[2023-06-28 03:04:15,447] [INFO] DFAST_QC pipeline started.
[2023-06-28 03:04:15,450] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 03:04:15,450] [INFO] DQC Reference Directory: /var/lib/cwl/stg46a22874-5b36-477a-906d-3cf2ba5ac326/dqc_reference
[2023-06-28 03:04:18,686] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 03:04:18,687] [INFO] Task started: Prodigal
[2023-06-28 03:04:18,687] [INFO] Running command: gunzip -c /var/lib/cwl/stg02c5851a-2b8a-4911-9535-1a81a5324323/GCA_944382655.1_BRZ_GD_bin93_genomic.fna.gz | prodigal -d GCA_944382655.1_BRZ_GD_bin93_genomic.fna/cds.fna -a GCA_944382655.1_BRZ_GD_bin93_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 03:04:24,733] [INFO] Task succeeded: Prodigal
[2023-06-28 03:04:24,733] [INFO] Task started: HMMsearch
[2023-06-28 03:04:24,733] [INFO] Running command: hmmsearch --tblout GCA_944382655.1_BRZ_GD_bin93_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46a22874-5b36-477a-906d-3cf2ba5ac326/dqc_reference/reference_markers.hmm GCA_944382655.1_BRZ_GD_bin93_genomic.fna/protein.faa > /dev/null
[2023-06-28 03:04:24,994] [INFO] Task succeeded: HMMsearch
[2023-06-28 03:04:24,996] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg02c5851a-2b8a-4911-9535-1a81a5324323/GCA_944382655.1_BRZ_GD_bin93_genomic.fna.gz]
[2023-06-28 03:04:25,029] [INFO] Query marker FASTA was written to GCA_944382655.1_BRZ_GD_bin93_genomic.fna/markers.fasta
[2023-06-28 03:04:25,030] [INFO] Task started: Blastn
[2023-06-28 03:04:25,030] [INFO] Running command: blastn -query GCA_944382655.1_BRZ_GD_bin93_genomic.fna/markers.fasta -db /var/lib/cwl/stg46a22874-5b36-477a-906d-3cf2ba5ac326/dqc_reference/reference_markers.fasta -out GCA_944382655.1_BRZ_GD_bin93_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 03:04:27,493] [INFO] Task succeeded: Blastn
[2023-06-28 03:04:27,498] [INFO] Selected 14 target genomes.
[2023-06-28 03:04:27,499] [INFO] Target genome list was writen to GCA_944382655.1_BRZ_GD_bin93_genomic.fna/target_genomes.txt
[2023-06-28 03:04:27,583] [INFO] Task started: fastANI
[2023-06-28 03:04:27,583] [INFO] Running command: fastANI --query /var/lib/cwl/stg02c5851a-2b8a-4911-9535-1a81a5324323/GCA_944382655.1_BRZ_GD_bin93_genomic.fna.gz --refList GCA_944382655.1_BRZ_GD_bin93_genomic.fna/target_genomes.txt --output GCA_944382655.1_BRZ_GD_bin93_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 03:04:34,642] [INFO] Task succeeded: fastANI
[2023-06-28 03:04:34,643] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46a22874-5b36-477a-906d-3cf2ba5ac326/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 03:04:34,643] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46a22874-5b36-477a-906d-3cf2ba5ac326/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 03:04:34,657] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 03:04:34,657] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 03:04:34,658] [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	80.5815	299	629	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	78.2263	174	629	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	77.8034	135	629	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	77.7659	138	629	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_025152575.1	214851	214851	type	True	77.7425	138	629	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_000157955.1	214851	214851	type	True	77.7165	140	629	95	below_threshold
Ruthenibacterium lactatiformans	strain=585-1	GCA_000949455.1	1550024	1550024	suspected-type	True	77.6893	126	629	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	77.6716	141	629	95	below_threshold
Faecalibacterium prausnitzii	strain=ATCC 27768	GCA_003324185.1	853	853	suspected-type	True	77.3888	138	629	95	below_threshold
Bittarella massiliensis	strain=GD6	GCA_001486165.1	1720313	1720313	type	True	77.2625	76	629	95	below_threshold
Anaerotruncus massiliensis	strain=AT3	GCA_900199635.1	1673720	1673720	type	True	76.26	60	629	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 03:04:34,660] [INFO] DFAST Taxonomy check result was written to GCA_944382655.1_BRZ_GD_bin93_genomic.fna/tc_result.tsv
[2023-06-28 03:04:34,660] [INFO] ===== Taxonomy check completed =====
[2023-06-28 03:04:34,660] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 03:04:34,661] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46a22874-5b36-477a-906d-3cf2ba5ac326/dqc_reference/checkm_data
[2023-06-28 03:04:34,662] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 03:04:34,690] [INFO] Task started: CheckM
[2023-06-28 03:04:34,691] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944382655.1_BRZ_GD_bin93_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944382655.1_BRZ_GD_bin93_genomic.fna/checkm_input GCA_944382655.1_BRZ_GD_bin93_genomic.fna/checkm_result
[2023-06-28 03:05:02,155] [INFO] Task succeeded: CheckM
[2023-06-28 03:05:02,156] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.28%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 03:05:02,175] [INFO] ===== Completeness check finished =====
[2023-06-28 03:05:02,175] [INFO] ===== Start GTDB Search =====
[2023-06-28 03:05:02,176] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944382655.1_BRZ_GD_bin93_genomic.fna/markers.fasta)
[2023-06-28 03:05:02,176] [INFO] Task started: Blastn
[2023-06-28 03:05:02,176] [INFO] Running command: blastn -query GCA_944382655.1_BRZ_GD_bin93_genomic.fna/markers.fasta -db /var/lib/cwl/stg46a22874-5b36-477a-906d-3cf2ba5ac326/dqc_reference/reference_markers_gtdb.fasta -out GCA_944382655.1_BRZ_GD_bin93_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 03:05:03,217] [INFO] Task succeeded: Blastn
[2023-06-28 03:05:03,221] [INFO] Selected 5 target genomes.
[2023-06-28 03:05:03,222] [INFO] Target genome list was writen to GCA_944382655.1_BRZ_GD_bin93_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 03:05:03,227] [INFO] Task started: fastANI
[2023-06-28 03:05:03,227] [INFO] Running command: fastANI --query /var/lib/cwl/stg02c5851a-2b8a-4911-9535-1a81a5324323/GCA_944382655.1_BRZ_GD_bin93_genomic.fna.gz --refList GCA_944382655.1_BRZ_GD_bin93_genomic.fna/target_genomes_gtdb.txt --output GCA_944382655.1_BRZ_GD_bin93_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 03:05:06,098] [INFO] Task succeeded: fastANI
[2023-06-28 03:05:06,104] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 03:05:06,105] [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_019114225.1	s__Fournierella pullicola	98.6605	564	629	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004558145.1	s__Fournierella excrementavium	91.4492	526	629	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	97.60	97.45	0.91	0.87	5	-
GCA_019116345.1	s__Fournierella merdipullorum	90.9644	470	629	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119025.1	s__Fournierella excrementigallinarum	90.4653	457	629	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118765.1	s__Fournierella merdavium	87.9391	459	629	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 03:05:06,107] [INFO] GTDB search result was written to GCA_944382655.1_BRZ_GD_bin93_genomic.fna/result_gtdb.tsv
[2023-06-28 03:05:06,107] [INFO] ===== GTDB Search completed =====
[2023-06-28 03:05:06,110] [INFO] DFAST_QC result json was written to GCA_944382655.1_BRZ_GD_bin93_genomic.fna/dqc_result.json
[2023-06-28 03:05:06,110] [INFO] DFAST_QC completed!
[2023-06-28 03:05:06,110] [INFO] Total running time: 0h0m51s