[2023-06-17 03:14:11,662] [INFO] DFAST_QC pipeline started.
[2023-06-17 03:14:11,671] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 03:14:11,671] [INFO] DQC Reference Directory: /var/lib/cwl/stg381e5141-bbd4-4db7-adb5-4414f9d14ae7/dqc_reference
[2023-06-17 03:14:13,951] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 03:14:13,952] [INFO] Task started: Prodigal
[2023-06-17 03:14:13,952] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f15e2d7-806a-42de-8fc6-92c9da6cddb2/GCA_905206785.1_ERR1600683-mag-bin.57_genomic.fna.gz | prodigal -d GCA_905206785.1_ERR1600683-mag-bin.57_genomic.fna/cds.fna -a GCA_905206785.1_ERR1600683-mag-bin.57_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 03:14:18,312] [INFO] Task succeeded: Prodigal
[2023-06-17 03:14:18,313] [INFO] Task started: HMMsearch
[2023-06-17 03:14:18,313] [INFO] Running command: hmmsearch --tblout GCA_905206785.1_ERR1600683-mag-bin.57_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg381e5141-bbd4-4db7-adb5-4414f9d14ae7/dqc_reference/reference_markers.hmm GCA_905206785.1_ERR1600683-mag-bin.57_genomic.fna/protein.faa > /dev/null
[2023-06-17 03:14:18,555] [INFO] Task succeeded: HMMsearch
[2023-06-17 03:14:18,556] [INFO] Found 6/6 markers.
[2023-06-17 03:14:18,578] [INFO] Query marker FASTA was written to GCA_905206785.1_ERR1600683-mag-bin.57_genomic.fna/markers.fasta
[2023-06-17 03:14:18,578] [INFO] Task started: Blastn
[2023-06-17 03:14:18,578] [INFO] Running command: blastn -query GCA_905206785.1_ERR1600683-mag-bin.57_genomic.fna/markers.fasta -db /var/lib/cwl/stg381e5141-bbd4-4db7-adb5-4414f9d14ae7/dqc_reference/reference_markers.fasta -out GCA_905206785.1_ERR1600683-mag-bin.57_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 03:14:19,269] [INFO] Task succeeded: Blastn
[2023-06-17 03:14:19,274] [INFO] Selected 26 target genomes.
[2023-06-17 03:14:19,275] [INFO] Target genome list was writen to GCA_905206785.1_ERR1600683-mag-bin.57_genomic.fna/target_genomes.txt
[2023-06-17 03:14:19,344] [INFO] Task started: fastANI
[2023-06-17 03:14:19,345] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f15e2d7-806a-42de-8fc6-92c9da6cddb2/GCA_905206785.1_ERR1600683-mag-bin.57_genomic.fna.gz --refList GCA_905206785.1_ERR1600683-mag-bin.57_genomic.fna/target_genomes.txt --output GCA_905206785.1_ERR1600683-mag-bin.57_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 03:14:34,790] [INFO] Task succeeded: fastANI
[2023-06-17 03:14:34,790] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg381e5141-bbd4-4db7-adb5-4414f9d14ae7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 03:14:34,791] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg381e5141-bbd4-4db7-adb5-4414f9d14ae7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 03:14:34,793] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 03:14:34,793] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 03:14:34,793] [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
--------------------------------------------------------------------------------
[2023-06-17 03:14:34,795] [INFO] DFAST Taxonomy check result was written to GCA_905206785.1_ERR1600683-mag-bin.57_genomic.fna/tc_result.tsv
[2023-06-17 03:14:34,795] [INFO] ===== Taxonomy check completed =====
[2023-06-17 03:14:34,796] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 03:14:34,796] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg381e5141-bbd4-4db7-adb5-4414f9d14ae7/dqc_reference/checkm_data
[2023-06-17 03:14:34,800] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 03:14:34,825] [INFO] Task started: CheckM
[2023-06-17 03:14:34,825] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905206785.1_ERR1600683-mag-bin.57_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905206785.1_ERR1600683-mag-bin.57_genomic.fna/checkm_input GCA_905206785.1_ERR1600683-mag-bin.57_genomic.fna/checkm_result
[2023-06-17 03:14:55,516] [INFO] Task succeeded: CheckM
[2023-06-17 03:14:55,518] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 03:14:55,540] [INFO] ===== Completeness check finished =====
[2023-06-17 03:14:55,540] [INFO] ===== Start GTDB Search =====
[2023-06-17 03:14:55,541] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905206785.1_ERR1600683-mag-bin.57_genomic.fna/markers.fasta)
[2023-06-17 03:14:55,541] [INFO] Task started: Blastn
[2023-06-17 03:14:55,541] [INFO] Running command: blastn -query GCA_905206785.1_ERR1600683-mag-bin.57_genomic.fna/markers.fasta -db /var/lib/cwl/stg381e5141-bbd4-4db7-adb5-4414f9d14ae7/dqc_reference/reference_markers_gtdb.fasta -out GCA_905206785.1_ERR1600683-mag-bin.57_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 03:14:56,710] [INFO] Task succeeded: Blastn
[2023-06-17 03:14:56,714] [INFO] Selected 17 target genomes.
[2023-06-17 03:14:56,714] [INFO] Target genome list was writen to GCA_905206785.1_ERR1600683-mag-bin.57_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 03:14:56,752] [INFO] Task started: fastANI
[2023-06-17 03:14:56,753] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f15e2d7-806a-42de-8fc6-92c9da6cddb2/GCA_905206785.1_ERR1600683-mag-bin.57_genomic.fna.gz --refList GCA_905206785.1_ERR1600683-mag-bin.57_genomic.fna/target_genomes_gtdb.txt --output GCA_905206785.1_ERR1600683-mag-bin.57_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 03:15:01,609] [INFO] Task succeeded: fastANI
[2023-06-17 03:15:01,624] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 03:15:01,624] [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_000432275.1	s__CAZU01 sp000432275	98.8097	481	558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__CAZU01	95.0	98.86	98.76	0.93	0.90	5	conclusive
GCA_001917175.1	s__51-20 sp001917175	79.3486	97	558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__51-20	95.0	99.01	98.90	0.93	0.93	4	-
GCA_018362935.1	s__CAZU01 sp018362935	78.1061	151	558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__CAZU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001917125.1	s__Scatocola faecipullorum	78.0552	129	558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__Scatocola	95.0	98.98	98.59	0.91	0.85	10	-
GCA_905210515.1	s__CAJLXD01 sp905210515	77.7325	74	558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__CAJLXD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551585.1	s__CAJLXD01 sp900551585	77.7081	93	558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__CAJLXD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017480995.1	s__CAZU01 sp017480995	77.7012	138	558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__CAZU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000436375.1	s__Scatacola_A faecigallinarum	77.698	128	558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__Scatacola_A	95.0	97.40	96.59	0.91	0.88	10	-
GCA_017626035.1	s__JAGAJR01 sp017626035	77.5987	115	558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__JAGAJR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017935485.1	s__MGBC133411 sp017935485	77.5449	100	558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__MGBC133411	95.0	98.32	98.32	0.87	0.87	2	-
GCA_910585375.1	s__MGBC133411 sp910585375	77.3599	113	558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__MGBC133411	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017452885.1	s__CAZU01 sp017452885	77.3042	80	558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__CAZU01	95.0	99.01	99.01	0.81	0.81	2	-
GCA_900540425.1	s__MGBC133411 sp900540425	77.1855	103	558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__MGBC133411	95.0	99.13	99.08	0.91	0.88	3	-
--------------------------------------------------------------------------------
[2023-06-17 03:15:01,626] [INFO] GTDB search result was written to GCA_905206785.1_ERR1600683-mag-bin.57_genomic.fna/result_gtdb.tsv
[2023-06-17 03:15:01,627] [INFO] ===== GTDB Search completed =====
[2023-06-17 03:15:01,630] [INFO] DFAST_QC result json was written to GCA_905206785.1_ERR1600683-mag-bin.57_genomic.fna/dqc_result.json
[2023-06-17 03:15:01,630] [INFO] DFAST_QC completed!
[2023-06-17 03:15:01,631] [INFO] Total running time: 0h0m50s