[2023-03-16 02:38:04,936] [INFO] DFAST_QC pipeline started.
[2023-03-16 02:38:04,936] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 02:38:04,936] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0fe271c-9c07-4d2e-b7f5-bc770579b9c4/dqc_reference
[2023-03-16 02:38:06,170] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 02:38:06,170] [INFO] Task started: Prodigal
[2023-03-16 02:38:06,170] [INFO] Running command: cat /var/lib/cwl/stge4109a73-8bc5-49bd-afe2-13eb21ba83bf/OceanDNA-b35287.fa | prodigal -d OceanDNA-b35287/cds.fna -a OceanDNA-b35287/protein.faa -g 11 -q > /dev/null
[2023-03-16 02:38:28,235] [INFO] Task succeeded: Prodigal
[2023-03-16 02:38:28,235] [INFO] Task started: HMMsearch
[2023-03-16 02:38:28,235] [INFO] Running command: hmmsearch --tblout OceanDNA-b35287/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0fe271c-9c07-4d2e-b7f5-bc770579b9c4/dqc_reference/reference_markers.hmm OceanDNA-b35287/protein.faa > /dev/null
[2023-03-16 02:38:28,470] [INFO] Task succeeded: HMMsearch
[2023-03-16 02:38:28,470] [INFO] Found 6/6 markers.
[2023-03-16 02:38:28,496] [INFO] Query marker FASTA was written to OceanDNA-b35287/markers.fasta
[2023-03-16 02:38:28,496] [INFO] Task started: Blastn
[2023-03-16 02:38:28,496] [INFO] Running command: blastn -query OceanDNA-b35287/markers.fasta -db /var/lib/cwl/stgd0fe271c-9c07-4d2e-b7f5-bc770579b9c4/dqc_reference/reference_markers.fasta -out OceanDNA-b35287/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:38:29,183] [INFO] Task succeeded: Blastn
[2023-03-16 02:38:29,184] [INFO] Selected 11 target genomes.
[2023-03-16 02:38:29,184] [INFO] Target genome list was writen to OceanDNA-b35287/target_genomes.txt
[2023-03-16 02:38:29,191] [INFO] Task started: fastANI
[2023-03-16 02:38:29,192] [INFO] Running command: fastANI --query /var/lib/cwl/stge4109a73-8bc5-49bd-afe2-13eb21ba83bf/OceanDNA-b35287.fa --refList OceanDNA-b35287/target_genomes.txt --output OceanDNA-b35287/fastani_result.tsv --threads 1
[2023-03-16 02:38:40,241] [INFO] Task succeeded: fastANI
[2023-03-16 02:38:40,242] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0fe271c-9c07-4d2e-b7f5-bc770579b9c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 02:38:40,242] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0fe271c-9c07-4d2e-b7f5-bc770579b9c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 02:38:40,249] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2023-03-16 02:38:40,249] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 02:38:40,249] [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 leiognathi	strain=ATCC 25521	GCA_000950415.1	553611	553611	type	True	96.5524	1196	1351	95	conclusive
Photobacterium leiognathi	strain=ATCC 25521	GCA_003026235.1	553611	553611	type	True	96.5032	1205	1351	95	conclusive
Photobacterium lucens	strain=CAIM 1937	GCA_009873615.1	2562949	2562949	type	True	92.937	1084	1351	95	below_threshold
Photobacterium angustum	strain=ATCC 25915	GCA_003026365.1	661	661	type	True	84.3301	1018	1351	95	below_threshold
Photobacterium angustum	strain=ATCC 25915	GCA_000950005.1	661	661	type	True	84.2741	1009	1351	95	below_threshold
Photobacterium iliopiscarium	strain=ATCC 51760	GCA_000950265.1	56192	56192	type	True	79.8335	537	1351	95	below_threshold
Photobacterium swingsii	strain=CECT 7576	GCA_024346715.1	680026	680026	type	True	79.155	371	1351	95	below_threshold
Photobacterium sanguinicancri	strain=CECT 7579	GCA_024346675.1	875932	875932	type	True	78.8843	381	1351	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	78.0654	193	1351	95	below_threshold
Aliivibrio fischeri	strain=DSM 507	GCA_023983475.1	668	668	suspected-type	True	77.8107	208	1351	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_024347315.1	693153	693153	type	True	77.7109	206	1351	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 02:38:40,250] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35287/tc_result.tsv
[2023-03-16 02:38:40,250] [INFO] ===== Taxonomy check completed =====
[2023-03-16 02:38:40,250] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 02:38:40,250] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0fe271c-9c07-4d2e-b7f5-bc770579b9c4/dqc_reference/checkm_data
[2023-03-16 02:38:40,251] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 02:38:40,256] [INFO] Task started: CheckM
[2023-03-16 02:38:40,256] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35287/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35287/checkm_input OceanDNA-b35287/checkm_result
[2023-03-16 02:39:35,927] [INFO] Task succeeded: CheckM
[2023-03-16 02:39:35,927] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.08%
Contamintation: 10.42%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-16 02:39:35,930] [INFO] ===== Completeness check finished =====
[2023-03-16 02:39:35,931] [INFO] ===== Start GTDB Search =====
[2023-03-16 02:39:35,931] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35287/markers.fasta)
[2023-03-16 02:39:35,931] [INFO] Task started: Blastn
[2023-03-16 02:39:35,931] [INFO] Running command: blastn -query OceanDNA-b35287/markers.fasta -db /var/lib/cwl/stgd0fe271c-9c07-4d2e-b7f5-bc770579b9c4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35287/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:39:36,986] [INFO] Task succeeded: Blastn
[2023-03-16 02:39:36,987] [INFO] Selected 6 target genomes.
[2023-03-16 02:39:36,987] [INFO] Target genome list was writen to OceanDNA-b35287/target_genomes_gtdb.txt
[2023-03-16 02:39:37,014] [INFO] Task started: fastANI
[2023-03-16 02:39:37,014] [INFO] Running command: fastANI --query /var/lib/cwl/stge4109a73-8bc5-49bd-afe2-13eb21ba83bf/OceanDNA-b35287.fa --refList OceanDNA-b35287/target_genomes_gtdb.txt --output OceanDNA-b35287/fastani_result_gtdb.tsv --threads 1
[2023-03-16 02:39:43,401] [INFO] Task succeeded: fastANI
[2023-03-16 02:39:43,405] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 02:39:43,405] [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_000950415.1	s__Photobacterium leiognathi	96.5524	1196	1351	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.11	96.59	0.91	0.88	15	conclusive
GCF_009873615.1	s__Photobacterium lucens	92.937	1084	1351	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.83	97.58	0.96	0.94	5	-
GCF_003026105.1	s__Photobacterium sp003026105	84.5601	1010	1351	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.17	99.06	0.96	0.95	8	-
GCF_003026365.1	s__Photobacterium angustum	84.3301	1018	1351	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.76	95.45	0.92	0.87	27	-
GCF_000153325.1	s__Photobacterium sp000153325	83.8634	980	1351	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954455.1	s__Photobacterium aquimaris	80.1183	576	1351	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.51	95.34	0.95	0.87	6	-
--------------------------------------------------------------------------------
[2023-03-16 02:39:43,405] [INFO] GTDB search result was written to OceanDNA-b35287/result_gtdb.tsv
[2023-03-16 02:39:43,406] [INFO] ===== GTDB Search completed =====
[2023-03-16 02:39:43,407] [INFO] DFAST_QC result json was written to OceanDNA-b35287/dqc_result.json
[2023-03-16 02:39:43,407] [INFO] DFAST_QC completed!
[2023-03-16 02:39:43,407] [INFO] Total running time: 0h1m38s