[2023-03-19 02:40:15,875] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:40:15,875] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:40:15,875] [INFO] DQC Reference Directory: /var/lib/cwl/stg64f13f14-0aa6-4902-a377-de05ac39d694/dqc_reference
[2023-03-19 02:40:16,995] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:40:16,995] [INFO] Task started: Prodigal
[2023-03-19 02:40:16,996] [INFO] Running command: cat /var/lib/cwl/stg2549f656-da0f-49d3-8f3f-ffd5c0dbb0ec/OceanDNA-b35286.fa | prodigal -d OceanDNA-b35286/cds.fna -a OceanDNA-b35286/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:40:24,468] [INFO] Task succeeded: Prodigal
[2023-03-19 02:40:24,469] [INFO] Task started: HMMsearch
[2023-03-19 02:40:24,469] [INFO] Running command: hmmsearch --tblout OceanDNA-b35286/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg64f13f14-0aa6-4902-a377-de05ac39d694/dqc_reference/reference_markers.hmm OceanDNA-b35286/protein.faa > /dev/null
[2023-03-19 02:40:24,641] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:40:24,642] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg2549f656-da0f-49d3-8f3f-ffd5c0dbb0ec/OceanDNA-b35286.fa]
[2023-03-19 02:40:24,666] [INFO] Query marker FASTA was written to OceanDNA-b35286/markers.fasta
[2023-03-19 02:40:24,667] [INFO] Task started: Blastn
[2023-03-19 02:40:24,667] [INFO] Running command: blastn -query OceanDNA-b35286/markers.fasta -db /var/lib/cwl/stg64f13f14-0aa6-4902-a377-de05ac39d694/dqc_reference/reference_markers.fasta -out OceanDNA-b35286/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:40:25,178] [INFO] Task succeeded: Blastn
[2023-03-19 02:40:25,181] [INFO] Selected 14 target genomes.
[2023-03-19 02:40:25,182] [INFO] Target genome list was writen to OceanDNA-b35286/target_genomes.txt
[2023-03-19 02:40:25,191] [INFO] Task started: fastANI
[2023-03-19 02:40:25,191] [INFO] Running command: fastANI --query /var/lib/cwl/stg2549f656-da0f-49d3-8f3f-ffd5c0dbb0ec/OceanDNA-b35286.fa --refList OceanDNA-b35286/target_genomes.txt --output OceanDNA-b35286/fastani_result.tsv --threads 1
[2023-03-19 02:40:33,895] [INFO] Task succeeded: fastANI
[2023-03-19 02:40:33,895] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg64f13f14-0aa6-4902-a377-de05ac39d694/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:40:33,895] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg64f13f14-0aa6-4902-a377-de05ac39d694/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:40:33,903] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2023-03-19 02:40:33,903] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-19 02:40:33,903] [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
Photobacterium angustum	strain=ATCC 25915	GCA_000950005.1	661	661	type	True	95.0465	228	234	95	conclusive
Photobacterium angustum	strain=ATCC 25915	GCA_003026365.1	661	661	type	True	94.9899	230	234	95	below_threshold
Photobacterium leiognathi	strain=ATCC 25521	GCA_000950415.1	553611	553611	type	True	84.9335	192	234	95	below_threshold
Photobacterium leiognathi	strain=ATCC 25521	GCA_003026235.1	553611	553611	type	True	84.8566	196	234	95	below_threshold
Photobacterium lucens	strain=CAIM 1937	GCA_009873615.1	2562949	2562949	type	True	84.1071	187	234	95	below_threshold
Photobacterium kishitanii	strain=ATCC BAA-1194	GCA_000950095.1	318456	318456	type	True	80.5476	121	234	95	below_threshold
Photobacterium toruni	strain=CECT 9189	GCA_024529955.1	1935446	1935446	type	True	80.4682	111	234	95	below_threshold
Photobacterium kishitanii	strain=ATCC:BAA-1194	GCA_003026355.1	318456	318456	type	True	80.465	127	234	95	below_threshold
Photobacterium kishitanii	strain=pjapo.1.1	GCA_003025975.1	318456	318456	type	True	80.4407	127	234	95	below_threshold
Photobacterium toruni	strain=CECT 9189	GCA_900166975.1	1935446	1935446	type	True	80.3883	111	234	95	below_threshold
Photobacterium swingsii	strain=CECT 7576	GCA_024346715.1	680026	680026	type	True	79.234	78	234	95	below_threshold
Aliivibrio fischeri	strain=DSM 507	GCA_023983475.1	668	668	suspected-type	True	78.0046	52	234	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 02:40:33,904] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35286/tc_result.tsv
[2023-03-19 02:40:33,906] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:40:33,907] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:40:33,907] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg64f13f14-0aa6-4902-a377-de05ac39d694/dqc_reference/checkm_data
[2023-03-19 02:40:33,907] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:40:33,913] [INFO] Task started: CheckM
[2023-03-19 02:40:33,913] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35286/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35286/checkm_input OceanDNA-b35286/checkm_result
[2023-03-19 02:40:58,440] [INFO] Task succeeded: CheckM
[2023-03-19 02:40:58,440] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.32%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:40:58,445] [INFO] ===== Completeness check finished =====
[2023-03-19 02:40:58,445] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:40:58,446] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35286/markers.fasta)
[2023-03-19 02:40:58,447] [INFO] Task started: Blastn
[2023-03-19 02:40:58,447] [INFO] Running command: blastn -query OceanDNA-b35286/markers.fasta -db /var/lib/cwl/stg64f13f14-0aa6-4902-a377-de05ac39d694/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35286/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:40:58,946] [INFO] Task succeeded: Blastn
[2023-03-19 02:40:58,947] [INFO] Selected 8 target genomes.
[2023-03-19 02:40:58,947] [INFO] Target genome list was writen to OceanDNA-b35286/target_genomes_gtdb.txt
[2023-03-19 02:40:58,957] [INFO] Task started: fastANI
[2023-03-19 02:40:58,957] [INFO] Running command: fastANI --query /var/lib/cwl/stg2549f656-da0f-49d3-8f3f-ffd5c0dbb0ec/OceanDNA-b35286.fa --refList OceanDNA-b35286/target_genomes_gtdb.txt --output OceanDNA-b35286/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:41:04,589] [INFO] Task succeeded: fastANI
[2023-03-19 02:41:04,595] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:41:04,595] [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_003026365.1	s__Photobacterium angustum	94.9899	230	234	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.76	95.45	0.92	0.87	27	-
GCF_003026105.1	s__Photobacterium sp003026105	93.9267	221	234	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.17	99.06	0.96	0.95	8	-
GCF_000153325.1	s__Photobacterium sp000153325	93.3693	222	234	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000950415.1	s__Photobacterium leiognathi	84.9335	192	234	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.11	96.59	0.91	0.88	15	-
GCF_009873615.1	s__Photobacterium lucens	84.1071	187	234	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.83	97.58	0.96	0.94	5	-
GCF_900185615.1	s__Photobacterium malacitanum	80.9392	118	234	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	95.08	95.06	0.91	0.91	6	-
GCF_003026355.1	s__Photobacterium kishitanii	80.465	127	234	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.67	97.61	0.95	0.91	24	-
GCF_900166975.1	s__Photobacterium toruni	80.3883	111	234	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:41:04,596] [INFO] GTDB search result was written to OceanDNA-b35286/result_gtdb.tsv
[2023-03-19 02:41:04,599] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:41:04,602] [INFO] DFAST_QC result json was written to OceanDNA-b35286/dqc_result.json
[2023-03-19 02:41:04,602] [INFO] DFAST_QC completed!
[2023-03-19 02:41:04,602] [INFO] Total running time: 0h0m49s