[2023-06-28 20:49:05,329] [INFO] DFAST_QC pipeline started.
[2023-06-28 20:49:05,331] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 20:49:05,331] [INFO] DQC Reference Directory: /var/lib/cwl/stg69c577c9-02a9-4034-8c16-8d403f34f8fe/dqc_reference
[2023-06-28 20:49:06,542] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 20:49:06,543] [INFO] Task started: Prodigal
[2023-06-28 20:49:06,544] [INFO] Running command: gunzip -c /var/lib/cwl/stg670358d3-138a-4c62-a249-a910047d606d/GCA_944324035.1_BRZ_QC_bin21_genomic.fna.gz | prodigal -d GCA_944324035.1_BRZ_QC_bin21_genomic.fna/cds.fna -a GCA_944324035.1_BRZ_QC_bin21_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 20:49:09,871] [INFO] Task succeeded: Prodigal
[2023-06-28 20:49:09,871] [INFO] Task started: HMMsearch
[2023-06-28 20:49:09,871] [INFO] Running command: hmmsearch --tblout GCA_944324035.1_BRZ_QC_bin21_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69c577c9-02a9-4034-8c16-8d403f34f8fe/dqc_reference/reference_markers.hmm GCA_944324035.1_BRZ_QC_bin21_genomic.fna/protein.faa > /dev/null
[2023-06-28 20:49:10,089] [INFO] Task succeeded: HMMsearch
[2023-06-28 20:49:10,090] [INFO] Found 6/6 markers.
[2023-06-28 20:49:10,112] [INFO] Query marker FASTA was written to GCA_944324035.1_BRZ_QC_bin21_genomic.fna/markers.fasta
[2023-06-28 20:49:10,112] [INFO] Task started: Blastn
[2023-06-28 20:49:10,112] [INFO] Running command: blastn -query GCA_944324035.1_BRZ_QC_bin21_genomic.fna/markers.fasta -db /var/lib/cwl/stg69c577c9-02a9-4034-8c16-8d403f34f8fe/dqc_reference/reference_markers.fasta -out GCA_944324035.1_BRZ_QC_bin21_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:49:10,697] [INFO] Task succeeded: Blastn
[2023-06-28 20:49:10,702] [INFO] Selected 16 target genomes.
[2023-06-28 20:49:10,703] [INFO] Target genome list was writen to GCA_944324035.1_BRZ_QC_bin21_genomic.fna/target_genomes.txt
[2023-06-28 20:49:10,706] [INFO] Task started: fastANI
[2023-06-28 20:49:10,706] [INFO] Running command: fastANI --query /var/lib/cwl/stg670358d3-138a-4c62-a249-a910047d606d/GCA_944324035.1_BRZ_QC_bin21_genomic.fna.gz --refList GCA_944324035.1_BRZ_QC_bin21_genomic.fna/target_genomes.txt --output GCA_944324035.1_BRZ_QC_bin21_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 20:49:18,802] [INFO] Task succeeded: fastANI
[2023-06-28 20:49:18,802] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69c577c9-02a9-4034-8c16-8d403f34f8fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 20:49:18,803] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69c577c9-02a9-4034-8c16-8d403f34f8fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 20:49:18,805] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 20:49:18,805] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 20:49:18,805] [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 20:49:18,817] [INFO] DFAST Taxonomy check result was written to GCA_944324035.1_BRZ_QC_bin21_genomic.fna/tc_result.tsv
[2023-06-28 20:49:18,818] [INFO] ===== Taxonomy check completed =====
[2023-06-28 20:49:18,818] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 20:49:18,818] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69c577c9-02a9-4034-8c16-8d403f34f8fe/dqc_reference/checkm_data
[2023-06-28 20:49:18,823] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 20:49:18,846] [INFO] Task started: CheckM
[2023-06-28 20:49:18,846] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944324035.1_BRZ_QC_bin21_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944324035.1_BRZ_QC_bin21_genomic.fna/checkm_input GCA_944324035.1_BRZ_QC_bin21_genomic.fna/checkm_result
[2023-06-28 20:49:36,305] [INFO] Task succeeded: CheckM
[2023-06-28 20:49:36,307] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.11%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 20:49:36,330] [INFO] ===== Completeness check finished =====
[2023-06-28 20:49:36,330] [INFO] ===== Start GTDB Search =====
[2023-06-28 20:49:36,331] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944324035.1_BRZ_QC_bin21_genomic.fna/markers.fasta)
[2023-06-28 20:49:36,331] [INFO] Task started: Blastn
[2023-06-28 20:49:36,331] [INFO] Running command: blastn -query GCA_944324035.1_BRZ_QC_bin21_genomic.fna/markers.fasta -db /var/lib/cwl/stg69c577c9-02a9-4034-8c16-8d403f34f8fe/dqc_reference/reference_markers_gtdb.fasta -out GCA_944324035.1_BRZ_QC_bin21_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:49:37,173] [INFO] Task succeeded: Blastn
[2023-06-28 20:49:37,178] [INFO] Selected 19 target genomes.
[2023-06-28 20:49:37,178] [INFO] Target genome list was writen to GCA_944324035.1_BRZ_QC_bin21_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 20:49:37,179] [INFO] Task started: fastANI
[2023-06-28 20:49:37,179] [INFO] Running command: fastANI --query /var/lib/cwl/stg670358d3-138a-4c62-a249-a910047d606d/GCA_944324035.1_BRZ_QC_bin21_genomic.fna.gz --refList GCA_944324035.1_BRZ_QC_bin21_genomic.fna/target_genomes_gtdb.txt --output GCA_944324035.1_BRZ_QC_bin21_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 20:49:43,704] [INFO] Task succeeded: fastANI
[2023-06-28 20:49:43,725] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 20:49:43,725] [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_900770525.1	s__UBA1221 sp900770525	78.5969	191	548	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA1221	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000431315.1	s__Scatousia sp000431315	78.266	146	548	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Scatousia	95.0	97.32	95.18	0.89	0.88	6	-
GCA_902777385.1	s__UBA1221 sp902777385	78.2463	163	548	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA1221	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017542305.1	s__UBA1221 sp017542305	78.1609	138	548	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA1221	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902760645.1	s__UBA1221 sp902760645	77.9922	170	548	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA1221	95.0	99.01	99.01	0.93	0.93	2	-
GCA_003150395.1	s__Scatenecus sp003150395	77.8907	121	548	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Scatenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000438175.1	s__Stercorousia faecigallinarum	77.8396	146	548	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	98.53	97.95	0.88	0.85	4	-
GCA_002350725.1	s__UBA1221 sp002350725	77.8321	129	548	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA1221	95.0	99.91	99.91	0.86	0.86	2	-
GCA_900761225.1	s__Stercorousia sp900761225	77.6256	123	548	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002309425.1	s__UBA1221 sp002309425	77.6236	122	548	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA1221	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554385.1	s__Scatousia sp900554385	77.6047	113	548	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Scatousia	95.0	99.41	98.83	0.97	0.96	3	-
GCA_000433095.1	s__Stercorousia sp000433095	77.5596	135	548	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	99.53	99.13	0.95	0.93	3	-
GCA_018711035.1	s__Scatousia excrementigallinarum	77.5187	142	548	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Scatousia	95.0	99.20	99.20	0.79	0.79	2	-
GCA_900551965.1	s__Zag111 sp900551965	77.4761	75	548	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551915.1	s__Scatenecus faecavium	77.3838	125	548	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Scatenecus	95.0	98.79	98.66	0.89	0.87	5	-
GCA_900548405.1	s__Stercorousia sp001917115	77.276	133	548	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	98.35	95.50	0.91	0.85	8	-
GCA_900320675.1	s__UBA1221 sp900320675	77.2591	117	548	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA1221	95.0	99.32	98.98	0.96	0.93	4	-
GCA_017467605.1	s__Zag111 sp017467605	77.1162	86	548	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017652265.1	s__Gastranaerophilus sp017652265	77.0447	66	548	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Gastranaerophilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 20:49:43,728] [INFO] GTDB search result was written to GCA_944324035.1_BRZ_QC_bin21_genomic.fna/result_gtdb.tsv
[2023-06-28 20:49:43,728] [INFO] ===== GTDB Search completed =====
[2023-06-28 20:49:43,731] [INFO] DFAST_QC result json was written to GCA_944324035.1_BRZ_QC_bin21_genomic.fna/dqc_result.json
[2023-06-28 20:49:43,732] [INFO] DFAST_QC completed!
[2023-06-28 20:49:43,732] [INFO] Total running time: 0h0m38s