[2023-06-05 07:16:23,882] [INFO] DFAST_QC pipeline started.
[2023-06-05 07:16:23,892] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 07:16:23,892] [INFO] DQC Reference Directory: /var/lib/cwl/stg18712944-1bfa-4d65-8855-98eb09d4f472/dqc_reference
[2023-06-05 07:16:27,031] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 07:16:27,032] [INFO] Task started: Prodigal
[2023-06-05 07:16:27,032] [INFO] Running command: gunzip -c /var/lib/cwl/stg7bb52579-c862-4d45-a99f-a0e0a9dabef6/GCA_934463485.1_ERR7738557_bin.147_genomic.fna.gz | prodigal -d GCA_934463485.1_ERR7738557_bin.147_genomic.fna/cds.fna -a GCA_934463485.1_ERR7738557_bin.147_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 07:16:29,654] [INFO] Task succeeded: Prodigal
[2023-06-05 07:16:29,655] [INFO] Task started: HMMsearch
[2023-06-05 07:16:29,655] [INFO] Running command: hmmsearch --tblout GCA_934463485.1_ERR7738557_bin.147_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18712944-1bfa-4d65-8855-98eb09d4f472/dqc_reference/reference_markers.hmm GCA_934463485.1_ERR7738557_bin.147_genomic.fna/protein.faa > /dev/null
[2023-06-05 07:16:29,900] [INFO] Task succeeded: HMMsearch
[2023-06-05 07:16:29,902] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg7bb52579-c862-4d45-a99f-a0e0a9dabef6/GCA_934463485.1_ERR7738557_bin.147_genomic.fna.gz]
[2023-06-05 07:16:29,924] [INFO] Query marker FASTA was written to GCA_934463485.1_ERR7738557_bin.147_genomic.fna/markers.fasta
[2023-06-05 07:16:29,924] [INFO] Task started: Blastn
[2023-06-05 07:16:29,924] [INFO] Running command: blastn -query GCA_934463485.1_ERR7738557_bin.147_genomic.fna/markers.fasta -db /var/lib/cwl/stg18712944-1bfa-4d65-8855-98eb09d4f472/dqc_reference/reference_markers.fasta -out GCA_934463485.1_ERR7738557_bin.147_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:16:30,529] [INFO] Task succeeded: Blastn
[2023-06-05 07:16:30,535] [INFO] Selected 7 target genomes.
[2023-06-05 07:16:30,536] [INFO] Target genome list was writen to GCA_934463485.1_ERR7738557_bin.147_genomic.fna/target_genomes.txt
[2023-06-05 07:16:30,538] [INFO] Task started: fastANI
[2023-06-05 07:16:30,538] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bb52579-c862-4d45-a99f-a0e0a9dabef6/GCA_934463485.1_ERR7738557_bin.147_genomic.fna.gz --refList GCA_934463485.1_ERR7738557_bin.147_genomic.fna/target_genomes.txt --output GCA_934463485.1_ERR7738557_bin.147_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 07:16:33,741] [INFO] Task succeeded: fastANI
[2023-06-05 07:16:33,741] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18712944-1bfa-4d65-8855-98eb09d4f472/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 07:16:33,741] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18712944-1bfa-4d65-8855-98eb09d4f472/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 07:16:33,743] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 07:16:33,743] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 07:16:33,743] [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
--------------------------------------------------------------------------------
[2023-06-05 07:16:33,745] [INFO] DFAST Taxonomy check result was written to GCA_934463485.1_ERR7738557_bin.147_genomic.fna/tc_result.tsv
[2023-06-05 07:16:33,746] [INFO] ===== Taxonomy check completed =====
[2023-06-05 07:16:33,746] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 07:16:33,746] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18712944-1bfa-4d65-8855-98eb09d4f472/dqc_reference/checkm_data
[2023-06-05 07:16:33,749] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 07:16:33,766] [INFO] Task started: CheckM
[2023-06-05 07:16:33,767] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934463485.1_ERR7738557_bin.147_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934463485.1_ERR7738557_bin.147_genomic.fna/checkm_input GCA_934463485.1_ERR7738557_bin.147_genomic.fna/checkm_result
[2023-06-05 07:16:52,839] [INFO] Task succeeded: CheckM
[2023-06-05 07:16:52,841] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.36%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 07:16:52,861] [INFO] ===== Completeness check finished =====
[2023-06-05 07:16:52,862] [INFO] ===== Start GTDB Search =====
[2023-06-05 07:16:52,862] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934463485.1_ERR7738557_bin.147_genomic.fna/markers.fasta)
[2023-06-05 07:16:52,863] [INFO] Task started: Blastn
[2023-06-05 07:16:52,863] [INFO] Running command: blastn -query GCA_934463485.1_ERR7738557_bin.147_genomic.fna/markers.fasta -db /var/lib/cwl/stg18712944-1bfa-4d65-8855-98eb09d4f472/dqc_reference/reference_markers_gtdb.fasta -out GCA_934463485.1_ERR7738557_bin.147_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:16:53,806] [INFO] Task succeeded: Blastn
[2023-06-05 07:16:53,812] [INFO] Selected 17 target genomes.
[2023-06-05 07:16:53,812] [INFO] Target genome list was writen to GCA_934463485.1_ERR7738557_bin.147_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 07:16:53,820] [INFO] Task started: fastANI
[2023-06-05 07:16:53,820] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bb52579-c862-4d45-a99f-a0e0a9dabef6/GCA_934463485.1_ERR7738557_bin.147_genomic.fna.gz --refList GCA_934463485.1_ERR7738557_bin.147_genomic.fna/target_genomes_gtdb.txt --output GCA_934463485.1_ERR7738557_bin.147_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 07:16:58,275] [INFO] Task succeeded: fastANI
[2023-06-05 07:16:58,291] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 07:16:58,291] [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_900547095.1	s__UBA737 sp900547095	96.5673	382	456	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	98.77	97.54	0.95	0.90	3	conclusive
GCA_002297415.1	s__UBA737 sp002297415	79.6606	205	456	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	99.54	99.54	0.81	0.81	3	-
GCA_002431945.1	s__UBA737 sp002431945	78.4917	87	456	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	97.08	96.44	0.77	0.66	6	-
GCA_905193585.1	s__UBA737 sp905193585	77.368	61	456	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547305.1	s__UBA737 sp900547305	77.3107	75	456	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	99.91	99.91	0.93	0.93	2	-
GCA_900547445.1	s__UBA737 sp900547445	76.8767	60	456	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	99.98	99.98	0.91	0.91	2	-
GCA_905211675.1	s__UBA737 sp905211675	76.5029	54	456	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 07:16:58,294] [INFO] GTDB search result was written to GCA_934463485.1_ERR7738557_bin.147_genomic.fna/result_gtdb.tsv
[2023-06-05 07:16:58,295] [INFO] ===== GTDB Search completed =====
[2023-06-05 07:16:58,299] [INFO] DFAST_QC result json was written to GCA_934463485.1_ERR7738557_bin.147_genomic.fna/dqc_result.json
[2023-06-05 07:16:58,299] [INFO] DFAST_QC completed!
[2023-06-05 07:16:58,300] [INFO] Total running time: 0h0m34s