[2023-03-16 23:55:45,541] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:55:45,541] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:55:45,541] [INFO] DQC Reference Directory: /var/lib/cwl/stg855d6867-b604-4d6c-85c6-0e76a65253c6/dqc_reference
[2023-03-16 23:55:46,664] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:55:46,664] [INFO] Task started: Prodigal
[2023-03-16 23:55:46,664] [INFO] Running command: cat /var/lib/cwl/stg53d7e67f-636c-4152-b025-0a089059163a/OceanDNA-b35184.fa | prodigal -d OceanDNA-b35184/cds.fna -a OceanDNA-b35184/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:56:07,339] [INFO] Task succeeded: Prodigal
[2023-03-16 23:56:07,339] [INFO] Task started: HMMsearch
[2023-03-16 23:56:07,339] [INFO] Running command: hmmsearch --tblout OceanDNA-b35184/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg855d6867-b604-4d6c-85c6-0e76a65253c6/dqc_reference/reference_markers.hmm OceanDNA-b35184/protein.faa > /dev/null
[2023-03-16 23:56:07,558] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:56:07,559] [INFO] Found 6/6 markers.
[2023-03-16 23:56:07,584] [INFO] Query marker FASTA was written to OceanDNA-b35184/markers.fasta
[2023-03-16 23:56:07,585] [INFO] Task started: Blastn
[2023-03-16 23:56:07,585] [INFO] Running command: blastn -query OceanDNA-b35184/markers.fasta -db /var/lib/cwl/stg855d6867-b604-4d6c-85c6-0e76a65253c6/dqc_reference/reference_markers.fasta -out OceanDNA-b35184/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:56:08,231] [INFO] Task succeeded: Blastn
[2023-03-16 23:56:08,232] [INFO] Selected 32 target genomes.
[2023-03-16 23:56:08,232] [INFO] Target genome list was writen to OceanDNA-b35184/target_genomes.txt
[2023-03-16 23:56:08,251] [INFO] Task started: fastANI
[2023-03-16 23:56:08,251] [INFO] Running command: fastANI --query /var/lib/cwl/stg53d7e67f-636c-4152-b025-0a089059163a/OceanDNA-b35184.fa --refList OceanDNA-b35184/target_genomes.txt --output OceanDNA-b35184/fastani_result.tsv --threads 1
[2023-03-16 23:56:28,396] [INFO] Task succeeded: fastANI
[2023-03-16 23:56:28,396] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg855d6867-b604-4d6c-85c6-0e76a65253c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:56:28,396] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg855d6867-b604-4d6c-85c6-0e76a65253c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:56:28,404] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:56:28,404] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 23:56:28,404] [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
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	76.5607	52	1286	95	below_threshold
Colwellia marinimaniae	strain=MTCD1	GCA_002207865.1	1513592	1513592	type	True	76.47	70	1286	95	below_threshold
Pseudoalteromonas ostreae	strain=hOe-66	GCA_018069805.1	2774154	2774154	type	True	76.3758	53	1286	95	below_threshold
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	76.3663	59	1286	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	76.1353	57	1286	95	below_threshold
Pseudoalteromonas tetraodonis	strain=NBRC 103034	GCA_007991235.1	43659	43659	suspected-type	True	76.104	53	1286	95	below_threshold
Pseudoalteromonas tetraodonis	strain=GFC	GCA_002310835.1	43659	43659	suspected-type	True	76.0676	56	1286	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	76.0354	74	1286	95	below_threshold
Pseudoalteromonas tunicata	strain=D2	GCA_000153245.1	314281	314281	type	True	75.9684	60	1286	95	below_threshold
Pseudoalteromonas tunicata	strain=D2	GCA_002310815.1	314281	314281	type	True	75.9245	62	1286	95	below_threshold
Pseudoalteromonas tunicata	strain=D2	GCA_003568825.1	314281	314281	type	True	75.9136	61	1286	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 23:56:28,404] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35184/tc_result.tsv
[2023-03-16 23:56:28,404] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:56:28,404] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:56:28,405] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg855d6867-b604-4d6c-85c6-0e76a65253c6/dqc_reference/checkm_data
[2023-03-16 23:56:28,405] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:56:28,717] [INFO] Task started: CheckM
[2023-03-16 23:56:28,717] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35184/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35184/checkm_input OceanDNA-b35184/checkm_result
[2023-03-16 23:57:21,082] [INFO] Task succeeded: CheckM
[2023-03-16 23:57:21,083] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.30%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 23:57:21,086] [INFO] ===== Completeness check finished =====
[2023-03-16 23:57:21,086] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:57:21,086] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35184/markers.fasta)
[2023-03-16 23:57:21,087] [INFO] Task started: Blastn
[2023-03-16 23:57:21,087] [INFO] Running command: blastn -query OceanDNA-b35184/markers.fasta -db /var/lib/cwl/stg855d6867-b604-4d6c-85c6-0e76a65253c6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35184/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:57:22,114] [INFO] Task succeeded: Blastn
[2023-03-16 23:57:22,115] [INFO] Selected 24 target genomes.
[2023-03-16 23:57:22,115] [INFO] Target genome list was writen to OceanDNA-b35184/target_genomes_gtdb.txt
[2023-03-16 23:57:22,711] [INFO] Task started: fastANI
[2023-03-16 23:57:22,711] [INFO] Running command: fastANI --query /var/lib/cwl/stg53d7e67f-636c-4152-b025-0a089059163a/OceanDNA-b35184.fa --refList OceanDNA-b35184/target_genomes_gtdb.txt --output OceanDNA-b35184/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:57:38,937] [INFO] Task succeeded: fastANI
[2023-03-16 23:57:38,946] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 23:57:38,946] [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_013214965.1	s__Psychrobium sp013214965	99.7704	1190	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychrobiaceae;g__Psychrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013214885.1	s__Psychrobium sp013214885	79.3556	284	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychrobiaceae;g__Psychrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214945.1	s__Psychrobium sp013214945	78.572	307	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychrobiaceae;g__Psychrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214905.1	s__Psychrobium sp013214905	78.3191	191	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychrobiaceae;g__Psychrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002835545.1	s__Psychrobium sp002835545	77.4386	168	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychrobiaceae;g__Psychrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001874365.1	s__Psychrobium sp001874365	76.9941	116	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychrobiaceae;g__Psychrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402495.1	s__Pseudoalteromonas sp018402495	76.6207	50	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902498845.1	s__Pseudoalteromonas rhizosphaerae	76.5622	52	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.81	97.24	0.86	0.81	17	-
GCF_001269985.1	s__Pseudoalteromonas sp001269985	76.5319	56	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.50	95.03	0.90	0.80	3	-
GCF_018069805.1	s__Pseudoalteromonas sp018069805	76.4533	52	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003061515.1	s__Cognaticolwellia sp003061515	76.422	55	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.05	98.05	0.90	0.90	2	-
GCF_018860585.1	s__Colwellia sp018860585	76.2696	50	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385555.1	s__Shewanella polaris	75.9062	59	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.84	97.84	0.89	0.89	2	-
GCF_002000085.1	s__Pseudocolwellia agarivorans	75.7762	55	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudocolwellia	95.0	95.36	95.36	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-03-16 23:57:38,947] [INFO] GTDB search result was written to OceanDNA-b35184/result_gtdb.tsv
[2023-03-16 23:57:38,947] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:57:38,948] [INFO] DFAST_QC result json was written to OceanDNA-b35184/dqc_result.json
[2023-03-16 23:57:38,948] [INFO] DFAST_QC completed!
[2023-03-16 23:57:38,948] [INFO] Total running time: 0h1m53s