[2023-03-17 02:42:34,226] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:42:34,226] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:42:34,226] [INFO] DQC Reference Directory: /var/lib/cwl/stg8655a6a0-53d3-49f5-9cdb-cd286024428e/dqc_reference
[2023-03-17 02:42:35,367] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:42:35,368] [INFO] Task started: Prodigal
[2023-03-17 02:42:35,368] [INFO] Running command: cat /var/lib/cwl/stg30c324f4-52fd-4b25-a173-3922c657a672/OceanDNA-b4322.fa | prodigal -d OceanDNA-b4322/cds.fna -a OceanDNA-b4322/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:42:40,029] [INFO] Task succeeded: Prodigal
[2023-03-17 02:42:40,030] [INFO] Task started: HMMsearch
[2023-03-17 02:42:40,030] [INFO] Running command: hmmsearch --tblout OceanDNA-b4322/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8655a6a0-53d3-49f5-9cdb-cd286024428e/dqc_reference/reference_markers.hmm OceanDNA-b4322/protein.faa > /dev/null
[2023-03-17 02:42:40,152] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:42:40,152] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg30c324f4-52fd-4b25-a173-3922c657a672/OceanDNA-b4322.fa]
[2023-03-17 02:42:40,158] [INFO] Query marker FASTA was written to OceanDNA-b4322/markers.fasta
[2023-03-17 02:42:40,159] [INFO] Task started: Blastn
[2023-03-17 02:42:40,159] [INFO] Running command: blastn -query OceanDNA-b4322/markers.fasta -db /var/lib/cwl/stg8655a6a0-53d3-49f5-9cdb-cd286024428e/dqc_reference/reference_markers.fasta -out OceanDNA-b4322/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:42:40,636] [INFO] Task succeeded: Blastn
[2023-03-17 02:42:40,637] [INFO] Selected 10 target genomes.
[2023-03-17 02:42:40,637] [INFO] Target genome list was writen to OceanDNA-b4322/target_genomes.txt
[2023-03-17 02:42:40,673] [INFO] Task started: fastANI
[2023-03-17 02:42:40,673] [INFO] Running command: fastANI --query /var/lib/cwl/stg30c324f4-52fd-4b25-a173-3922c657a672/OceanDNA-b4322.fa --refList OceanDNA-b4322/target_genomes.txt --output OceanDNA-b4322/fastani_result.tsv --threads 1
[2023-03-17 02:42:44,690] [INFO] Task succeeded: fastANI
[2023-03-17 02:42:44,691] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8655a6a0-53d3-49f5-9cdb-cd286024428e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:42:44,691] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8655a6a0-53d3-49f5-9cdb-cd286024428e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:42:44,691] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:42:44,691] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 02:42:44,691] [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
--------------------------------------------------------------------------------
[2023-03-17 02:42:44,691] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4322/tc_result.tsv
[2023-03-17 02:42:44,692] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:42:44,692] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:42:44,692] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8655a6a0-53d3-49f5-9cdb-cd286024428e/dqc_reference/checkm_data
[2023-03-17 02:42:44,695] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:42:44,781] [INFO] Task started: CheckM
[2023-03-17 02:42:44,781] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4322/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4322/checkm_input OceanDNA-b4322/checkm_result
[2023-03-17 02:43:02,144] [INFO] Task succeeded: CheckM
[2023-03-17 02:43:02,144] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:43:02,145] [INFO] ===== Completeness check finished =====
[2023-03-17 02:43:02,145] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:43:02,146] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4322/markers.fasta)
[2023-03-17 02:43:02,147] [INFO] Task started: Blastn
[2023-03-17 02:43:02,147] [INFO] Running command: blastn -query OceanDNA-b4322/markers.fasta -db /var/lib/cwl/stg8655a6a0-53d3-49f5-9cdb-cd286024428e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4322/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:43:02,770] [INFO] Task succeeded: Blastn
[2023-03-17 02:43:02,771] [INFO] Selected 11 target genomes.
[2023-03-17 02:43:02,771] [INFO] Target genome list was writen to OceanDNA-b4322/target_genomes_gtdb.txt
[2023-03-17 02:43:02,785] [INFO] Task started: fastANI
[2023-03-17 02:43:02,785] [INFO] Running command: fastANI --query /var/lib/cwl/stg30c324f4-52fd-4b25-a173-3922c657a672/OceanDNA-b4322.fa --refList OceanDNA-b4322/target_genomes_gtdb.txt --output OceanDNA-b4322/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:43:05,549] [INFO] Task succeeded: fastANI
[2023-03-17 02:43:05,555] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 02:43:05,555] [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_002457315.1	s__MED-G16 sp002457315	93.7201	215	260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002696995.1	s__MED-G16 sp002696995	83.8398	165	260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	95.99	95.99	0.74	0.74	2	-
GCA_902634135.1	s__MED-G16 sp902634135	79.1597	81	260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002697405.1	s__MED-G16 sp002697405	78.8738	104	260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	98.03	98.03	0.62	0.62	2	-
GCA_902626505.1	s__MED-G16 sp902626505	78.3361	124	260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701745.1	s__MED-G16 sp002701745	77.8241	96	260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	96.78	96.78	0.79	0.79	2	-
GCA_902523065.1	s__MED-G16 sp902523065	76.996	74	260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	96.84	95.61	0.92	0.88	9	-
GCA_002692105.1	s__MED-G16 sp002692105	76.7446	80	260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	97.44	97.02	0.77	0.72	3	-
GCA_002702205.1	s__MED-G16 sp002702205	76.7124	64	260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:43:05,555] [INFO] GTDB search result was written to OceanDNA-b4322/result_gtdb.tsv
[2023-03-17 02:43:05,555] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:43:05,556] [INFO] DFAST_QC result json was written to OceanDNA-b4322/dqc_result.json
[2023-03-17 02:43:05,556] [INFO] DFAST_QC completed!
[2023-03-17 02:43:05,556] [INFO] Total running time: 0h0m31s