Blastn
[2023-03-15 12:35:17,614] [INFO] Selected 26 target genomes.
[2023-03-15 12:35:17,614] [INFO] Target genome list was writen to OceanDNA-b7473/target_genomes_gtdb.txt
[2023-03-15 12:35:17,841] [INFO] Task started: fastANI
[2023-03-15 12:35:17,841] [INFO] Running command: fastANI --query /var/lib/cwl/stg958e87b3-8cd5-481a-add7-3cf62a75933d/OceanDNA-b7473.fa --refList OceanDNA-b7473/target_genomes_gtdb.txt --output OceanDNA-b7473/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:35:34,345] [INFO] Task succeeded: fastANI
[2023-03-15 12:35:34,355] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 12:35:34,356] [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
GCA_002710685.1	s__Leeuwenhoekiella sp002710685	84.5871	152	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900129005.1	s__Leeuwenhoekiella marinoflava	77.4343	177	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000687915.1	s__Leeuwenhoekiella sp000687915	77.3007	192	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004104375.1	s__Leeuwenhoekiella aequorea	77.2956	152	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004104075.1	s__Leeuwenhoekiella polynyae	77.1533	184	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152985.1	s__Leeuwenhoekiella blandensis	77.0939	165	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	97.86	97.58	0.89	0.73	11	-
GCF_004104055.1	s__Leeuwenhoekiella aestuarii	77.0111	189	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.75	99.75	0.97	0.97	2	-
GCF_900130045.1	s__Leeuwenhoekiella palythoae	76.9098	183	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	96.69	96.09	0.92	0.86	9	-
GCA_002708845.1	s__Leeuwenhoekiella sp002708845	76.7148	142	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.96	99.95	0.93	0.90	5	-
GCF_900168045.1	s__Salegentibacter holothuriorum	76.0739	77	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000520995.1	s__Aquimarina macrocephali	75.9278	62	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142975.1	s__Salegentibacter salegens	75.9097	82	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900299525.1	s__Aquimarina sp900299525	75.8271	59	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000355805.1	s__Dokdonia sp000355805	75.8243	71	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422365.1	s__Mesoflavibacter zeaxanthinifaciens	75.7945	64	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	97.07	97.05	0.91	0.91	3	-
GCF_000430645.1	s__Aquimarina latercula	75.7808	62	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.44	98.41	0.94	0.92	4	-
GCF_002846555.1	s__Aquimarina sp002846555	75.7167	58	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900299505.1	s__Aquimarina sp900299505	75.5903	61	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 12:35:34,357] [INFO] GTDB search result was written to OceanDNA-b7473/result_gtdb.tsv
[2023-03-15 12:35:34,360] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:35:34,364] [INFO] DFAST_QC result json was written to OceanDNA-b7473/dqc_result.json
[2023-03-15 12:35:34,364] [INFO] DFAST_QC completed!
[2023-03-15 12:35:34,364] [INFO] Total running time: 0h1m43s