[2023-06-13 08:52:11,580] [INFO] DFAST_QC pipeline started.
[2023-06-13 08:52:11,584] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 08:52:11,584] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe2623c7-75c5-4559-8acf-831e7fbcabd4/dqc_reference
[2023-06-13 08:52:13,047] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 08:52:13,048] [INFO] Task started: Prodigal
[2023-06-13 08:52:13,048] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ed7df26-9a31-4751-9835-2963f3f11327/GCA_022747045.1_ASM2274704v1_genomic.fna.gz | prodigal -d GCA_022747045.1_ASM2274704v1_genomic.fna/cds.fna -a GCA_022747045.1_ASM2274704v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 08:52:23,373] [INFO] Task succeeded: Prodigal
[2023-06-13 08:52:23,373] [INFO] Task started: HMMsearch
[2023-06-13 08:52:23,373] [INFO] Running command: hmmsearch --tblout GCA_022747045.1_ASM2274704v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe2623c7-75c5-4559-8acf-831e7fbcabd4/dqc_reference/reference_markers.hmm GCA_022747045.1_ASM2274704v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 08:52:23,667] [INFO] Task succeeded: HMMsearch
[2023-06-13 08:52:23,668] [INFO] Found 6/6 markers.
[2023-06-13 08:52:23,717] [INFO] Query marker FASTA was written to GCA_022747045.1_ASM2274704v1_genomic.fna/markers.fasta
[2023-06-13 08:52:23,717] [INFO] Task started: Blastn
[2023-06-13 08:52:23,718] [INFO] Running command: blastn -query GCA_022747045.1_ASM2274704v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe2623c7-75c5-4559-8acf-831e7fbcabd4/dqc_reference/reference_markers.fasta -out GCA_022747045.1_ASM2274704v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:52:24,461] [INFO] Task succeeded: Blastn
[2023-06-13 08:52:24,466] [INFO] Selected 20 target genomes.
[2023-06-13 08:52:24,466] [INFO] Target genome list was writen to GCA_022747045.1_ASM2274704v1_genomic.fna/target_genomes.txt
[2023-06-13 08:52:24,469] [INFO] Task started: fastANI
[2023-06-13 08:52:24,469] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ed7df26-9a31-4751-9835-2963f3f11327/GCA_022747045.1_ASM2274704v1_genomic.fna.gz --refList GCA_022747045.1_ASM2274704v1_genomic.fna/target_genomes.txt --output GCA_022747045.1_ASM2274704v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 08:52:36,269] [INFO] Task succeeded: fastANI
[2023-06-13 08:52:36,269] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe2623c7-75c5-4559-8acf-831e7fbcabd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 08:52:36,270] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe2623c7-75c5-4559-8acf-831e7fbcabd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 08:52:36,285] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2023-06-13 08:52:36,285] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 08:52:36,285] [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
Ruthenibacterium lactatiformans	strain=585-1	GCA_000949455.1	1550024	1550024	suspected-type	True	99.2929	916	1047	95	conclusive
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	77.4102	187	1047	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	77.166	100	1047	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	77.1344	107	1047	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	77.1274	109	1047	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_025152575.1	214851	214851	type	True	76.9958	90	1047	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_000157955.1	214851	214851	type	True	76.9682	92	1047	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	76.9222	61	1047	95	below_threshold
Faecalibacterium prausnitzii	strain=ATCC 27768	GCA_003324185.1	853	853	suspected-type	True	76.8752	123	1047	95	below_threshold
Bittarella massiliensis	strain=GD6	GCA_001486165.1	1720313	1720313	type	True	76.8649	66	1047	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	76.7586	58	1047	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	76.7563	118	1047	95	below_threshold
Anaerotruncus massiliensis	strain=AT3	GCA_900199635.1	1673720	1673720	type	True	76.5422	72	1047	95	below_threshold
Anaerotruncus rubiinfantis	strain=MT15	GCA_900078395.1	1720200	1720200	type	True	76.1123	50	1047	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 08:52:36,290] [INFO] DFAST Taxonomy check result was written to GCA_022747045.1_ASM2274704v1_genomic.fna/tc_result.tsv
[2023-06-13 08:52:36,291] [INFO] ===== Taxonomy check completed =====
[2023-06-13 08:52:36,291] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 08:52:36,291] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe2623c7-75c5-4559-8acf-831e7fbcabd4/dqc_reference/checkm_data
[2023-06-13 08:52:36,293] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 08:52:36,335] [INFO] Task started: CheckM
[2023-06-13 08:52:36,335] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022747045.1_ASM2274704v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022747045.1_ASM2274704v1_genomic.fna/checkm_input GCA_022747045.1_ASM2274704v1_genomic.fna/checkm_result
[2023-06-13 08:53:10,797] [INFO] Task succeeded: CheckM
[2023-06-13 08:53:10,798] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 08:53:10,818] [INFO] ===== Completeness check finished =====
[2023-06-13 08:53:10,818] [INFO] ===== Start GTDB Search =====
[2023-06-13 08:53:10,819] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022747045.1_ASM2274704v1_genomic.fna/markers.fasta)
[2023-06-13 08:53:10,819] [INFO] Task started: Blastn
[2023-06-13 08:53:10,819] [INFO] Running command: blastn -query GCA_022747045.1_ASM2274704v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe2623c7-75c5-4559-8acf-831e7fbcabd4/dqc_reference/reference_markers_gtdb.fasta -out GCA_022747045.1_ASM2274704v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:53:12,039] [INFO] Task succeeded: Blastn
[2023-06-13 08:53:12,043] [INFO] Selected 18 target genomes.
[2023-06-13 08:53:12,044] [INFO] Target genome list was writen to GCA_022747045.1_ASM2274704v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 08:53:12,054] [INFO] Task started: fastANI
[2023-06-13 08:53:12,054] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ed7df26-9a31-4751-9835-2963f3f11327/GCA_022747045.1_ASM2274704v1_genomic.fna.gz --refList GCA_022747045.1_ASM2274704v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022747045.1_ASM2274704v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 08:53:20,303] [INFO] Task succeeded: fastANI
[2023-06-13 08:53:20,324] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 08:53:20,324] [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_000949455.1	s__Ruthenibacterium lactatiformans	99.2929	916	1047	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruthenibacterium	95.0	98.75	98.24	0.81	0.72	47	conclusive
GCA_014799685.1	s__Ruthenibacterium sp014799685	79.6271	335	1047	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruthenibacterium	95.0	97.75	97.75	0.71	0.71	2	-
GCA_910587145.1	s__Ruthenibacterium sp013316265	79.3964	319	1047	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruthenibacterium	95.0	99.81	99.81	0.95	0.95	2	-
GCA_905212515.1	s__Ruthenibacterium sp905212515	78.9717	246	1047	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruthenibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019113785.1	s__Ruthenibacterium merdigallinarum	78.7764	254	1047	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruthenibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546885.1	s__Ruthenibacterium merdipullorum	78.447	201	1047	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruthenibacterium	95.0	99.05	98.69	0.88	0.82	7	-
GCF_002160015.1	s__Anaerofilum faecale	78.3647	213	1047	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerofilum	95.0	98.90	98.89	0.95	0.94	3	-
GCA_018380115.1	s__Ruthenibacterium sp018380115	78.2967	230	1047	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruthenibacterium	95.0	97.78	95.38	0.91	0.83	6	-
GCA_019116345.1	s__Fournierella merdipullorum	77.9811	178	1047	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	77.9338	179	1047	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159185.1	s__Fournierella sp002159185	77.8201	172	1047	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_019117205.1	s__Fournierella merdigallinarum	77.8149	168	1047	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002160145.1	s__Fournierella sp002160145	77.6291	183	1047	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	98.11	98.11	0.91	0.91	2	-
GCA_019119495.1	s__Gemmiger stercorigallinarum	77.5997	127	1047	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	98.30	97.15	0.83	0.66	4	-
GCF_014287275.1	s__Pygmaiobacter sp014287275	77.3307	187	1047	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Pygmaiobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 08:53:20,327] [INFO] GTDB search result was written to GCA_022747045.1_ASM2274704v1_genomic.fna/result_gtdb.tsv
[2023-06-13 08:53:20,329] [INFO] ===== GTDB Search completed =====
[2023-06-13 08:53:20,335] [INFO] DFAST_QC result json was written to GCA_022747045.1_ASM2274704v1_genomic.fna/dqc_result.json
[2023-06-13 08:53:20,336] [INFO] DFAST_QC completed!
[2023-06-13 08:53:20,336] [INFO] Total running time: 0h1m9s