[2023-03-18 23:27:53,079] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:27:53,079] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:27:53,079] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ee09e32-9141-4ac7-b20d-929079d10b01/dqc_reference
[2023-03-18 23:27:54,275] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:27:54,276] [INFO] Task started: Prodigal
[2023-03-18 23:27:54,277] [INFO] Running command: cat /var/lib/cwl/stg7f3110b1-43dc-4a8e-b50e-d02f0a277549/OceanDNA-b12487.fa | prodigal -d OceanDNA-b12487/cds.fna -a OceanDNA-b12487/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:28:03,074] [INFO] Task succeeded: Prodigal
[2023-03-18 23:28:03,074] [INFO] Task started: HMMsearch
[2023-03-18 23:28:03,075] [INFO] Running command: hmmsearch --tblout OceanDNA-b12487/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ee09e32-9141-4ac7-b20d-929079d10b01/dqc_reference/reference_markers.hmm OceanDNA-b12487/protein.faa > /dev/null
[2023-03-18 23:28:03,243] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:28:03,244] [INFO] Found 6/6 markers.
[2023-03-18 23:28:03,258] [INFO] Query marker FASTA was written to OceanDNA-b12487/markers.fasta
[2023-03-18 23:28:03,259] [INFO] Task started: Blastn
[2023-03-18 23:28:03,259] [INFO] Running command: blastn -query OceanDNA-b12487/markers.fasta -db /var/lib/cwl/stg1ee09e32-9141-4ac7-b20d-929079d10b01/dqc_reference/reference_markers.fasta -out OceanDNA-b12487/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:28:05,793] [INFO] Task succeeded: Blastn
[2023-03-18 23:28:05,794] [INFO] Selected 35 target genomes.
[2023-03-18 23:28:05,794] [INFO] Target genome list was writen to OceanDNA-b12487/target_genomes.txt
[2023-03-18 23:28:05,814] [INFO] Task started: fastANI
[2023-03-18 23:28:05,814] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f3110b1-43dc-4a8e-b50e-d02f0a277549/OceanDNA-b12487.fa --refList OceanDNA-b12487/target_genomes.txt --output OceanDNA-b12487/fastani_result.tsv --threads 1
[2023-03-18 23:28:23,424] [INFO] Task succeeded: fastANI
[2023-03-18 23:28:23,424] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ee09e32-9141-4ac7-b20d-929079d10b01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:28:23,424] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ee09e32-9141-4ac7-b20d-929079d10b01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:28:23,424] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:28:23,424] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:28:23,425] [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 23:28:23,425] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12487/tc_result.tsv
[2023-03-18 23:28:23,425] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:28:23,425] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:28:23,425] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ee09e32-9141-4ac7-b20d-929079d10b01/dqc_reference/checkm_data
[2023-03-18 23:28:23,428] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:28:23,432] [INFO] Task started: CheckM
[2023-03-18 23:28:23,432] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12487/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12487/checkm_input OceanDNA-b12487/checkm_result
[2023-03-18 23:28:50,426] [INFO] Task succeeded: CheckM
[2023-03-18 23:28:50,427] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.14%
Contamintation: 5.21%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 23:28:50,429] [INFO] ===== Completeness check finished =====
[2023-03-18 23:28:50,429] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:28:50,429] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12487/markers.fasta)
[2023-03-18 23:28:50,431] [INFO] Task started: Blastn
[2023-03-18 23:28:50,431] [INFO] Running command: blastn -query OceanDNA-b12487/markers.fasta -db /var/lib/cwl/stg1ee09e32-9141-4ac7-b20d-929079d10b01/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12487/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:28:51,285] [INFO] Task succeeded: Blastn
[2023-03-18 23:28:51,286] [INFO] Selected 28 target genomes.
[2023-03-18 23:28:51,286] [INFO] Target genome list was writen to OceanDNA-b12487/target_genomes_gtdb.txt
[2023-03-18 23:28:51,307] [INFO] Task started: fastANI
[2023-03-18 23:28:51,307] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f3110b1-43dc-4a8e-b50e-d02f0a277549/OceanDNA-b12487.fa --refList OceanDNA-b12487/target_genomes_gtdb.txt --output OceanDNA-b12487/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:29:00,261] [INFO] Task succeeded: fastANI
[2023-03-18 23:29:00,268] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:29:00,268] [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_002721285.1	s__SP287 sp002721285	98.5781	244	474	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__SP287	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002686655.1	s__MED-G20 sp002686655	77.1644	131	474	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	96.65	96.65	0.87	0.87	2	-
GCA_002457645.1	s__MED-G20 sp002457645	76.8603	81	474	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002723085.1	s__GCA-2723085 sp002723085	76.729	127	474	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__GCA-2723085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691605.1	s__MED-G20 sp002691605	76.6529	98	474	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	96.19	95.12	0.79	0.76	3	-
GCA_905182525.1	s__MED-G20 sp905182525	76.6525	136	474	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	96.07	96.07	0.86	0.86	2	-
GCA_016780365.1	s__MED-G20 sp016780365	76.6502	93	474	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	98.18	97.06	0.79	0.71	6	-
GCA_905181675.1	s__MED-G20 sp905181675	76.5706	86	474	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002713405.1	s__MED-G20 sp002713405	76.5496	102	474	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002716065.1	s__GCA-2716065 sp002716065	76.1944	61	474	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__GCA-2716065	95.0	97.60	97.60	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-03-18 23:29:00,268] [INFO] GTDB search result was written to OceanDNA-b12487/result_gtdb.tsv
[2023-03-18 23:29:00,268] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:29:00,269] [INFO] DFAST_QC result json was written to OceanDNA-b12487/dqc_result.json
[2023-03-18 23:29:00,269] [INFO] DFAST_QC completed!
[2023-03-18 23:29:00,269] [INFO] Total running time: 0h1m7s