[2023-03-17 02:49:37,485] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:49:37,485] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:49:37,485] [INFO] DQC Reference Directory: /var/lib/cwl/stgb47379d6-0fa3-4150-afb0-3ebae97bf0e2/dqc_reference
[2023-03-17 02:49:38,706] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:49:38,706] [INFO] Task started: Prodigal
[2023-03-17 02:49:38,706] [INFO] Running command: cat /var/lib/cwl/stgdb9164ea-becb-4cc0-869c-9b55492cbf5f/OceanDNA-b8602.fa | prodigal -d OceanDNA-b8602/cds.fna -a OceanDNA-b8602/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:49:43,086] [INFO] Task succeeded: Prodigal
[2023-03-17 02:49:43,086] [INFO] Task started: HMMsearch
[2023-03-17 02:49:43,087] [INFO] Running command: hmmsearch --tblout OceanDNA-b8602/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb47379d6-0fa3-4150-afb0-3ebae97bf0e2/dqc_reference/reference_markers.hmm OceanDNA-b8602/protein.faa > /dev/null
[2023-03-17 02:49:43,271] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:49:43,272] [INFO] Found 6/6 markers.
[2023-03-17 02:49:43,279] [INFO] Query marker FASTA was written to OceanDNA-b8602/markers.fasta
[2023-03-17 02:49:43,279] [INFO] Task started: Blastn
[2023-03-17 02:49:43,279] [INFO] Running command: blastn -query OceanDNA-b8602/markers.fasta -db /var/lib/cwl/stgb47379d6-0fa3-4150-afb0-3ebae97bf0e2/dqc_reference/reference_markers.fasta -out OceanDNA-b8602/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:49:43,857] [INFO] Task succeeded: Blastn
[2023-03-17 02:49:43,858] [INFO] Selected 35 target genomes.
[2023-03-17 02:49:43,858] [INFO] Target genome list was writen to OceanDNA-b8602/target_genomes.txt
[2023-03-17 02:49:44,214] [INFO] Task started: fastANI
[2023-03-17 02:49:44,214] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb9164ea-becb-4cc0-869c-9b55492cbf5f/OceanDNA-b8602.fa --refList OceanDNA-b8602/target_genomes.txt --output OceanDNA-b8602/fastani_result.tsv --threads 1
[2023-03-17 02:50:01,636] [INFO] Task succeeded: fastANI
[2023-03-17 02:50:01,636] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb47379d6-0fa3-4150-afb0-3ebae97bf0e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:50:01,637] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb47379d6-0fa3-4150-afb0-3ebae97bf0e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:50:01,637] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:50:01,637] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 02:50:01,637] [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 02:50:01,637] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8602/tc_result.tsv
[2023-03-17 02:50:01,637] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:50:01,637] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:50:01,637] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb47379d6-0fa3-4150-afb0-3ebae97bf0e2/dqc_reference/checkm_data
[2023-03-17 02:50:01,640] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:50:01,642] [INFO] Task started: CheckM
[2023-03-17 02:50:01,642] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8602/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8602/checkm_input OceanDNA-b8602/checkm_result
[2023-03-17 02:50:18,888] [INFO] Task succeeded: CheckM
[2023-03-17 02:50:18,889] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:50:18,891] [INFO] ===== Completeness check finished =====
[2023-03-17 02:50:18,891] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:50:18,891] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8602/markers.fasta)
[2023-03-17 02:50:18,892] [INFO] Task started: Blastn
[2023-03-17 02:50:18,893] [INFO] Running command: blastn -query OceanDNA-b8602/markers.fasta -db /var/lib/cwl/stgb47379d6-0fa3-4150-afb0-3ebae97bf0e2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8602/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:50:19,825] [INFO] Task succeeded: Blastn
[2023-03-17 02:50:19,827] [INFO] Selected 22 target genomes.
[2023-03-17 02:50:19,827] [INFO] Target genome list was writen to OceanDNA-b8602/target_genomes_gtdb.txt
[2023-03-17 02:50:19,930] [INFO] Task started: fastANI
[2023-03-17 02:50:19,930] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb9164ea-becb-4cc0-869c-9b55492cbf5f/OceanDNA-b8602.fa --refList OceanDNA-b8602/target_genomes_gtdb.txt --output OceanDNA-b8602/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:50:25,380] [INFO] Task succeeded: fastANI
[2023-03-17 02:50:25,388] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 02:50:25,388] [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_002729755.1	s__MED-G11 sp002729755	95.1877	204	242	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	95.15	95.15	0.85	0.85	2	conclusive
GCA_902586435.1	s__MED-G11 sp902586435	83.7794	156	242	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	96.29	96.26	0.76	0.71	5	-
GCA_018646865.1	s__MED-G11 sp014239615	78.0935	84	242	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	99.76	99.49	0.92	0.80	17	-
GCA_902514615.1	s__MED-G11 sp902514615	77.7459	73	242	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239665.1	s__MED-G11 sp014239665	77.6696	72	242	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	96.49	96.27	0.81	0.77	10	-
GCA_004213645.1	s__MED-G11 sp004213645	77.4159	62	242	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	97.96	97.96	0.74	0.74	2	-
GCA_002457075.1	s__MED-G11 sp002457075	77.111	69	242	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	98.35	98.35	0.79	0.79	2	-
GCA_902617285.1	s__MED-G11 sp902617285	76.8722	61	242	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	96.97	95.44	0.83	0.80	4	-
GCA_902593165.1	s__MED-G11 sp902593165	76.7139	64	242	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	96.69	96.69	0.86	0.86	2	-
GCA_902620455.1	s__MED-G11 sp902620455	76.7117	88	242	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	99.20	98.53	0.88	0.86	7	-
GCA_902523665.1	s__MED-G11 sp902523665	76.6004	57	242	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902622595.1	s__MED-G11 sp902622595	76.2369	78	242	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	96.81	96.16	0.93	0.91	12	-
--------------------------------------------------------------------------------
[2023-03-17 02:50:25,390] [INFO] GTDB search result was written to OceanDNA-b8602/result_gtdb.tsv
[2023-03-17 02:50:25,393] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:50:25,397] [INFO] DFAST_QC result json was written to OceanDNA-b8602/dqc_result.json
[2023-03-17 02:50:25,397] [INFO] DFAST_QC completed!
[2023-03-17 02:50:25,397] [INFO] Total running time: 0h0m48s