[2023-03-19 05:04:10,730] [INFO] DFAST_QC pipeline started.
[2023-03-19 05:04:10,730] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 05:04:10,730] [INFO] DQC Reference Directory: /var/lib/cwl/stgeabc9bd3-369b-4979-84d6-5a45da96fd43/dqc_reference
[2023-03-19 05:04:11,996] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 05:04:11,997] [INFO] Task started: Prodigal
[2023-03-19 05:04:11,997] [INFO] Running command: cat /var/lib/cwl/stg744bbb0e-7e33-420f-bdc6-5e87817b1f6a/OceanDNA-b41877.fa | prodigal -d OceanDNA-b41877/cds.fna -a OceanDNA-b41877/protein.faa -g 11 -q > /dev/null
[2023-03-19 05:04:17,138] [INFO] Task succeeded: Prodigal
[2023-03-19 05:04:17,139] [INFO] Task started: HMMsearch
[2023-03-19 05:04:17,139] [INFO] Running command: hmmsearch --tblout OceanDNA-b41877/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeabc9bd3-369b-4979-84d6-5a45da96fd43/dqc_reference/reference_markers.hmm OceanDNA-b41877/protein.faa > /dev/null
[2023-03-19 05:04:17,326] [INFO] Task succeeded: HMMsearch
[2023-03-19 05:04:17,327] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg744bbb0e-7e33-420f-bdc6-5e87817b1f6a/OceanDNA-b41877.fa]
[2023-03-19 05:04:17,336] [INFO] Query marker FASTA was written to OceanDNA-b41877/markers.fasta
[2023-03-19 05:04:17,338] [INFO] Task started: Blastn
[2023-03-19 05:04:17,338] [INFO] Running command: blastn -query OceanDNA-b41877/markers.fasta -db /var/lib/cwl/stgeabc9bd3-369b-4979-84d6-5a45da96fd43/dqc_reference/reference_markers.fasta -out OceanDNA-b41877/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:04:17,924] [INFO] Task succeeded: Blastn
[2023-03-19 05:04:17,925] [INFO] Selected 15 target genomes.
[2023-03-19 05:04:17,925] [INFO] Target genome list was writen to OceanDNA-b41877/target_genomes.txt
[2023-03-19 05:04:17,960] [INFO] Task started: fastANI
[2023-03-19 05:04:17,960] [INFO] Running command: fastANI --query /var/lib/cwl/stg744bbb0e-7e33-420f-bdc6-5e87817b1f6a/OceanDNA-b41877.fa --refList OceanDNA-b41877/target_genomes.txt --output OceanDNA-b41877/fastani_result.tsv --threads 1
[2023-03-19 05:04:22,309] [INFO] Task succeeded: fastANI
[2023-03-19 05:04:22,309] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeabc9bd3-369b-4979-84d6-5a45da96fd43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 05:04:22,309] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeabc9bd3-369b-4979-84d6-5a45da96fd43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 05:04:22,309] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 05:04:22,309] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 05:04:22,310] [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
--------------------------------------------------------------------------------
[2023-03-19 05:04:22,310] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41877/tc_result.tsv
[2023-03-19 05:04:22,310] [INFO] ===== Taxonomy check completed =====
[2023-03-19 05:04:22,310] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 05:04:22,310] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeabc9bd3-369b-4979-84d6-5a45da96fd43/dqc_reference/checkm_data
[2023-03-19 05:04:22,313] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 05:04:22,315] [INFO] Task started: CheckM
[2023-03-19 05:04:22,316] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41877/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41877/checkm_input OceanDNA-b41877/checkm_result
[2023-03-19 05:04:41,202] [INFO] Task succeeded: CheckM
[2023-03-19 05:04:41,203] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 2.75%
Strain heterogeneity: 71.43%
--------------------------------------------------------------------------------
[2023-03-19 05:04:41,205] [INFO] ===== Completeness check finished =====
[2023-03-19 05:04:41,205] [INFO] ===== Start GTDB Search =====
[2023-03-19 05:04:41,205] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41877/markers.fasta)
[2023-03-19 05:04:41,206] [INFO] Task started: Blastn
[2023-03-19 05:04:41,206] [INFO] Running command: blastn -query OceanDNA-b41877/markers.fasta -db /var/lib/cwl/stgeabc9bd3-369b-4979-84d6-5a45da96fd43/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41877/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:04:41,905] [INFO] Task succeeded: Blastn
[2023-03-19 05:04:41,906] [INFO] Selected 17 target genomes.
[2023-03-19 05:04:41,906] [INFO] Target genome list was writen to OceanDNA-b41877/target_genomes_gtdb.txt
[2023-03-19 05:04:41,947] [INFO] Task started: fastANI
[2023-03-19 05:04:41,947] [INFO] Running command: fastANI --query /var/lib/cwl/stg744bbb0e-7e33-420f-bdc6-5e87817b1f6a/OceanDNA-b41877.fa --refList OceanDNA-b41877/target_genomes_gtdb.txt --output OceanDNA-b41877/fastani_result_gtdb.tsv --threads 1
[2023-03-19 05:04:45,211] [INFO] Task succeeded: fastANI
[2023-03-19 05:04:45,219] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 05:04:45,219] [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_902557645.1	s__MED-G78 sp902558645	99.0017	296	330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G78	95.0	98.05	95.16	0.89	0.87	6	conclusive
GCA_902509965.1	s__MED-G78 sp902509965	79.9714	162	330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G78	95.0	96.76	96.76	0.83	0.83	2	-
GCA_905181645.1	s__MED-G78 sp905181645	79.1657	200	330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G78	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181955.1	s__MED-G78 sp905181955	78.7589	213	330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G78	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902514105.1	s__MED-G78 sp902514105	78.5626	118	330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G78	95.0	98.38	98.38	0.65	0.65	2	-
GCA_000385055.1	s__SCGC-AAA076-P13 sp000385055	77.6721	57	330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	98.19	98.19	0.89	0.89	2	-
GCA_902558095.1	s__SAR86A sp902558095	77.1675	51	330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010024215.1	s__SCGC-AAA076-P13 sp010024215	77.0345	61	330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	98.04	96.58	0.74	0.68	5	-
GCA_902617045.1	s__SAR86A sp902617045	76.9952	51	330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.06	95.32	0.86	0.86	4	-
GCA_902563835.1	s__SAR86A sp902563835	76.9143	52	330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902557965.1	s__SAR86A sp902557965	76.8522	54	330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.42	97.04	0.73	0.71	3	-
GCA_902591925.1	s__SAR86A sp902591925	76.6945	67	330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.32	97.27	0.90	0.89	3	-
--------------------------------------------------------------------------------
[2023-03-19 05:04:45,219] [INFO] GTDB search result was written to OceanDNA-b41877/result_gtdb.tsv
[2023-03-19 05:04:45,219] [INFO] ===== GTDB Search completed =====
[2023-03-19 05:04:45,220] [INFO] DFAST_QC result json was written to OceanDNA-b41877/dqc_result.json
[2023-03-19 05:04:45,220] [INFO] DFAST_QC completed!
[2023-03-19 05:04:45,220] [INFO] Total running time: 0h0m34s