[2023-03-16 11:24:27,614] [INFO] DFAST_QC pipeline started.
[2023-03-16 11:24:27,614] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 11:24:27,614] [INFO] DQC Reference Directory: /var/lib/cwl/stg2755364a-151e-4979-a3a5-c654ca8a4516/dqc_reference
[2023-03-16 11:24:28,822] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 11:24:28,823] [INFO] Task started: Prodigal
[2023-03-16 11:24:28,823] [INFO] Running command: cat /var/lib/cwl/stg442e22f6-13d0-460b-8a5f-f686a36749ed/OceanDNA-b42278.fa | prodigal -d OceanDNA-b42278/cds.fna -a OceanDNA-b42278/protein.faa -g 11 -q > /dev/null
[2023-03-16 11:24:34,073] [INFO] Task succeeded: Prodigal
[2023-03-16 11:24:34,073] [INFO] Task started: HMMsearch
[2023-03-16 11:24:34,073] [INFO] Running command: hmmsearch --tblout OceanDNA-b42278/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2755364a-151e-4979-a3a5-c654ca8a4516/dqc_reference/reference_markers.hmm OceanDNA-b42278/protein.faa > /dev/null
[2023-03-16 11:24:34,242] [INFO] Task succeeded: HMMsearch
[2023-03-16 11:24:34,243] [INFO] Found 6/6 markers.
[2023-03-16 11:24:34,251] [INFO] Query marker FASTA was written to OceanDNA-b42278/markers.fasta
[2023-03-16 11:24:34,252] [INFO] Task started: Blastn
[2023-03-16 11:24:34,252] [INFO] Running command: blastn -query OceanDNA-b42278/markers.fasta -db /var/lib/cwl/stg2755364a-151e-4979-a3a5-c654ca8a4516/dqc_reference/reference_markers.fasta -out OceanDNA-b42278/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:24:34,795] [INFO] Task succeeded: Blastn
[2023-03-16 11:24:34,796] [INFO] Selected 19 target genomes.
[2023-03-16 11:24:34,796] [INFO] Target genome list was writen to OceanDNA-b42278/target_genomes.txt
[2023-03-16 11:24:34,806] [INFO] Task started: fastANI
[2023-03-16 11:24:34,806] [INFO] Running command: fastANI --query /var/lib/cwl/stg442e22f6-13d0-460b-8a5f-f686a36749ed/OceanDNA-b42278.fa --refList OceanDNA-b42278/target_genomes.txt --output OceanDNA-b42278/fastani_result.tsv --threads 1
[2023-03-16 11:24:43,693] [INFO] Task succeeded: fastANI
[2023-03-16 11:24:43,693] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2755364a-151e-4979-a3a5-c654ca8a4516/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 11:24:43,694] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2755364a-151e-4979-a3a5-c654ca8a4516/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 11:24:43,694] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 11:24:43,694] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 11:24:43,694] [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
--------------------------------------------------------------------------------
[2023-03-16 11:24:43,694] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42278/tc_result.tsv
[2023-03-16 11:24:43,694] [INFO] ===== Taxonomy check completed =====
[2023-03-16 11:24:43,694] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 11:24:43,694] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2755364a-151e-4979-a3a5-c654ca8a4516/dqc_reference/checkm_data
[2023-03-16 11:24:43,697] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 11:24:43,699] [INFO] Task started: CheckM
[2023-03-16 11:24:43,699] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42278/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42278/checkm_input OceanDNA-b42278/checkm_result
[2023-03-16 11:25:09,766] [INFO] Task succeeded: CheckM
[2023-03-16 11:25:09,766] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.91%
Contamintation: 6.77%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 11:25:09,768] [INFO] ===== Completeness check finished =====
[2023-03-16 11:25:09,768] [INFO] ===== Start GTDB Search =====
[2023-03-16 11:25:09,768] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42278/markers.fasta)
[2023-03-16 11:25:09,768] [INFO] Task started: Blastn
[2023-03-16 11:25:09,768] [INFO] Running command: blastn -query OceanDNA-b42278/markers.fasta -db /var/lib/cwl/stg2755364a-151e-4979-a3a5-c654ca8a4516/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42278/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:25:12,105] [INFO] Task succeeded: Blastn
[2023-03-16 11:25:12,106] [INFO] Selected 17 target genomes.
[2023-03-16 11:25:12,106] [INFO] Target genome list was writen to OceanDNA-b42278/target_genomes_gtdb.txt
[2023-03-16 11:25:12,427] [INFO] Task started: fastANI
[2023-03-16 11:25:12,427] [INFO] Running command: fastANI --query /var/lib/cwl/stg442e22f6-13d0-460b-8a5f-f686a36749ed/OceanDNA-b42278.fa --refList OceanDNA-b42278/target_genomes_gtdb.txt --output OceanDNA-b42278/fastani_result_gtdb.tsv --threads 1
[2023-03-16 11:25:16,332] [INFO] Task succeeded: fastANI
[2023-03-16 11:25:16,341] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 11:25:16,341] [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_902591925.1	s__SAR86A sp902591925	98.3159	307	332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.32	97.27	0.90	0.89	3	conclusive
GCA_902617045.1	s__SAR86A sp902617045	91.3578	255	332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.06	95.32	0.86	0.86	4	-
GCA_902547295.1	s__SAR86A sp902547295	91.3155	218	332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004212975.1	s__SAR86A sp004212975	91.1098	201	332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.30	95.02	0.85	0.76	8	-
GCA_902541175.1	s__SAR86A sp902541175	90.8816	257	332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.65	95.31	0.89	0.85	3	-
GCA_902612915.1	s__SAR86A sp902612915	90.7882	242	332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.80	95.61	0.84	0.75	10	-
GCA_902630885.1	s__SAR86A sp902630885	82.5181	222	332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902631785.1	s__SAR86A sp902631785	82.3463	220	332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.84	96.84	0.79	0.79	2	-
GCA_000252525.1	s__SAR86A sp000252525	81.0778	162	332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.49	95.25	0.88	0.84	16	-
GCA_002690725.1	s__SAR86A sp002690725	80.3183	159	332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	95.15	95.15	0.80	0.80	2	-
GCA_902556105.1	s__SAR86A sp902556105	79.0251	130	332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902559345.1	s__SAR86A sp902559345	78.3821	109	332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902563835.1	s__SAR86A sp902563835	78.3666	131	332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902516285.1	s__SAR86A sp902516285	78.0548	116	332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.51	96.51	0.92	0.92	2	-
GCA_003213495.1	s__SAR86A sp003213495	78.0359	154	332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	98.20	96.41	0.97	0.94	3	-
GCA_902557705.1	s__SCGC-AAA076-P13 sp902557705	76.8812	59	332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 11:25:16,342] [INFO] GTDB search result was written to OceanDNA-b42278/result_gtdb.tsv
[2023-03-16 11:25:16,342] [INFO] ===== GTDB Search completed =====
[2023-03-16 11:25:16,343] [INFO] DFAST_QC result json was written to OceanDNA-b42278/dqc_result.json
[2023-03-16 11:25:16,343] [INFO] DFAST_QC completed!
[2023-03-16 11:25:16,343] [INFO] Total running time: 0h0m49s