[2023-06-30 16:28:54,068] [INFO] DFAST_QC pipeline started.
[2023-06-30 16:28:54,087] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 16:28:54,087] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e1694b1-c9eb-49e9-9268-4b65a2850589/dqc_reference
[2023-06-30 16:28:56,563] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 16:28:56,564] [INFO] Task started: Prodigal
[2023-06-30 16:28:56,565] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b1cee74-51ad-4805-8d09-8a20b8de1943/GCA_903844735.1_freshwater_MAG_---_Loclat_bin-10216_genomic.fna.gz | prodigal -d GCA_903844735.1_freshwater_MAG_---_Loclat_bin-10216_genomic.fna/cds.fna -a GCA_903844735.1_freshwater_MAG_---_Loclat_bin-10216_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 16:29:12,192] [INFO] Task succeeded: Prodigal
[2023-06-30 16:29:12,192] [INFO] Task started: HMMsearch
[2023-06-30 16:29:12,192] [INFO] Running command: hmmsearch --tblout GCA_903844735.1_freshwater_MAG_---_Loclat_bin-10216_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e1694b1-c9eb-49e9-9268-4b65a2850589/dqc_reference/reference_markers.hmm GCA_903844735.1_freshwater_MAG_---_Loclat_bin-10216_genomic.fna/protein.faa > /dev/null
[2023-06-30 16:29:12,555] [INFO] Task succeeded: HMMsearch
[2023-06-30 16:29:12,556] [INFO] Found 6/6 markers.
[2023-06-30 16:29:12,613] [INFO] Query marker FASTA was written to GCA_903844735.1_freshwater_MAG_---_Loclat_bin-10216_genomic.fna/markers.fasta
[2023-06-30 16:29:12,613] [INFO] Task started: Blastn
[2023-06-30 16:29:12,614] [INFO] Running command: blastn -query GCA_903844735.1_freshwater_MAG_---_Loclat_bin-10216_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e1694b1-c9eb-49e9-9268-4b65a2850589/dqc_reference/reference_markers.fasta -out GCA_903844735.1_freshwater_MAG_---_Loclat_bin-10216_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 16:29:13,212] [INFO] Task succeeded: Blastn
[2023-06-30 16:29:13,217] [INFO] Selected 20 target genomes.
[2023-06-30 16:29:13,217] [INFO] Target genome list was writen to GCA_903844735.1_freshwater_MAG_---_Loclat_bin-10216_genomic.fna/target_genomes.txt
[2023-06-30 16:29:13,228] [INFO] Task started: fastANI
[2023-06-30 16:29:13,228] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b1cee74-51ad-4805-8d09-8a20b8de1943/GCA_903844735.1_freshwater_MAG_---_Loclat_bin-10216_genomic.fna.gz --refList GCA_903844735.1_freshwater_MAG_---_Loclat_bin-10216_genomic.fna/target_genomes.txt --output GCA_903844735.1_freshwater_MAG_---_Loclat_bin-10216_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 16:29:29,000] [INFO] Task succeeded: fastANI
[2023-06-30 16:29:29,001] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e1694b1-c9eb-49e9-9268-4b65a2850589/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 16:29:29,001] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e1694b1-c9eb-49e9-9268-4b65a2850589/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 16:29:29,013] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 16:29:29,013] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 16:29:29,013] [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
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	74.9453	69	1727	95	below_threshold
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	74.8431	83	1727	95	below_threshold
Acuticoccus kandeliae	strain=J103	GCA_003073115.1	2073160	2073160	type	True	74.6933	58	1727	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	74.6856	76	1727	95	below_threshold
Lentzea albida	strain=DSM 44437	GCA_900111005.1	65499	65499	type	True	74.5919	68	1727	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 16:29:29,018] [INFO] DFAST Taxonomy check result was written to GCA_903844735.1_freshwater_MAG_---_Loclat_bin-10216_genomic.fna/tc_result.tsv
[2023-06-30 16:29:29,018] [INFO] ===== Taxonomy check completed =====
[2023-06-30 16:29:29,019] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 16:29:29,019] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e1694b1-c9eb-49e9-9268-4b65a2850589/dqc_reference/checkm_data
[2023-06-30 16:29:29,021] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 16:29:29,077] [INFO] Task started: CheckM
[2023-06-30 16:29:29,078] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903844735.1_freshwater_MAG_---_Loclat_bin-10216_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903844735.1_freshwater_MAG_---_Loclat_bin-10216_genomic.fna/checkm_input GCA_903844735.1_freshwater_MAG_---_Loclat_bin-10216_genomic.fna/checkm_result
[2023-06-30 16:30:14,875] [INFO] Task succeeded: CheckM
[2023-06-30 16:30:14,876] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 16:30:14,901] [INFO] ===== Completeness check finished =====
[2023-06-30 16:30:14,902] [INFO] ===== Start GTDB Search =====
[2023-06-30 16:30:14,902] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903844735.1_freshwater_MAG_---_Loclat_bin-10216_genomic.fna/markers.fasta)
[2023-06-30 16:30:14,903] [INFO] Task started: Blastn
[2023-06-30 16:30:14,903] [INFO] Running command: blastn -query GCA_903844735.1_freshwater_MAG_---_Loclat_bin-10216_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e1694b1-c9eb-49e9-9268-4b65a2850589/dqc_reference/reference_markers_gtdb.fasta -out GCA_903844735.1_freshwater_MAG_---_Loclat_bin-10216_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 16:30:15,681] [INFO] Task succeeded: Blastn
[2023-06-30 16:30:15,686] [INFO] Selected 19 target genomes.
[2023-06-30 16:30:15,686] [INFO] Target genome list was writen to GCA_903844735.1_freshwater_MAG_---_Loclat_bin-10216_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 16:30:15,715] [INFO] Task started: fastANI
[2023-06-30 16:30:15,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b1cee74-51ad-4805-8d09-8a20b8de1943/GCA_903844735.1_freshwater_MAG_---_Loclat_bin-10216_genomic.fna.gz --refList GCA_903844735.1_freshwater_MAG_---_Loclat_bin-10216_genomic.fna/target_genomes_gtdb.txt --output GCA_903844735.1_freshwater_MAG_---_Loclat_bin-10216_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 16:30:28,206] [INFO] Task succeeded: fastANI
[2023-06-30 16:30:28,216] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 16:30:28,216] [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_903844735.1	s__CAIMUX01 sp903844735	100.0	1721	1727	d__Bacteria;p__Eisenbacteria;c__RBG-16-71-46;o__CAIMUX01;f__CAIMUX01;g__CAIMUX01	95.0	99.95	99.95	0.96	0.96	2	conclusive
GCA_016867495.1	s__VGJL01 sp016867495	75.9455	67	1727	d__Bacteria;p__Eisenbacteria;c__RBG-16-71-46;o__CAIMUX01;f__VGJL01;g__VGJL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903921835.1	s__CAIXRL01 sp903921835	75.5992	55	1727	d__Bacteria;p__Eisenbacteria;c__RBG-16-71-46;o__RBG-16-71-46;f__RBG-16-71-46;g__CAIXRL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235265.1	s__JACRLI01 sp016235265	75.3803	55	1727	d__Bacteria;p__Eisenbacteria;c__RBG-16-71-46;o__RBG-16-71-46;f__JACRLI01;g__JACRLI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111005.1	s__Lentzea albida	74.5919	68	1727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 16:30:28,218] [INFO] GTDB search result was written to GCA_903844735.1_freshwater_MAG_---_Loclat_bin-10216_genomic.fna/result_gtdb.tsv
[2023-06-30 16:30:28,219] [INFO] ===== GTDB Search completed =====
[2023-06-30 16:30:28,222] [INFO] DFAST_QC result json was written to GCA_903844735.1_freshwater_MAG_---_Loclat_bin-10216_genomic.fna/dqc_result.json
[2023-06-30 16:30:28,222] [INFO] DFAST_QC completed!
[2023-06-30 16:30:28,222] [INFO] Total running time: 0h1m34s