[2023-06-28 12:00:32,276] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:00:32,278] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:00:32,278] [INFO] DQC Reference Directory: /var/lib/cwl/stg039ecf67-5203-4454-993b-72ffc309e1f2/dqc_reference
[2023-06-28 12:00:33,583] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:00:33,584] [INFO] Task started: Prodigal
[2023-06-28 12:00:33,584] [INFO] Running command: gunzip -c /var/lib/cwl/stg04f0134c-8473-42cb-97d3-9a08704ceba9/GCA_020719085.1_ASM2071908v1_genomic.fna.gz | prodigal -d GCA_020719085.1_ASM2071908v1_genomic.fna/cds.fna -a GCA_020719085.1_ASM2071908v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:00:46,931] [INFO] Task succeeded: Prodigal
[2023-06-28 12:00:46,932] [INFO] Task started: HMMsearch
[2023-06-28 12:00:46,932] [INFO] Running command: hmmsearch --tblout GCA_020719085.1_ASM2071908v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg039ecf67-5203-4454-993b-72ffc309e1f2/dqc_reference/reference_markers.hmm GCA_020719085.1_ASM2071908v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:00:47,210] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:00:47,212] [INFO] Found 6/6 markers.
[2023-06-28 12:00:47,241] [INFO] Query marker FASTA was written to GCA_020719085.1_ASM2071908v1_genomic.fna/markers.fasta
[2023-06-28 12:00:47,241] [INFO] Task started: Blastn
[2023-06-28 12:00:47,241] [INFO] Running command: blastn -query GCA_020719085.1_ASM2071908v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg039ecf67-5203-4454-993b-72ffc309e1f2/dqc_reference/reference_markers.fasta -out GCA_020719085.1_ASM2071908v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:00:47,886] [INFO] Task succeeded: Blastn
[2023-06-28 12:00:47,890] [INFO] Selected 33 target genomes.
[2023-06-28 12:00:47,890] [INFO] Target genome list was writen to GCA_020719085.1_ASM2071908v1_genomic.fna/target_genomes.txt
[2023-06-28 12:00:47,902] [INFO] Task started: fastANI
[2023-06-28 12:00:47,903] [INFO] Running command: fastANI --query /var/lib/cwl/stg04f0134c-8473-42cb-97d3-9a08704ceba9/GCA_020719085.1_ASM2071908v1_genomic.fna.gz --refList GCA_020719085.1_ASM2071908v1_genomic.fna/target_genomes.txt --output GCA_020719085.1_ASM2071908v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:01:06,751] [INFO] Task succeeded: fastANI
[2023-06-28 12:01:06,752] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg039ecf67-5203-4454-993b-72ffc309e1f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:01:06,752] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg039ecf67-5203-4454-993b-72ffc309e1f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:01:06,754] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:01:06,754] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 12:01:06,754] [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
--------------------------------------------------------------------------------
[2023-06-28 12:01:06,756] [INFO] DFAST Taxonomy check result was written to GCA_020719085.1_ASM2071908v1_genomic.fna/tc_result.tsv
[2023-06-28 12:01:06,757] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:01:06,757] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:01:06,757] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg039ecf67-5203-4454-993b-72ffc309e1f2/dqc_reference/checkm_data
[2023-06-28 12:01:06,761] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:01:06,795] [INFO] Task started: CheckM
[2023-06-28 12:01:06,796] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020719085.1_ASM2071908v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020719085.1_ASM2071908v1_genomic.fna/checkm_input GCA_020719085.1_ASM2071908v1_genomic.fna/checkm_result
[2023-06-28 12:01:51,508] [INFO] Task succeeded: CheckM
[2023-06-28 12:01:51,510] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.18%
Contamintation: 0.93%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:01:51,534] [INFO] ===== Completeness check finished =====
[2023-06-28 12:01:51,534] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:01:51,536] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020719085.1_ASM2071908v1_genomic.fna/markers.fasta)
[2023-06-28 12:01:51,536] [INFO] Task started: Blastn
[2023-06-28 12:01:51,536] [INFO] Running command: blastn -query GCA_020719085.1_ASM2071908v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg039ecf67-5203-4454-993b-72ffc309e1f2/dqc_reference/reference_markers_gtdb.fasta -out GCA_020719085.1_ASM2071908v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:01:52,377] [INFO] Task succeeded: Blastn
[2023-06-28 12:01:52,381] [INFO] Selected 21 target genomes.
[2023-06-28 12:01:52,381] [INFO] Target genome list was writen to GCA_020719085.1_ASM2071908v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:01:52,398] [INFO] Task started: fastANI
[2023-06-28 12:01:52,398] [INFO] Running command: fastANI --query /var/lib/cwl/stg04f0134c-8473-42cb-97d3-9a08704ceba9/GCA_020719085.1_ASM2071908v1_genomic.fna.gz --refList GCA_020719085.1_ASM2071908v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020719085.1_ASM2071908v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:02:05,831] [INFO] Task succeeded: fastANI
[2023-06-28 12:02:05,842] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 12:02:05,842] [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_002325785.1	s__SR-FBR-E99 sp002325785	79.9695	436	824	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__SR-FBR-E99	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002402965.1	s__SR-FBR-E99 sp002402965	78.9481	373	824	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__SR-FBR-E99	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002383485.1	s__SR-FBR-E99 sp002383485	78.7093	321	824	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__SR-FBR-E99	95.0	99.98	99.98	0.99	0.99	2	-
GCA_002403305.1	s__SR-FBR-E99 sp002403305	78.5263	368	824	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__SR-FBR-E99	95.0	99.96	99.90	0.97	0.95	5	-
GCA_011620595.1	s__SR-FBR-E99 sp011620595	78.2035	335	824	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__SR-FBR-E99	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003250475.1	s__SR-FBR-E99 sp003250475	78.1164	267	824	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__SR-FBR-E99	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018262715.1	s__SR-FBR-E99 sp018262715	78.0076	294	824	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__SR-FBR-E99	95.0	99.48	99.48	0.89	0.86	3	-
GCA_002409145.1	s__SR-FBR-E99 sp002409145	77.9411	259	824	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__SR-FBR-E99	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012514255.1	s__SR-FBR-E99 sp012514255	77.5953	242	824	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__SR-FBR-E99	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009881065.1	s__SR-FBR-E99 sp009881065	77.4323	210	824	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__SR-FBR-E99	95.0	99.27	99.14	0.89	0.83	7	-
GCA_017882245.1	s__SR-FBR-E99 sp017882245	76.9866	140	824	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__SR-FBR-E99	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:02:05,846] [INFO] GTDB search result was written to GCA_020719085.1_ASM2071908v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:02:05,847] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:02:05,850] [INFO] DFAST_QC result json was written to GCA_020719085.1_ASM2071908v1_genomic.fna/dqc_result.json
[2023-06-28 12:02:05,850] [INFO] DFAST_QC completed!
[2023-06-28 12:02:05,850] [INFO] Total running time: 0h1m34s