[2023-06-27 20:56:34,811] [INFO] DFAST_QC pipeline started.
[2023-06-27 20:56:34,814] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 20:56:34,815] [INFO] DQC Reference Directory: /var/lib/cwl/stg21087211-b64f-4d4b-a1e7-acb5c1928268/dqc_reference
[2023-06-27 20:56:36,079] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 20:56:36,080] [INFO] Task started: Prodigal
[2023-06-27 20:56:36,080] [INFO] Running command: gunzip -c /var/lib/cwl/stg94fe1593-c02b-4735-9bfc-42959add648f/GCA_002310155.1_ASM231015v1_genomic.fna.gz | prodigal -d GCA_002310155.1_ASM231015v1_genomic.fna/cds.fna -a GCA_002310155.1_ASM231015v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 20:56:41,067] [INFO] Task succeeded: Prodigal
[2023-06-27 20:56:41,067] [INFO] Task started: HMMsearch
[2023-06-27 20:56:41,067] [INFO] Running command: hmmsearch --tblout GCA_002310155.1_ASM231015v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg21087211-b64f-4d4b-a1e7-acb5c1928268/dqc_reference/reference_markers.hmm GCA_002310155.1_ASM231015v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 20:56:41,332] [INFO] Task succeeded: HMMsearch
[2023-06-27 20:56:41,333] [INFO] Found 6/6 markers.
[2023-06-27 20:56:41,361] [INFO] Query marker FASTA was written to GCA_002310155.1_ASM231015v1_genomic.fna/markers.fasta
[2023-06-27 20:56:41,361] [INFO] Task started: Blastn
[2023-06-27 20:56:41,362] [INFO] Running command: blastn -query GCA_002310155.1_ASM231015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21087211-b64f-4d4b-a1e7-acb5c1928268/dqc_reference/reference_markers.fasta -out GCA_002310155.1_ASM231015v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 20:56:41,975] [INFO] Task succeeded: Blastn
[2023-06-27 20:56:41,979] [INFO] Selected 20 target genomes.
[2023-06-27 20:56:41,979] [INFO] Target genome list was writen to GCA_002310155.1_ASM231015v1_genomic.fna/target_genomes.txt
[2023-06-27 20:56:41,982] [INFO] Task started: fastANI
[2023-06-27 20:56:41,982] [INFO] Running command: fastANI --query /var/lib/cwl/stg94fe1593-c02b-4735-9bfc-42959add648f/GCA_002310155.1_ASM231015v1_genomic.fna.gz --refList GCA_002310155.1_ASM231015v1_genomic.fna/target_genomes.txt --output GCA_002310155.1_ASM231015v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 20:56:52,888] [INFO] Task succeeded: fastANI
[2023-06-27 20:56:52,889] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg21087211-b64f-4d4b-a1e7-acb5c1928268/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 20:56:52,890] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg21087211-b64f-4d4b-a1e7-acb5c1928268/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 20:56:52,891] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 20:56:52,891] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 20:56:52,892] [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
--------------------------------------------------------------------------------
[2023-06-27 20:56:52,893] [INFO] DFAST Taxonomy check result was written to GCA_002310155.1_ASM231015v1_genomic.fna/tc_result.tsv
[2023-06-27 20:56:52,894] [INFO] ===== Taxonomy check completed =====
[2023-06-27 20:56:52,894] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 20:56:52,895] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg21087211-b64f-4d4b-a1e7-acb5c1928268/dqc_reference/checkm_data
[2023-06-27 20:56:52,897] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 20:56:52,926] [INFO] Task started: CheckM
[2023-06-27 20:56:52,926] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002310155.1_ASM231015v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002310155.1_ASM231015v1_genomic.fna/checkm_input GCA_002310155.1_ASM231015v1_genomic.fna/checkm_result
[2023-06-27 20:57:14,739] [INFO] Task succeeded: CheckM
[2023-06-27 20:57:14,740] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 20:57:14,761] [INFO] ===== Completeness check finished =====
[2023-06-27 20:57:14,761] [INFO] ===== Start GTDB Search =====
[2023-06-27 20:57:14,762] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002310155.1_ASM231015v1_genomic.fna/markers.fasta)
[2023-06-27 20:57:14,762] [INFO] Task started: Blastn
[2023-06-27 20:57:14,762] [INFO] Running command: blastn -query GCA_002310155.1_ASM231015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21087211-b64f-4d4b-a1e7-acb5c1928268/dqc_reference/reference_markers_gtdb.fasta -out GCA_002310155.1_ASM231015v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 20:57:15,669] [INFO] Task succeeded: Blastn
[2023-06-27 20:57:15,674] [INFO] Selected 12 target genomes.
[2023-06-27 20:57:15,675] [INFO] Target genome list was writen to GCA_002310155.1_ASM231015v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 20:57:15,684] [INFO] Task started: fastANI
[2023-06-27 20:57:15,684] [INFO] Running command: fastANI --query /var/lib/cwl/stg94fe1593-c02b-4735-9bfc-42959add648f/GCA_002310155.1_ASM231015v1_genomic.fna.gz --refList GCA_002310155.1_ASM231015v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002310155.1_ASM231015v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 20:57:22,141] [INFO] Task succeeded: fastANI
[2023-06-27 20:57:22,156] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 20:57:22,156] [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_002310155.1	s__Firm-16 sp002310155	100.0	679	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Firm-16	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017519205.1	s__Firm-16 sp017519205	84.0268	394	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Firm-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017617525.1	s__Firm-16 sp017617525	83.7385	440	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Firm-16	95.0	98.00	98.00	0.90	0.90	2	-
GCA_017561715.1	s__Firm-16 sp017561715	83.6271	435	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Firm-16	95.0	97.23	97.10	0.89	0.87	4	-
GCA_900317035.1	s__Firm-16 sp900317035	83.2291	428	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Firm-16	95.0	98.62	96.93	0.90	0.81	6	-
GCA_017961235.1	s__Firm-16 sp017961235	82.978	473	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Firm-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002368805.1	s__Firm-16 sp002368805	82.9017	422	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Firm-16	95.0	98.86	98.65	0.90	0.86	4	-
GCA_017428545.1	s__Firm-16 sp017428545	82.4533	441	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Firm-16	95.0	98.00	97.90	0.86	0.80	3	-
GCA_016287245.1	s__Firm-16 sp016287245	82.0284	403	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Firm-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017551865.1	s__Firm-16 sp017551865	81.8746	399	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Firm-16	95.0	96.84	96.84	0.88	0.88	2	-
GCA_905235455.1	s__Firm-16 sp905235455	81.6501	333	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Firm-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017649745.1	s__Saccharofermentans sp017649745	78.8326	57	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Saccharofermentans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 20:57:22,158] [INFO] GTDB search result was written to GCA_002310155.1_ASM231015v1_genomic.fna/result_gtdb.tsv
[2023-06-27 20:57:22,159] [INFO] ===== GTDB Search completed =====
[2023-06-27 20:57:22,162] [INFO] DFAST_QC result json was written to GCA_002310155.1_ASM231015v1_genomic.fna/dqc_result.json
[2023-06-27 20:57:22,162] [INFO] DFAST_QC completed!
[2023-06-27 20:57:22,162] [INFO] Total running time: 0h0m47s