[2023-06-28 16:54:01,449] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:54:01,451] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:54:01,451] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d2db9b1-7e2c-4ff7-a009-256788feaeb2/dqc_reference
[2023-06-28 16:54:02,733] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:54:02,734] [INFO] Task started: Prodigal
[2023-06-28 16:54:02,735] [INFO] Running command: gunzip -c /var/lib/cwl/stgcca18f60-3545-4f44-aed9-6e9b5e2aa477/GCA_944382865.1_BRZ_HV_bin45_genomic.fna.gz | prodigal -d GCA_944382865.1_BRZ_HV_bin45_genomic.fna/cds.fna -a GCA_944382865.1_BRZ_HV_bin45_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:54:10,112] [INFO] Task succeeded: Prodigal
[2023-06-28 16:54:10,112] [INFO] Task started: HMMsearch
[2023-06-28 16:54:10,112] [INFO] Running command: hmmsearch --tblout GCA_944382865.1_BRZ_HV_bin45_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d2db9b1-7e2c-4ff7-a009-256788feaeb2/dqc_reference/reference_markers.hmm GCA_944382865.1_BRZ_HV_bin45_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:54:10,361] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:54:10,362] [INFO] Found 6/6 markers.
[2023-06-28 16:54:10,393] [INFO] Query marker FASTA was written to GCA_944382865.1_BRZ_HV_bin45_genomic.fna/markers.fasta
[2023-06-28 16:54:10,393] [INFO] Task started: Blastn
[2023-06-28 16:54:10,393] [INFO] Running command: blastn -query GCA_944382865.1_BRZ_HV_bin45_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d2db9b1-7e2c-4ff7-a009-256788feaeb2/dqc_reference/reference_markers.fasta -out GCA_944382865.1_BRZ_HV_bin45_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:54:11,129] [INFO] Task succeeded: Blastn
[2023-06-28 16:54:11,136] [INFO] Selected 14 target genomes.
[2023-06-28 16:54:11,137] [INFO] Target genome list was writen to GCA_944382865.1_BRZ_HV_bin45_genomic.fna/target_genomes.txt
[2023-06-28 16:54:11,142] [INFO] Task started: fastANI
[2023-06-28 16:54:11,143] [INFO] Running command: fastANI --query /var/lib/cwl/stgcca18f60-3545-4f44-aed9-6e9b5e2aa477/GCA_944382865.1_BRZ_HV_bin45_genomic.fna.gz --refList GCA_944382865.1_BRZ_HV_bin45_genomic.fna/target_genomes.txt --output GCA_944382865.1_BRZ_HV_bin45_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:54:19,901] [INFO] Task succeeded: fastANI
[2023-06-28 16:54:19,901] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d2db9b1-7e2c-4ff7-a009-256788feaeb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:54:19,902] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d2db9b1-7e2c-4ff7-a009-256788feaeb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:54:19,912] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:54:19,913] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 16:54:19,913] [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
Subdoligranulum variabile	strain=DSM 15176	GCA_025152575.1	214851	214851	type	True	78.554	250	802	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_000157955.1	214851	214851	type	True	78.5005	251	802	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	77.5598	144	802	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	77.348	136	802	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	77.3033	137	802	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	77.2898	135	802	95	below_threshold
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	76.6251	123	802	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 16:54:19,915] [INFO] DFAST Taxonomy check result was written to GCA_944382865.1_BRZ_HV_bin45_genomic.fna/tc_result.tsv
[2023-06-28 16:54:19,915] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:54:19,915] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:54:19,916] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d2db9b1-7e2c-4ff7-a009-256788feaeb2/dqc_reference/checkm_data
[2023-06-28 16:54:19,917] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:54:19,943] [INFO] Task started: CheckM
[2023-06-28 16:54:19,944] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944382865.1_BRZ_HV_bin45_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944382865.1_BRZ_HV_bin45_genomic.fna/checkm_input GCA_944382865.1_BRZ_HV_bin45_genomic.fna/checkm_result
[2023-06-28 16:54:46,558] [INFO] Task succeeded: CheckM
[2023-06-28 16:54:46,559] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 16:54:46,589] [INFO] ===== Completeness check finished =====
[2023-06-28 16:54:46,590] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:54:46,590] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944382865.1_BRZ_HV_bin45_genomic.fna/markers.fasta)
[2023-06-28 16:54:46,591] [INFO] Task started: Blastn
[2023-06-28 16:54:46,591] [INFO] Running command: blastn -query GCA_944382865.1_BRZ_HV_bin45_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d2db9b1-7e2c-4ff7-a009-256788feaeb2/dqc_reference/reference_markers_gtdb.fasta -out GCA_944382865.1_BRZ_HV_bin45_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:54:47,875] [INFO] Task succeeded: Blastn
[2023-06-28 16:54:47,880] [INFO] Selected 11 target genomes.
[2023-06-28 16:54:47,880] [INFO] Target genome list was writen to GCA_944382865.1_BRZ_HV_bin45_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:54:47,904] [INFO] Task started: fastANI
[2023-06-28 16:54:47,904] [INFO] Running command: fastANI --query /var/lib/cwl/stgcca18f60-3545-4f44-aed9-6e9b5e2aa477/GCA_944382865.1_BRZ_HV_bin45_genomic.fna.gz --refList GCA_944382865.1_BRZ_HV_bin45_genomic.fna/target_genomes_gtdb.txt --output GCA_944382865.1_BRZ_HV_bin45_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:54:53,168] [INFO] Task succeeded: fastANI
[2023-06-28 16:54:53,182] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 16:54:53,183] [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_900548355.1	s__Gemmiger avicola	98.5673	677	802	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	98.64	98.58	0.86	0.84	5	conclusive
GCA_019119835.1	s__Gemmiger stercoravium	81.1977	442	802	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	98.20	98.14	0.89	0.85	3	-
GCA_019119365.1	s__Gemmiger stercoripullorum	81.0627	446	802	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	98.12	98.12	0.82	0.82	2	-
GCF_016900095.1	s__Gemmiger formicilis_A	79.9154	389	802	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019115045.1	s__Gemmiger excrementipullorum	79.4997	325	802	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119495.1	s__Gemmiger stercorigallinarum	79.4846	299	802	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	98.30	97.15	0.83	0.66	4	-
GCA_905214345.1	s__Gemmiger sp905214345	79.444	375	802	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004561545.1	s__Gemmiger sp004561545	78.7573	229	802	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014982805.1	s__Gemmiger sp014982805	78.7572	275	802	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116485.1	s__Gemmiger excrementavium	78.243	264	802	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 16:54:53,185] [INFO] GTDB search result was written to GCA_944382865.1_BRZ_HV_bin45_genomic.fna/result_gtdb.tsv
[2023-06-28 16:54:53,185] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:54:53,189] [INFO] DFAST_QC result json was written to GCA_944382865.1_BRZ_HV_bin45_genomic.fna/dqc_result.json
[2023-06-28 16:54:53,189] [INFO] DFAST_QC completed!
[2023-06-28 16:54:53,189] [INFO] Total running time: 0h0m52s