[2023-03-18 04:38:00,431] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:38:00,431] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:38:00,431] [INFO] DQC Reference Directory: /var/lib/cwl/stg9850ecf8-f5a3-4287-a6cc-f279db86cc23/dqc_reference
[2023-03-18 04:38:01,536] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:38:01,536] [INFO] Task started: Prodigal
[2023-03-18 04:38:01,536] [INFO] Running command: cat /var/lib/cwl/stg40bdb2e5-c148-4199-8665-1da6bb135d4a/OceanDNA-b42307.fa | prodigal -d OceanDNA-b42307/cds.fna -a OceanDNA-b42307/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:38:06,587] [INFO] Task succeeded: Prodigal
[2023-03-18 04:38:06,587] [INFO] Task started: HMMsearch
[2023-03-18 04:38:06,587] [INFO] Running command: hmmsearch --tblout OceanDNA-b42307/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9850ecf8-f5a3-4287-a6cc-f279db86cc23/dqc_reference/reference_markers.hmm OceanDNA-b42307/protein.faa > /dev/null
[2023-03-18 04:38:06,732] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:38:06,733] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg40bdb2e5-c148-4199-8665-1da6bb135d4a/OceanDNA-b42307.fa]
[2023-03-18 04:38:06,742] [INFO] Query marker FASTA was written to OceanDNA-b42307/markers.fasta
[2023-03-18 04:38:06,742] [INFO] Task started: Blastn
[2023-03-18 04:38:06,743] [INFO] Running command: blastn -query OceanDNA-b42307/markers.fasta -db /var/lib/cwl/stg9850ecf8-f5a3-4287-a6cc-f279db86cc23/dqc_reference/reference_markers.fasta -out OceanDNA-b42307/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:38:07,182] [INFO] Task succeeded: Blastn
[2023-03-18 04:38:07,183] [INFO] Selected 15 target genomes.
[2023-03-18 04:38:07,184] [INFO] Target genome list was writen to OceanDNA-b42307/target_genomes.txt
[2023-03-18 04:38:07,193] [INFO] Task started: fastANI
[2023-03-18 04:38:07,193] [INFO] Running command: fastANI --query /var/lib/cwl/stg40bdb2e5-c148-4199-8665-1da6bb135d4a/OceanDNA-b42307.fa --refList OceanDNA-b42307/target_genomes.txt --output OceanDNA-b42307/fastani_result.tsv --threads 1
[2023-03-18 04:38:12,959] [INFO] Task succeeded: fastANI
[2023-03-18 04:38:12,960] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9850ecf8-f5a3-4287-a6cc-f279db86cc23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:38:12,960] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9850ecf8-f5a3-4287-a6cc-f279db86cc23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:38:12,960] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:38:12,960] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 04:38:12,960] [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
--------------------------------------------------------------------------------
[2023-03-18 04:38:12,960] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42307/tc_result.tsv
[2023-03-18 04:38:12,961] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:38:12,961] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:38:12,961] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9850ecf8-f5a3-4287-a6cc-f279db86cc23/dqc_reference/checkm_data
[2023-03-18 04:38:12,964] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:38:12,966] [INFO] Task started: CheckM
[2023-03-18 04:38:12,967] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42307/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42307/checkm_input OceanDNA-b42307/checkm_result
[2023-03-18 04:38:31,090] [INFO] Task succeeded: CheckM
[2023-03-18 04:38:31,091] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:38:31,093] [INFO] ===== Completeness check finished =====
[2023-03-18 04:38:31,093] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:38:31,093] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42307/markers.fasta)
[2023-03-18 04:38:31,094] [INFO] Task started: Blastn
[2023-03-18 04:38:31,095] [INFO] Running command: blastn -query OceanDNA-b42307/markers.fasta -db /var/lib/cwl/stg9850ecf8-f5a3-4287-a6cc-f279db86cc23/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42307/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:38:31,532] [INFO] Task succeeded: Blastn
[2023-03-18 04:38:31,534] [INFO] Selected 11 target genomes.
[2023-03-18 04:38:31,534] [INFO] Target genome list was writen to OceanDNA-b42307/target_genomes_gtdb.txt
[2023-03-18 04:38:31,543] [INFO] Task started: fastANI
[2023-03-18 04:38:31,543] [INFO] Running command: fastANI --query /var/lib/cwl/stg40bdb2e5-c148-4199-8665-1da6bb135d4a/OceanDNA-b42307.fa --refList OceanDNA-b42307/target_genomes_gtdb.txt --output OceanDNA-b42307/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:38:33,820] [INFO] Task succeeded: fastANI
[2023-03-18 04:38:33,827] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 04:38:33,827] [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_002721465.1	s__SAR86A sp002721465	99.1288	224	315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.78	96.78	0.69	0.69	2	conclusive
GCA_902516285.1	s__SAR86A sp902516285	93.6047	250	315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.51	96.51	0.92	0.92	2	-
GCA_902528875.1	s__SAR86A sp902528875	92.6039	239	315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902582355.1	s__SAR86A sp902582355	78.2426	99	315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	98.87	98.87	0.67	0.67	2	-
GCA_902556105.1	s__SAR86A sp902556105	77.9237	106	315	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	77.6136	105	315	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	77.5557	110	315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.42	97.04	0.73	0.71	3	-
GCA_002690725.1	s__SAR86A sp002690725	77.4163	94	315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	95.15	95.15	0.80	0.80	2	-
GCA_002710265.1	s__SAR86A sp002710265	77.2177	90	315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003213495.1	s__SAR86A sp003213495	77.1329	118	315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	98.20	96.41	0.97	0.94	3	-
GCA_902591565.1	s__SCGC-AAA076-P13 sp902591565	76.3149	70	315	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	-
--------------------------------------------------------------------------------
[2023-03-18 04:38:33,827] [INFO] GTDB search result was written to OceanDNA-b42307/result_gtdb.tsv
[2023-03-18 04:38:33,862] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:38:33,864] [INFO] DFAST_QC result json was written to OceanDNA-b42307/dqc_result.json
[2023-03-18 04:38:33,864] [INFO] DFAST_QC completed!
[2023-03-18 04:38:33,864] [INFO] Total running time: 0h0m33s