[2023-06-28 16:31:17,391] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:31:17,393] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:31:17,393] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1f17c62-7681-4959-b48f-1e382bcd4c75/dqc_reference
[2023-06-28 16:31:18,630] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:31:18,630] [INFO] Task started: Prodigal
[2023-06-28 16:31:18,630] [INFO] Running command: gunzip -c /var/lib/cwl/stg442623cc-c707-443f-9fdc-b6250ee61d23/GCA_944363595.1_E24_bin45_genomic.fna.gz | prodigal -d GCA_944363595.1_E24_bin45_genomic.fna/cds.fna -a GCA_944363595.1_E24_bin45_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:31:20,269] [INFO] Task succeeded: Prodigal
[2023-06-28 16:31:20,269] [INFO] Task started: HMMsearch
[2023-06-28 16:31:20,269] [INFO] Running command: hmmsearch --tblout GCA_944363595.1_E24_bin45_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1f17c62-7681-4959-b48f-1e382bcd4c75/dqc_reference/reference_markers.hmm GCA_944363595.1_E24_bin45_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:31:20,474] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:31:20,476] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg442623cc-c707-443f-9fdc-b6250ee61d23/GCA_944363595.1_E24_bin45_genomic.fna.gz]
[2023-06-28 16:31:20,491] [INFO] Query marker FASTA was written to GCA_944363595.1_E24_bin45_genomic.fna/markers.fasta
[2023-06-28 16:31:20,491] [INFO] Task started: Blastn
[2023-06-28 16:31:20,491] [INFO] Running command: blastn -query GCA_944363595.1_E24_bin45_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1f17c62-7681-4959-b48f-1e382bcd4c75/dqc_reference/reference_markers.fasta -out GCA_944363595.1_E24_bin45_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:31:21,025] [INFO] Task succeeded: Blastn
[2023-06-28 16:31:21,029] [INFO] Selected 23 target genomes.
[2023-06-28 16:31:21,029] [INFO] Target genome list was writen to GCA_944363595.1_E24_bin45_genomic.fna/target_genomes.txt
[2023-06-28 16:31:21,039] [INFO] Task started: fastANI
[2023-06-28 16:31:21,040] [INFO] Running command: fastANI --query /var/lib/cwl/stg442623cc-c707-443f-9fdc-b6250ee61d23/GCA_944363595.1_E24_bin45_genomic.fna.gz --refList GCA_944363595.1_E24_bin45_genomic.fna/target_genomes.txt --output GCA_944363595.1_E24_bin45_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:31:30,067] [INFO] Task succeeded: fastANI
[2023-06-28 16:31:30,068] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1f17c62-7681-4959-b48f-1e382bcd4c75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:31:30,068] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1f17c62-7681-4959-b48f-1e382bcd4c75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:31:30,069] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:31:30,069] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 16:31:30,069] [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 16:31:30,071] [INFO] DFAST Taxonomy check result was written to GCA_944363595.1_E24_bin45_genomic.fna/tc_result.tsv
[2023-06-28 16:31:30,072] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:31:30,072] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:31:30,072] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1f17c62-7681-4959-b48f-1e382bcd4c75/dqc_reference/checkm_data
[2023-06-28 16:31:30,074] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:31:30,088] [INFO] Task started: CheckM
[2023-06-28 16:31:30,088] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944363595.1_E24_bin45_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944363595.1_E24_bin45_genomic.fna/checkm_input GCA_944363595.1_E24_bin45_genomic.fna/checkm_result
[2023-06-28 16:31:41,965] [INFO] Task succeeded: CheckM
[2023-06-28 16:31:41,966] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 16:31:41,984] [INFO] ===== Completeness check finished =====
[2023-06-28 16:31:41,985] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:31:41,985] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944363595.1_E24_bin45_genomic.fna/markers.fasta)
[2023-06-28 16:31:41,985] [INFO] Task started: Blastn
[2023-06-28 16:31:41,985] [INFO] Running command: blastn -query GCA_944363595.1_E24_bin45_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1f17c62-7681-4959-b48f-1e382bcd4c75/dqc_reference/reference_markers_gtdb.fasta -out GCA_944363595.1_E24_bin45_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:31:42,740] [INFO] Task succeeded: Blastn
[2023-06-28 16:31:42,743] [INFO] Selected 25 target genomes.
[2023-06-28 16:31:42,744] [INFO] Target genome list was writen to GCA_944363595.1_E24_bin45_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:31:42,755] [INFO] Task started: fastANI
[2023-06-28 16:31:42,755] [INFO] Running command: fastANI --query /var/lib/cwl/stg442623cc-c707-443f-9fdc-b6250ee61d23/GCA_944363595.1_E24_bin45_genomic.fna.gz --refList GCA_944363595.1_E24_bin45_genomic.fna/target_genomes_gtdb.txt --output GCA_944363595.1_E24_bin45_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:31:47,987] [INFO] Task succeeded: fastANI
[2023-06-28 16:31:47,993] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 16:31:47,993] [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_017432825.1	s__RUG11198 sp017432825	76.9549	51	374	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG11198	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017409025.1	s__RUG705 sp017409025	76.6021	59	374	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG705	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548425.1	s__CAG-302 sp900548425	76.5878	62	374	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-302	95.0	99.47	98.99	0.91	0.87	3	-
GCA_900543825.1	s__CAG-302 sp900543825	76.4651	60	374	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-302	95.0	98.18	98.11	0.88	0.87	3	-
GCA_001916775.1	s__CAG-302 sp001916775	76.3733	66	374	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-302	95.0	95.82	95.12	0.84	0.77	8	-
GCA_900772445.1	s__HGM10818 sp900772445	76.3696	52	374	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__HGM10818	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905211265.1	s__HGM10818 sp905211265	76.2227	77	374	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__HGM10818	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 16:31:47,995] [INFO] GTDB search result was written to GCA_944363595.1_E24_bin45_genomic.fna/result_gtdb.tsv
[2023-06-28 16:31:47,995] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:31:47,998] [INFO] DFAST_QC result json was written to GCA_944363595.1_E24_bin45_genomic.fna/dqc_result.json
[2023-06-28 16:31:47,998] [INFO] DFAST_QC completed!
[2023-06-28 16:31:47,998] [INFO] Total running time: 0h0m31s