[2024-01-24 13:25:28,962] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:28,964] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:28,965] [INFO] DQC Reference Directory: /var/lib/cwl/stgab7b48f9-827b-44b8-b71b-b1010dd7d5c7/dqc_reference
[2024-01-24 13:25:30,423] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:30,424] [INFO] Task started: Prodigal
[2024-01-24 13:25:30,424] [INFO] Running command: gunzip -c /var/lib/cwl/stge857d1e3-24ee-461a-9993-5588a86d7639/GCF_900604345.1_PRJEB24952_genomic.fna.gz | prodigal -d GCF_900604345.1_PRJEB24952_genomic.fna/cds.fna -a GCF_900604345.1_PRJEB24952_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:39,097] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:39,097] [INFO] Task started: HMMsearch
[2024-01-24 13:25:39,097] [INFO] Running command: hmmsearch --tblout GCF_900604345.1_PRJEB24952_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab7b48f9-827b-44b8-b71b-b1010dd7d5c7/dqc_reference/reference_markers.hmm GCF_900604345.1_PRJEB24952_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:39,351] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:39,352] [INFO] Found 6/6 markers.
[2024-01-24 13:25:39,376] [INFO] Query marker FASTA was written to GCF_900604345.1_PRJEB24952_genomic.fna/markers.fasta
[2024-01-24 13:25:39,376] [INFO] Task started: Blastn
[2024-01-24 13:25:39,376] [INFO] Running command: blastn -query GCF_900604345.1_PRJEB24952_genomic.fna/markers.fasta -db /var/lib/cwl/stgab7b48f9-827b-44b8-b71b-b1010dd7d5c7/dqc_reference/reference_markers.fasta -out GCF_900604345.1_PRJEB24952_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:40,027] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:40,031] [INFO] Selected 31 target genomes.
[2024-01-24 13:25:40,032] [INFO] Target genome list was writen to GCF_900604345.1_PRJEB24952_genomic.fna/target_genomes.txt
[2024-01-24 13:25:40,360] [INFO] Task started: fastANI
[2024-01-24 13:25:40,360] [INFO] Running command: fastANI --query /var/lib/cwl/stge857d1e3-24ee-461a-9993-5588a86d7639/GCF_900604345.1_PRJEB24952_genomic.fna.gz --refList GCF_900604345.1_PRJEB24952_genomic.fna/target_genomes.txt --output GCF_900604345.1_PRJEB24952_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:01,027] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:01,028] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab7b48f9-827b-44b8-b71b-b1010dd7d5c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:01,029] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab7b48f9-827b-44b8-b71b-b1010dd7d5c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:01,040] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:26:01,040] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:26:01,041] [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
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	77.4806	51	807	95	below_threshold
Gehongia tenuis	strain=NSJ-53	GCA_014384795.1	2763655	2763655	type	True	76.785	58	807	95	below_threshold
Corallococcus exiguus	strain=DSM 14696	GCA_009909105.1	83462	83462	type	True	75.059	69	807	95	below_threshold
Corallococcus interemptor	strain=AB047A	GCA_003668875.1	2316720	2316720	type	True	75.0444	64	807	95	below_threshold
Corallococcus llansteffanensis	strain=CA051B	GCA_003612055.1	2316731	2316731	type	True	74.8946	69	807	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	74.7964	90	807	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:01,043] [INFO] DFAST Taxonomy check result was written to GCF_900604345.1_PRJEB24952_genomic.fna/tc_result.tsv
[2024-01-24 13:26:01,044] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:01,044] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:01,044] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab7b48f9-827b-44b8-b71b-b1010dd7d5c7/dqc_reference/checkm_data
[2024-01-24 13:26:01,046] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:01,071] [INFO] Task started: CheckM
[2024-01-24 13:26:01,071] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900604345.1_PRJEB24952_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900604345.1_PRJEB24952_genomic.fna/checkm_input GCF_900604345.1_PRJEB24952_genomic.fna/checkm_result
[2024-01-24 13:26:30,194] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:30,196] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:30,214] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:30,215] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:30,215] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900604345.1_PRJEB24952_genomic.fna/markers.fasta)
[2024-01-24 13:26:30,215] [INFO] Task started: Blastn
[2024-01-24 13:26:30,216] [INFO] Running command: blastn -query GCF_900604345.1_PRJEB24952_genomic.fna/markers.fasta -db /var/lib/cwl/stgab7b48f9-827b-44b8-b71b-b1010dd7d5c7/dqc_reference/reference_markers_gtdb.fasta -out GCF_900604345.1_PRJEB24952_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:31,156] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:31,160] [INFO] Selected 24 target genomes.
[2024-01-24 13:26:31,160] [INFO] Target genome list was writen to GCF_900604345.1_PRJEB24952_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:31,247] [INFO] Task started: fastANI
[2024-01-24 13:26:31,248] [INFO] Running command: fastANI --query /var/lib/cwl/stge857d1e3-24ee-461a-9993-5588a86d7639/GCF_900604345.1_PRJEB24952_genomic.fna.gz --refList GCF_900604345.1_PRJEB24952_genomic.fna/target_genomes_gtdb.txt --output GCF_900604345.1_PRJEB24952_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:42,538] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:42,555] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:42,556] [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
GCF_900604345.1	s__MARSEILLE-P3954 sp900604345	100.0	806	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__MARSEILLE-P3954;g__MARSEILLE-P3954	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900550525.1	s__Aphodomorpha intestinavium	77.6538	63	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__Aphodomorpha	95.0	98.57	98.50	0.86	0.85	3	-
GCA_904393115.1	s__Spyradocola merdavium	77.1411	101	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA1750;g__Spyradocola	95.0	98.74	98.61	0.95	0.94	8	-
GCA_002492415.1	s__Spyradocola sp002492415	76.8954	64	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA1750;g__Spyradocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018712885.1	s__Pullichristensenella stercoripullorum	76.6124	50	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Pullichristensenella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018716505.1	s__Faecaligallichristensenella faecipullorum	76.6025	58	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Faecaligallichristensenella	95.0	98.68	98.68	0.86	0.86	2	-
GCA_017432405.1	s__UBA2862 sp017432405	76.5945	64	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902764285.1	s__UBA2862 sp902764285	76.5759	76	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902801165.1	s__UBA2862 sp902801165	76.5603	78	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004563405.1	s__SFTH01 sp004563405	76.4361	71	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__SFTH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004554085.1	s__SFTH01 sp004554085	76.3396	72	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__SFTH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017410455.1	s__UBA11524 sp017410455	76.1999	66	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017936765.1	s__UBA11524 sp017936765	75.6142	50	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	96.73	96.73	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:42,557] [INFO] GTDB search result was written to GCF_900604345.1_PRJEB24952_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:42,558] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:42,561] [INFO] DFAST_QC result json was written to GCF_900604345.1_PRJEB24952_genomic.fna/dqc_result.json
[2024-01-24 13:26:42,561] [INFO] DFAST_QC completed!
[2024-01-24 13:26:42,561] [INFO] Total running time: 0h1m14s