[2023-03-16 04:39:48,540] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:39:48,540] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:39:48,541] [INFO] DQC Reference Directory: /var/lib/cwl/stg44f37e0c-aa26-436e-a4f3-c0a15b563c76/dqc_reference
[2023-03-16 04:39:49,677] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:39:49,677] [INFO] Task started: Prodigal
[2023-03-16 04:39:49,678] [INFO] Running command: cat /var/lib/cwl/stg8ddd3bfc-9770-458c-80b9-80b8cdd83a34/OceanDNA-b32496.fa | prodigal -d OceanDNA-b32496/cds.fna -a OceanDNA-b32496/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:39:55,426] [INFO] Task succeeded: Prodigal
[2023-03-16 04:39:55,426] [INFO] Task started: HMMsearch
[2023-03-16 04:39:55,427] [INFO] Running command: hmmsearch --tblout OceanDNA-b32496/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44f37e0c-aa26-436e-a4f3-c0a15b563c76/dqc_reference/reference_markers.hmm OceanDNA-b32496/protein.faa > /dev/null
[2023-03-16 04:39:55,569] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:39:55,569] [INFO] Found 6/6 markers.
[2023-03-16 04:39:55,579] [INFO] Query marker FASTA was written to OceanDNA-b32496/markers.fasta
[2023-03-16 04:39:55,579] [INFO] Task started: Blastn
[2023-03-16 04:39:55,580] [INFO] Running command: blastn -query OceanDNA-b32496/markers.fasta -db /var/lib/cwl/stg44f37e0c-aa26-436e-a4f3-c0a15b563c76/dqc_reference/reference_markers.fasta -out OceanDNA-b32496/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:39:56,080] [INFO] Task succeeded: Blastn
[2023-03-16 04:39:56,081] [INFO] Selected 11 target genomes.
[2023-03-16 04:39:56,081] [INFO] Target genome list was writen to OceanDNA-b32496/target_genomes.txt
[2023-03-16 04:39:56,087] [INFO] Task started: fastANI
[2023-03-16 04:39:56,087] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ddd3bfc-9770-458c-80b9-80b8cdd83a34/OceanDNA-b32496.fa --refList OceanDNA-b32496/target_genomes.txt --output OceanDNA-b32496/fastani_result.tsv --threads 1
[2023-03-16 04:39:59,575] [INFO] Task succeeded: fastANI
[2023-03-16 04:39:59,576] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44f37e0c-aa26-436e-a4f3-c0a15b563c76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:39:59,576] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44f37e0c-aa26-436e-a4f3-c0a15b563c76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:39:59,576] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:39:59,576] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:39:59,576] [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 04:39:59,676] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32496/tc_result.tsv
[2023-03-16 04:39:59,676] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:39:59,677] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:39:59,677] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44f37e0c-aa26-436e-a4f3-c0a15b563c76/dqc_reference/checkm_data
[2023-03-16 04:39:59,687] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:39:59,907] [INFO] Task started: CheckM
[2023-03-16 04:39:59,907] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32496/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32496/checkm_input OceanDNA-b32496/checkm_result
[2023-03-16 04:40:19,815] [INFO] Task succeeded: CheckM
[2023-03-16 04:40:19,816] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 5.73%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 04:40:19,817] [INFO] ===== Completeness check finished =====
[2023-03-16 04:40:19,817] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:40:19,818] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32496/markers.fasta)
[2023-03-16 04:40:19,819] [INFO] Task started: Blastn
[2023-03-16 04:40:19,819] [INFO] Running command: blastn -query OceanDNA-b32496/markers.fasta -db /var/lib/cwl/stg44f37e0c-aa26-436e-a4f3-c0a15b563c76/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32496/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:40:20,683] [INFO] Task succeeded: Blastn
[2023-03-16 04:40:20,684] [INFO] Selected 17 target genomes.
[2023-03-16 04:40:20,684] [INFO] Target genome list was writen to OceanDNA-b32496/target_genomes_gtdb.txt
[2023-03-16 04:40:20,704] [INFO] Task started: fastANI
[2023-03-16 04:40:20,704] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ddd3bfc-9770-458c-80b9-80b8cdd83a34/OceanDNA-b32496.fa --refList OceanDNA-b32496/target_genomes_gtdb.txt --output OceanDNA-b32496/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:40:24,149] [INFO] Task succeeded: fastANI
[2023-03-16 04:40:24,156] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:40:24,156] [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_902536485.1	s__GCA-002690875 sp902536485	77.3762	97	385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-002690875	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902618535.1	s__GCA-002690875 sp902618535	77.2693	115	385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-002690875	95.0	97.44	97.44	0.66	0.66	2	-
GCA_002689325.1	s__GCA-002690875 sp002689325	77.2503	137	385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-002690875	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902537615.1	s__GCA-002690875 sp902537615	77.0701	128	385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-002690875	95.0	96.75	96.75	0.77	0.77	2	-
GCA_002690875.1	s__GCA-002690875 sp002690875	77.0193	133	385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-002690875	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902536655.1	s__GCA-2691245 sp902536655	76.2389	57	385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-2691245	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002712255.1	s__MED-G10 sp002712255	76.2244	103	385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__MED-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902547955.1	s__MED-G10 sp902547955	76.1936	76	385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__MED-G10	95.0	97.61	97.06	0.82	0.80	5	-
GCA_002457065.1	s__MED-G10 sp002457065	75.9355	63	385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__MED-G10	95.0	97.75	96.52	0.68	0.65	3	-
GCA_002167825.1	s__TMED13 sp002167825	75.7946	54	385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__TMED13	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-16 04:40:24,156] [INFO] GTDB search result was written to OceanDNA-b32496/result_gtdb.tsv
[2023-03-16 04:40:24,156] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:40:24,157] [INFO] DFAST_QC result json was written to OceanDNA-b32496/dqc_result.json
[2023-03-16 04:40:24,157] [INFO] DFAST_QC completed!
[2023-03-16 04:40:24,157] [INFO] Total running time: 0h0m36s