[2023-06-17 12:35:23,398] [INFO] DFAST_QC pipeline started.
[2023-06-17 12:35:23,400] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 12:35:23,401] [INFO] DQC Reference Directory: /var/lib/cwl/stg05181f2d-066b-4ddb-8c09-6a266db8dc7a/dqc_reference
[2023-06-17 12:35:25,351] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 12:35:25,352] [INFO] Task started: Prodigal
[2023-06-17 12:35:25,352] [INFO] Running command: gunzip -c /var/lib/cwl/stg600bfe88-7e23-45f3-a8ca-13983e2bb101/GCA_905477775.1_0.2_20180319_Bin_18_alpha_genomic.fna.gz | prodigal -d GCA_905477775.1_0.2_20180319_Bin_18_alpha_genomic.fna/cds.fna -a GCA_905477775.1_0.2_20180319_Bin_18_alpha_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 12:35:28,214] [INFO] Task succeeded: Prodigal
[2023-06-17 12:35:28,215] [INFO] Task started: HMMsearch
[2023-06-17 12:35:28,215] [INFO] Running command: hmmsearch --tblout GCA_905477775.1_0.2_20180319_Bin_18_alpha_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05181f2d-066b-4ddb-8c09-6a266db8dc7a/dqc_reference/reference_markers.hmm GCA_905477775.1_0.2_20180319_Bin_18_alpha_genomic.fna/protein.faa > /dev/null
[2023-06-17 12:35:28,454] [INFO] Task succeeded: HMMsearch
[2023-06-17 12:35:28,456] [INFO] Found 6/6 markers.
[2023-06-17 12:35:28,475] [INFO] Query marker FASTA was written to GCA_905477775.1_0.2_20180319_Bin_18_alpha_genomic.fna/markers.fasta
[2023-06-17 12:35:28,476] [INFO] Task started: Blastn
[2023-06-17 12:35:28,476] [INFO] Running command: blastn -query GCA_905477775.1_0.2_20180319_Bin_18_alpha_genomic.fna/markers.fasta -db /var/lib/cwl/stg05181f2d-066b-4ddb-8c09-6a266db8dc7a/dqc_reference/reference_markers.fasta -out GCA_905477775.1_0.2_20180319_Bin_18_alpha_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 12:35:29,951] [INFO] Task succeeded: Blastn
[2023-06-17 12:35:29,956] [INFO] Selected 29 target genomes.
[2023-06-17 12:35:29,956] [INFO] Target genome list was writen to GCA_905477775.1_0.2_20180319_Bin_18_alpha_genomic.fna/target_genomes.txt
[2023-06-17 12:35:29,972] [INFO] Task started: fastANI
[2023-06-17 12:35:29,972] [INFO] Running command: fastANI --query /var/lib/cwl/stg600bfe88-7e23-45f3-a8ca-13983e2bb101/GCA_905477775.1_0.2_20180319_Bin_18_alpha_genomic.fna.gz --refList GCA_905477775.1_0.2_20180319_Bin_18_alpha_genomic.fna/target_genomes.txt --output GCA_905477775.1_0.2_20180319_Bin_18_alpha_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 12:35:45,635] [INFO] Task succeeded: fastANI
[2023-06-17 12:35:45,636] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05181f2d-066b-4ddb-8c09-6a266db8dc7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 12:35:45,636] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05181f2d-066b-4ddb-8c09-6a266db8dc7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 12:35:45,638] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 12:35:45,638] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 12:35:45,639] [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 12:35:45,641] [INFO] DFAST Taxonomy check result was written to GCA_905477775.1_0.2_20180319_Bin_18_alpha_genomic.fna/tc_result.tsv
[2023-06-17 12:35:45,642] [INFO] ===== Taxonomy check completed =====
[2023-06-17 12:35:45,642] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 12:35:45,643] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05181f2d-066b-4ddb-8c09-6a266db8dc7a/dqc_reference/checkm_data
[2023-06-17 12:35:45,647] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 12:35:45,664] [INFO] Task started: CheckM
[2023-06-17 12:35:45,664] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905477775.1_0.2_20180319_Bin_18_alpha_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905477775.1_0.2_20180319_Bin_18_alpha_genomic.fna/checkm_input GCA_905477775.1_0.2_20180319_Bin_18_alpha_genomic.fna/checkm_result
[2023-06-17 12:36:02,052] [INFO] Task succeeded: CheckM
[2023-06-17 12:36:02,053] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 12:36:02,073] [INFO] ===== Completeness check finished =====
[2023-06-17 12:36:02,074] [INFO] ===== Start GTDB Search =====
[2023-06-17 12:36:02,074] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905477775.1_0.2_20180319_Bin_18_alpha_genomic.fna/markers.fasta)
[2023-06-17 12:36:02,074] [INFO] Task started: Blastn
[2023-06-17 12:36:02,075] [INFO] Running command: blastn -query GCA_905477775.1_0.2_20180319_Bin_18_alpha_genomic.fna/markers.fasta -db /var/lib/cwl/stg05181f2d-066b-4ddb-8c09-6a266db8dc7a/dqc_reference/reference_markers_gtdb.fasta -out GCA_905477775.1_0.2_20180319_Bin_18_alpha_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 12:36:03,055] [INFO] Task succeeded: Blastn
[2023-06-17 12:36:03,060] [INFO] Selected 9 target genomes.
[2023-06-17 12:36:03,060] [INFO] Target genome list was writen to GCA_905477775.1_0.2_20180319_Bin_18_alpha_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 12:36:03,072] [INFO] Task started: fastANI
[2023-06-17 12:36:03,072] [INFO] Running command: fastANI --query /var/lib/cwl/stg600bfe88-7e23-45f3-a8ca-13983e2bb101/GCA_905477775.1_0.2_20180319_Bin_18_alpha_genomic.fna.gz --refList GCA_905477775.1_0.2_20180319_Bin_18_alpha_genomic.fna/target_genomes_gtdb.txt --output GCA_905477775.1_0.2_20180319_Bin_18_alpha_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 12:36:05,141] [INFO] Task succeeded: fastANI
[2023-06-17 12:36:05,149] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 12:36:05,149] [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_004214015.1	s__MED-G11 sp004214015	97.7699	210	330	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	97.90	97.77	0.83	0.80	4	conclusive
GCA_016777325.1	s__MED-G11 sp016777325	92.0055	185	330	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902509805.1	s__MED-G11 sp902509805	90.2867	153	330	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	97.79	97.79	0.58	0.58	2	-
GCA_018646865.1	s__MED-G11 sp014239615	86.2734	268	330	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	99.76	99.49	0.92	0.80	17	-
GCA_902514615.1	s__MED-G11 sp902514615	84.4993	218	330	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239665.1	s__MED-G11 sp014239665	83.909	240	330	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	96.49	96.27	0.81	0.77	10	-
GCA_002457075.1	s__MED-G11 sp002457075	83.3221	190	330	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	98.35	98.35	0.79	0.79	2	-
GCA_902622595.1	s__MED-G11 sp902622595	78.9542	198	330	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	96.81	96.16	0.93	0.91	12	-
GCA_016780245.1	s__MED-G11 sp016780245	78.7438	134	330	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	99.94	99.94	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-06-17 12:36:05,151] [INFO] GTDB search result was written to GCA_905477775.1_0.2_20180319_Bin_18_alpha_genomic.fna/result_gtdb.tsv
[2023-06-17 12:36:05,152] [INFO] ===== GTDB Search completed =====
[2023-06-17 12:36:05,155] [INFO] DFAST_QC result json was written to GCA_905477775.1_0.2_20180319_Bin_18_alpha_genomic.fna/dqc_result.json
[2023-06-17 12:36:05,155] [INFO] DFAST_QC completed!
[2023-06-17 12:36:05,155] [INFO] Total running time: 0h0m42s