[2023-06-30 04:11:46,735] [INFO] DFAST_QC pipeline started.
[2023-06-30 04:11:46,737] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 04:11:46,737] [INFO] DQC Reference Directory: /var/lib/cwl/stg697a1b42-c8fa-4674-940a-990ae478c1aa/dqc_reference
[2023-06-30 04:11:49,660] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 04:11:49,661] [INFO] Task started: Prodigal
[2023-06-30 04:11:49,661] [INFO] Running command: gunzip -c /var/lib/cwl/stg958f4923-bd0a-40a7-84f4-bf4f288449d3/GCA_900757295.1_ERS537306_66_genomic.fna.gz | prodigal -d GCA_900757295.1_ERS537306_66_genomic.fna/cds.fna -a GCA_900757295.1_ERS537306_66_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 04:11:51,389] [INFO] Task succeeded: Prodigal
[2023-06-30 04:11:51,389] [INFO] Task started: HMMsearch
[2023-06-30 04:11:51,389] [INFO] Running command: hmmsearch --tblout GCA_900757295.1_ERS537306_66_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg697a1b42-c8fa-4674-940a-990ae478c1aa/dqc_reference/reference_markers.hmm GCA_900757295.1_ERS537306_66_genomic.fna/protein.faa > /dev/null
[2023-06-30 04:11:51,603] [INFO] Task succeeded: HMMsearch
[2023-06-30 04:11:51,604] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg958f4923-bd0a-40a7-84f4-bf4f288449d3/GCA_900757295.1_ERS537306_66_genomic.fna.gz]
[2023-06-30 04:11:51,623] [INFO] Query marker FASTA was written to GCA_900757295.1_ERS537306_66_genomic.fna/markers.fasta
[2023-06-30 04:11:51,624] [INFO] Task started: Blastn
[2023-06-30 04:11:51,624] [INFO] Running command: blastn -query GCA_900757295.1_ERS537306_66_genomic.fna/markers.fasta -db /var/lib/cwl/stg697a1b42-c8fa-4674-940a-990ae478c1aa/dqc_reference/reference_markers.fasta -out GCA_900757295.1_ERS537306_66_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:11:53,440] [INFO] Task succeeded: Blastn
[2023-06-30 04:11:53,446] [INFO] Selected 25 target genomes.
[2023-06-30 04:11:53,447] [INFO] Target genome list was writen to GCA_900757295.1_ERS537306_66_genomic.fna/target_genomes.txt
[2023-06-30 04:11:53,449] [INFO] Task started: fastANI
[2023-06-30 04:11:53,450] [INFO] Running command: fastANI --query /var/lib/cwl/stg958f4923-bd0a-40a7-84f4-bf4f288449d3/GCA_900757295.1_ERS537306_66_genomic.fna.gz --refList GCA_900757295.1_ERS537306_66_genomic.fna/target_genomes.txt --output GCA_900757295.1_ERS537306_66_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 04:12:04,046] [INFO] Task succeeded: fastANI
[2023-06-30 04:12:04,047] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg697a1b42-c8fa-4674-940a-990ae478c1aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 04:12:04,048] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg697a1b42-c8fa-4674-940a-990ae478c1aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 04:12:04,051] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 04:12:04,052] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 04:12:04,052] [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
--------------------------------------------------------------------------------
[2023-06-30 04:12:04,055] [INFO] DFAST Taxonomy check result was written to GCA_900757295.1_ERS537306_66_genomic.fna/tc_result.tsv
[2023-06-30 04:12:04,056] [INFO] ===== Taxonomy check completed =====
[2023-06-30 04:12:04,056] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 04:12:04,057] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg697a1b42-c8fa-4674-940a-990ae478c1aa/dqc_reference/checkm_data
[2023-06-30 04:12:04,061] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 04:12:04,079] [INFO] Task started: CheckM
[2023-06-30 04:12:04,079] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900757295.1_ERS537306_66_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900757295.1_ERS537306_66_genomic.fna/checkm_input GCA_900757295.1_ERS537306_66_genomic.fna/checkm_result
[2023-06-30 04:12:18,189] [INFO] Task succeeded: CheckM
[2023-06-30 04:12:18,190] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 04:12:18,217] [INFO] ===== Completeness check finished =====
[2023-06-30 04:12:18,218] [INFO] ===== Start GTDB Search =====
[2023-06-30 04:12:18,218] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900757295.1_ERS537306_66_genomic.fna/markers.fasta)
[2023-06-30 04:12:18,219] [INFO] Task started: Blastn
[2023-06-30 04:12:18,219] [INFO] Running command: blastn -query GCA_900757295.1_ERS537306_66_genomic.fna/markers.fasta -db /var/lib/cwl/stg697a1b42-c8fa-4674-940a-990ae478c1aa/dqc_reference/reference_markers_gtdb.fasta -out GCA_900757295.1_ERS537306_66_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:12:19,064] [INFO] Task succeeded: Blastn
[2023-06-30 04:12:19,069] [INFO] Selected 25 target genomes.
[2023-06-30 04:12:19,069] [INFO] Target genome list was writen to GCA_900757295.1_ERS537306_66_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 04:12:19,079] [INFO] Task started: fastANI
[2023-06-30 04:12:19,079] [INFO] Running command: fastANI --query /var/lib/cwl/stg958f4923-bd0a-40a7-84f4-bf4f288449d3/GCA_900757295.1_ERS537306_66_genomic.fna.gz --refList GCA_900757295.1_ERS537306_66_genomic.fna/target_genomes_gtdb.txt --output GCA_900757295.1_ERS537306_66_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 04:12:25,296] [INFO] Task succeeded: fastANI
[2023-06-30 04:12:25,312] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 04:12:25,312] [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_900757295.1	s__HGM10766 sp900757295	100.0	345	355	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__HGM10766	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015059425.1	s__Caccenecus sp015059425	77.2505	64	355	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Caccenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000433255.1	s__CAG-605 sp000433255	77.069	51	355	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-605	95.0	96.75	95.28	0.93	0.90	4	-
GCA_017435485.1	s__RGIG1752 sp017435485	76.9164	57	355	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RGIG1752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017398945.1	s__RGIG1752 sp017398945	76.7601	67	355	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RGIG1752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015059485.1	s__RUG14121 sp015059485	76.7387	65	355	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG14121	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016296185.1	s__Coprovivens sp016296185	76.6769	70	355	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Coprovivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587775.1	s__MGBC162267 sp910587775	76.6654	56	355	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__MGBC162267	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002438065.1	s__CAG-533 sp002438065	76.5192	66	355	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-533	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549285.1	s__Caccenecus sp900549285	76.2863	56	355	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Caccenecus	95.0	99.98	99.96	0.98	0.96	3	-
GCA_000438195.1	s__Caccenecus sp000438195	76.199	55	355	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Caccenecus	95.0	99.99	99.99	0.98	0.98	3	-
GCA_910587065.1	s__CAG-582 sp910587065	75.9703	53	355	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-582	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 04:12:25,315] [INFO] GTDB search result was written to GCA_900757295.1_ERS537306_66_genomic.fna/result_gtdb.tsv
[2023-06-30 04:12:25,315] [INFO] ===== GTDB Search completed =====
[2023-06-30 04:12:25,319] [INFO] DFAST_QC result json was written to GCA_900757295.1_ERS537306_66_genomic.fna/dqc_result.json
[2023-06-30 04:12:25,319] [INFO] DFAST_QC completed!
[2023-06-30 04:12:25,319] [INFO] Total running time: 0h0m39s