[2023-06-28 12:02:30,595] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:02:30,597] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:02:30,598] [INFO] DQC Reference Directory: /var/lib/cwl/stga61d8d7e-5f70-47f4-9aa6-4d7f61bc8225/dqc_reference
[2023-06-28 12:02:31,899] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:02:31,900] [INFO] Task started: Prodigal
[2023-06-28 12:02:31,900] [INFO] Running command: gunzip -c /var/lib/cwl/stga6be6fd0-065c-49b5-b757-c155454067a4/GCA_015069505.1_ASM1506950v1_genomic.fna.gz | prodigal -d GCA_015069505.1_ASM1506950v1_genomic.fna/cds.fna -a GCA_015069505.1_ASM1506950v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:02:34,469] [INFO] Task succeeded: Prodigal
[2023-06-28 12:02:34,470] [INFO] Task started: HMMsearch
[2023-06-28 12:02:34,470] [INFO] Running command: hmmsearch --tblout GCA_015069505.1_ASM1506950v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga61d8d7e-5f70-47f4-9aa6-4d7f61bc8225/dqc_reference/reference_markers.hmm GCA_015069505.1_ASM1506950v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:02:34,702] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:02:34,703] [INFO] Found 6/6 markers.
[2023-06-28 12:02:34,721] [INFO] Query marker FASTA was written to GCA_015069505.1_ASM1506950v1_genomic.fna/markers.fasta
[2023-06-28 12:02:34,722] [INFO] Task started: Blastn
[2023-06-28 12:02:34,722] [INFO] Running command: blastn -query GCA_015069505.1_ASM1506950v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga61d8d7e-5f70-47f4-9aa6-4d7f61bc8225/dqc_reference/reference_markers.fasta -out GCA_015069505.1_ASM1506950v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:02:35,350] [INFO] Task succeeded: Blastn
[2023-06-28 12:02:35,355] [INFO] Selected 23 target genomes.
[2023-06-28 12:02:35,355] [INFO] Target genome list was writen to GCA_015069505.1_ASM1506950v1_genomic.fna/target_genomes.txt
[2023-06-28 12:02:35,370] [INFO] Task started: fastANI
[2023-06-28 12:02:35,370] [INFO] Running command: fastANI --query /var/lib/cwl/stga6be6fd0-065c-49b5-b757-c155454067a4/GCA_015069505.1_ASM1506950v1_genomic.fna.gz --refList GCA_015069505.1_ASM1506950v1_genomic.fna/target_genomes.txt --output GCA_015069505.1_ASM1506950v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:02:46,075] [INFO] Task succeeded: fastANI
[2023-06-28 12:02:46,076] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga61d8d7e-5f70-47f4-9aa6-4d7f61bc8225/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:02:46,076] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga61d8d7e-5f70-47f4-9aa6-4d7f61bc8225/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:02:46,078] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:02:46,078] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 12:02:46,079] [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
--------------------------------------------------------------------------------
[2023-06-28 12:02:46,081] [INFO] DFAST Taxonomy check result was written to GCA_015069505.1_ASM1506950v1_genomic.fna/tc_result.tsv
[2023-06-28 12:02:46,082] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:02:46,082] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:02:46,083] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga61d8d7e-5f70-47f4-9aa6-4d7f61bc8225/dqc_reference/checkm_data
[2023-06-28 12:02:46,087] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:02:46,108] [INFO] Task started: CheckM
[2023-06-28 12:02:46,109] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015069505.1_ASM1506950v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015069505.1_ASM1506950v1_genomic.fna/checkm_input GCA_015069505.1_ASM1506950v1_genomic.fna/checkm_result
[2023-06-28 12:03:02,803] [INFO] Task succeeded: CheckM
[2023-06-28 12:03:02,805] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.38%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 12:03:02,830] [INFO] ===== Completeness check finished =====
[2023-06-28 12:03:02,831] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:03:02,831] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015069505.1_ASM1506950v1_genomic.fna/markers.fasta)
[2023-06-28 12:03:02,831] [INFO] Task started: Blastn
[2023-06-28 12:03:02,831] [INFO] Running command: blastn -query GCA_015069505.1_ASM1506950v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga61d8d7e-5f70-47f4-9aa6-4d7f61bc8225/dqc_reference/reference_markers_gtdb.fasta -out GCA_015069505.1_ASM1506950v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:03:03,942] [INFO] Task succeeded: Blastn
[2023-06-28 12:03:03,947] [INFO] Selected 20 target genomes.
[2023-06-28 12:03:03,948] [INFO] Target genome list was writen to GCA_015069505.1_ASM1506950v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:03:03,968] [INFO] Task started: fastANI
[2023-06-28 12:03:03,969] [INFO] Running command: fastANI --query /var/lib/cwl/stga6be6fd0-065c-49b5-b757-c155454067a4/GCA_015069505.1_ASM1506950v1_genomic.fna.gz --refList GCA_015069505.1_ASM1506950v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015069505.1_ASM1506950v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:03:09,551] [INFO] Task succeeded: fastANI
[2023-06-28 12:03:09,568] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:03:09,569] [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_015069505.1	s__UBA1259 sp015069505	99.9999	400	404	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA1259	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905211955.1	s__UBA1259 sp905211955	78.4082	65	404	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA1259	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015055725.1	s__UBA1259 sp015055725	78.1912	79	404	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA1259	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017502525.1	s__UBA1259 sp017502525	78.0622	86	404	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA1259	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017465145.1	s__UBA1259 sp017465145	78.0418	80	404	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA1259	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017648525.1	s__UBA1259 sp017648525	77.9181	72	404	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA1259	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017621955.1	s__UBA1259 sp017621955	77.9101	75	404	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA1259	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900769565.1	s__UBA1259 sp900769565	77.8507	71	404	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA1259	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015055945.1	s__UBA1259 sp015055945	77.8168	72	404	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA1259	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904501795.1	s__UBA1259 sp904501795	77.7244	85	404	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA1259	95.0	100.00	100.00	0.99	0.99	2	-
GCA_017397305.1	s__UBA1259 sp017397305	77.6775	76	404	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA1259	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017399035.1	s__UBA1259 sp017399035	77.6662	69	404	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA1259	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015055805.1	s__UBA1259 sp015055805	77.6047	83	404	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA1259	95.0	98.31	98.31	0.82	0.82	2	-
GCA_017554545.1	s__UBA1259 sp017554545	77.4788	52	404	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA1259	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017399945.1	s__UBA1259 sp017399945	77.458	77	404	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA1259	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902767225.1	s__UBA1259 sp902767225	77.2504	50	404	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA1259	95.0	98.80	98.80	0.92	0.92	2	-
GCA_015069265.1	s__UBA1259 sp015069265	77.136	72	404	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA1259	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904502225.1	s__UBA1259 sp904502225	76.8919	72	404	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA1259	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-28 12:03:09,571] [INFO] GTDB search result was written to GCA_015069505.1_ASM1506950v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:03:09,572] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:03:09,575] [INFO] DFAST_QC result json was written to GCA_015069505.1_ASM1506950v1_genomic.fna/dqc_result.json
[2023-06-28 12:03:09,575] [INFO] DFAST_QC completed!
[2023-06-28 12:03:09,575] [INFO] Total running time: 0h0m39s