[2023-06-17 11:44:00,005] [INFO] DFAST_QC pipeline started.
[2023-06-17 11:44:00,009] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 11:44:00,009] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0c73b65-019e-4ef3-bd2a-da9a236d61f0/dqc_reference
[2023-06-17 11:44:01,751] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 11:44:01,752] [INFO] Task started: Prodigal
[2023-06-17 11:44:01,752] [INFO] Running command: gunzip -c /var/lib/cwl/stge0e6ceae-1279-4727-a852-ca62f8a00754/GCA_003331865.1_ASM333186v1_genomic.fna.gz | prodigal -d GCA_003331865.1_ASM333186v1_genomic.fna/cds.fna -a GCA_003331865.1_ASM333186v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 11:44:03,991] [INFO] Task succeeded: Prodigal
[2023-06-17 11:44:03,991] [INFO] Task started: HMMsearch
[2023-06-17 11:44:03,991] [INFO] Running command: hmmsearch --tblout GCA_003331865.1_ASM333186v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0c73b65-019e-4ef3-bd2a-da9a236d61f0/dqc_reference/reference_markers.hmm GCA_003331865.1_ASM333186v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 11:44:04,216] [INFO] Task succeeded: HMMsearch
[2023-06-17 11:44:04,217] [INFO] Found 6/6 markers.
[2023-06-17 11:44:04,235] [INFO] Query marker FASTA was written to GCA_003331865.1_ASM333186v1_genomic.fna/markers.fasta
[2023-06-17 11:44:04,235] [INFO] Task started: Blastn
[2023-06-17 11:44:04,235] [INFO] Running command: blastn -query GCA_003331865.1_ASM333186v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0c73b65-019e-4ef3-bd2a-da9a236d61f0/dqc_reference/reference_markers.fasta -out GCA_003331865.1_ASM333186v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:44:05,750] [INFO] Task succeeded: Blastn
[2023-06-17 11:44:05,757] [INFO] Selected 23 target genomes.
[2023-06-17 11:44:05,758] [INFO] Target genome list was writen to GCA_003331865.1_ASM333186v1_genomic.fna/target_genomes.txt
[2023-06-17 11:44:05,812] [INFO] Task started: fastANI
[2023-06-17 11:44:05,813] [INFO] Running command: fastANI --query /var/lib/cwl/stge0e6ceae-1279-4727-a852-ca62f8a00754/GCA_003331865.1_ASM333186v1_genomic.fna.gz --refList GCA_003331865.1_ASM333186v1_genomic.fna/target_genomes.txt --output GCA_003331865.1_ASM333186v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 11:44:18,536] [INFO] Task succeeded: fastANI
[2023-06-17 11:44:18,537] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0c73b65-019e-4ef3-bd2a-da9a236d61f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 11:44:18,537] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0c73b65-019e-4ef3-bd2a-da9a236d61f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 11:44:18,539] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 11:44:18,540] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 11:44:18,540] [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 11:44:18,543] [INFO] DFAST Taxonomy check result was written to GCA_003331865.1_ASM333186v1_genomic.fna/tc_result.tsv
[2023-06-17 11:44:18,544] [INFO] ===== Taxonomy check completed =====
[2023-06-17 11:44:18,544] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 11:44:18,544] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0c73b65-019e-4ef3-bd2a-da9a236d61f0/dqc_reference/checkm_data
[2023-06-17 11:44:18,549] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 11:44:18,564] [INFO] Task started: CheckM
[2023-06-17 11:44:18,564] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003331865.1_ASM333186v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003331865.1_ASM333186v1_genomic.fna/checkm_input GCA_003331865.1_ASM333186v1_genomic.fna/checkm_result
[2023-06-17 11:44:33,603] [INFO] Task succeeded: CheckM
[2023-06-17 11:44:33,605] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.73%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 11:44:33,626] [INFO] ===== Completeness check finished =====
[2023-06-17 11:44:33,627] [INFO] ===== Start GTDB Search =====
[2023-06-17 11:44:33,627] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003331865.1_ASM333186v1_genomic.fna/markers.fasta)
[2023-06-17 11:44:33,628] [INFO] Task started: Blastn
[2023-06-17 11:44:33,628] [INFO] Running command: blastn -query GCA_003331865.1_ASM333186v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0c73b65-019e-4ef3-bd2a-da9a236d61f0/dqc_reference/reference_markers_gtdb.fasta -out GCA_003331865.1_ASM333186v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:44:34,447] [INFO] Task succeeded: Blastn
[2023-06-17 11:44:34,451] [INFO] Selected 15 target genomes.
[2023-06-17 11:44:34,451] [INFO] Target genome list was writen to GCA_003331865.1_ASM333186v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 11:44:34,461] [INFO] Task started: fastANI
[2023-06-17 11:44:34,462] [INFO] Running command: fastANI --query /var/lib/cwl/stge0e6ceae-1279-4727-a852-ca62f8a00754/GCA_003331865.1_ASM333186v1_genomic.fna.gz --refList GCA_003331865.1_ASM333186v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003331865.1_ASM333186v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 11:44:39,211] [INFO] Task succeeded: fastANI
[2023-06-17 11:44:39,228] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 11:44:39,229] [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_004214185.1	s__MAG-121220-bin8 sp004214185	96.514	217	260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	96.26	95.81	0.84	0.82	5	conclusive
GCA_902635895.1	s__MAG-121220-bin8 sp902635895	79.8975	134	260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	96.57	96.57	0.70	0.70	2	-
GCA_902559035.1	s__MAG-121220-bin8 sp902559035	79.3787	165	260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	96.40	96.04	0.82	0.79	6	-
GCA_016780345.1	s__MAG-121220-bin8 sp016780345	79.2939	133	260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.67	99.67	0.79	0.79	2	-
GCA_902510655.1	s__MAG-121220-bin8 sp902510655	78.433	91	260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182765.1	s__MAG-121220-bin8 sp905182765	78.3758	131	260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700465.1	s__MAG-121220-bin8 sp002700465	78.2486	106	260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.15	98.67	0.80	0.80	3	-
GCA_018662905.1	s__MAG-121220-bin8 sp018662905	77.9428	93	260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.06	99.06	0.75	0.75	2	-
GCA_014239275.1	s__MAG-121220-bin8 sp014239275	77.5245	87	260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.08	98.67	0.74	0.67	4	-
GCA_905181625.1	s__MAG-121220-bin8 sp905181625	77.4643	98	260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012959395.1	s__MAG-121220-bin8 sp012959395	77.3718	97	260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	97.96	97.81	0.81	0.77	13	-
GCA_902511755.1	s__MAG-121220-bin8 sp902511755	77.2711	75	260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.22	98.71	0.74	0.72	3	-
GCA_003331265.1	s__MAG-121220-bin8 sp003331265	77.1839	93	260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181705.1	s__MAG-121220-bin8 sp905181705	76.91	98	260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 11:44:39,231] [INFO] GTDB search result was written to GCA_003331865.1_ASM333186v1_genomic.fna/result_gtdb.tsv
[2023-06-17 11:44:39,232] [INFO] ===== GTDB Search completed =====
[2023-06-17 11:44:39,237] [INFO] DFAST_QC result json was written to GCA_003331865.1_ASM333186v1_genomic.fna/dqc_result.json
[2023-06-17 11:44:39,238] [INFO] DFAST_QC completed!
[2023-06-17 11:44:39,238] [INFO] Total running time: 0h0m39s