[2023-03-17 05:59:11,034] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:59:11,034] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:59:11,034] [INFO] DQC Reference Directory: /var/lib/cwl/stg84f0abe9-a13c-4c2b-b3f6-e309c0fbdffd/dqc_reference
[2023-03-17 05:59:12,175] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:59:12,175] [INFO] Task started: Prodigal
[2023-03-17 05:59:12,176] [INFO] Running command: cat /var/lib/cwl/stg0a9ff74e-ed40-41a3-9713-3f764985da2e/OceanDNA-b11187.fa | prodigal -d OceanDNA-b11187/cds.fna -a OceanDNA-b11187/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:59:23,918] [INFO] Task succeeded: Prodigal
[2023-03-17 05:59:23,918] [INFO] Task started: HMMsearch
[2023-03-17 05:59:23,918] [INFO] Running command: hmmsearch --tblout OceanDNA-b11187/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84f0abe9-a13c-4c2b-b3f6-e309c0fbdffd/dqc_reference/reference_markers.hmm OceanDNA-b11187/protein.faa > /dev/null
[2023-03-17 05:59:24,076] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:59:24,077] [INFO] Found 6/6 markers.
[2023-03-17 05:59:24,091] [INFO] Query marker FASTA was written to OceanDNA-b11187/markers.fasta
[2023-03-17 05:59:24,091] [INFO] Task started: Blastn
[2023-03-17 05:59:24,091] [INFO] Running command: blastn -query OceanDNA-b11187/markers.fasta -db /var/lib/cwl/stg84f0abe9-a13c-4c2b-b3f6-e309c0fbdffd/dqc_reference/reference_markers.fasta -out OceanDNA-b11187/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:59:24,617] [INFO] Task succeeded: Blastn
[2023-03-17 05:59:24,618] [INFO] Selected 30 target genomes.
[2023-03-17 05:59:24,618] [INFO] Target genome list was writen to OceanDNA-b11187/target_genomes.txt
[2023-03-17 05:59:24,629] [INFO] Task started: fastANI
[2023-03-17 05:59:24,629] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a9ff74e-ed40-41a3-9713-3f764985da2e/OceanDNA-b11187.fa --refList OceanDNA-b11187/target_genomes.txt --output OceanDNA-b11187/fastani_result.tsv --threads 1
[2023-03-17 05:59:39,232] [INFO] Task succeeded: fastANI
[2023-03-17 05:59:39,233] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84f0abe9-a13c-4c2b-b3f6-e309c0fbdffd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:59:39,233] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84f0abe9-a13c-4c2b-b3f6-e309c0fbdffd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:59:39,233] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:59:39,233] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 05:59:39,233] [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 05:59:39,233] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11187/tc_result.tsv
[2023-03-17 05:59:39,233] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:59:39,234] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:59:39,234] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84f0abe9-a13c-4c2b-b3f6-e309c0fbdffd/dqc_reference/checkm_data
[2023-03-17 05:59:39,236] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:59:39,239] [INFO] Task started: CheckM
[2023-03-17 05:59:39,239] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11187/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11187/checkm_input OceanDNA-b11187/checkm_result
[2023-03-17 06:00:13,478] [INFO] Task succeeded: CheckM
[2023-03-17 06:00:13,479] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 6.71%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 06:00:13,481] [INFO] ===== Completeness check finished =====
[2023-03-17 06:00:13,481] [INFO] ===== Start GTDB Search =====
[2023-03-17 06:00:13,481] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11187/markers.fasta)
[2023-03-17 06:00:13,481] [INFO] Task started: Blastn
[2023-03-17 06:00:13,481] [INFO] Running command: blastn -query OceanDNA-b11187/markers.fasta -db /var/lib/cwl/stg84f0abe9-a13c-4c2b-b3f6-e309c0fbdffd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11187/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:00:14,437] [INFO] Task succeeded: Blastn
[2023-03-17 06:00:14,438] [INFO] Selected 20 target genomes.
[2023-03-17 06:00:14,438] [INFO] Target genome list was writen to OceanDNA-b11187/target_genomes_gtdb.txt
[2023-03-17 06:00:14,635] [INFO] Task started: fastANI
[2023-03-17 06:00:14,635] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a9ff74e-ed40-41a3-9713-3f764985da2e/OceanDNA-b11187.fa --refList OceanDNA-b11187/target_genomes_gtdb.txt --output OceanDNA-b11187/fastani_result_gtdb.tsv --threads 1
[2023-03-17 06:00:20,687] [INFO] Task succeeded: fastANI
[2023-03-17 06:00:20,696] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 06:00:20,697] [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_009936675.1	s__UBA8316 sp009936675	89.8964	300	468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.40	99.39	0.87	0.79	3	-
GCA_002390455.1	s__UBA8316 sp002390455	85.54	322	468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.09	98.50	0.88	0.83	3	-
GCA_002364535.1	s__UBA8316 sp002364535	81.3372	319	468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.85	99.85	0.95	0.95	2	-
GCA_018623955.1	s__UBA8316 sp018623955	81.0871	177	468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902619315.1	s__UBA8316 sp902619315	79.5034	190	468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002687665.1	s__UBA8316 sp002687665	79.4247	199	468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002336305.1	s__UBA8316 sp002336305	78.8518	193	468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018647605.1	s__UBA8316 sp018647605	78.6696	183	468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002711215.1	s__UBA8316 sp002711215	78.0038	152	468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	100.00	100.00	0.95	0.95	2	-
GCA_902609035.1	s__UBA8316 sp902609035	77.8874	103	468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017857815.1	s__UBA8316 sp017857815	77.3685	56	468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003538555.1	s__UBA8316 sp003538555	76.8994	57	468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	98.54	98.54	0.88	0.88	2	-
GCA_902515395.1	s__UBA8316 sp902515395	76.6092	62	468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	96.55	96.55	0.73	0.73	2	-
GCA_902590705.1	s__UBA8316 sp902590705	76.5115	65	468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.92	99.92	0.88	0.88	2	-
GCA_905182575.1	s__UBA8316 sp905182575	76.4788	52	468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	95.72	95.72	0.87	0.87	2	-
GCA_902584445.1	s__UBA8316 sp902584445	76.2005	64	468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 06:00:20,697] [INFO] GTDB search result was written to OceanDNA-b11187/result_gtdb.tsv
[2023-03-17 06:00:20,697] [INFO] ===== GTDB Search completed =====
[2023-03-17 06:00:20,698] [INFO] DFAST_QC result json was written to OceanDNA-b11187/dqc_result.json
[2023-03-17 06:00:20,698] [INFO] DFAST_QC completed!
[2023-03-17 06:00:20,698] [INFO] Total running time: 0h1m10s