[2023-06-04 19:18:18,549] [INFO] DFAST_QC pipeline started.
[2023-06-04 19:18:18,552] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 19:18:18,552] [INFO] DQC Reference Directory: /var/lib/cwl/stg19f987bd-8e88-41c6-8e9f-a4ed2b4c7208/dqc_reference
[2023-06-04 19:18:20,247] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 19:18:20,248] [INFO] Task started: Prodigal
[2023-06-04 19:18:20,248] [INFO] Running command: gunzip -c /var/lib/cwl/stg085e6d32-ad5a-4c29-a133-81f1391b3025/GCA_004555405.1_ASM455540v1_genomic.fna.gz | prodigal -d GCA_004555405.1_ASM455540v1_genomic.fna/cds.fna -a GCA_004555405.1_ASM455540v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 19:18:27,024] [INFO] Task succeeded: Prodigal
[2023-06-04 19:18:27,025] [INFO] Task started: HMMsearch
[2023-06-04 19:18:27,025] [INFO] Running command: hmmsearch --tblout GCA_004555405.1_ASM455540v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19f987bd-8e88-41c6-8e9f-a4ed2b4c7208/dqc_reference/reference_markers.hmm GCA_004555405.1_ASM455540v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 19:18:27,267] [INFO] Task succeeded: HMMsearch
[2023-06-04 19:18:27,268] [INFO] Found 6/6 markers.
[2023-06-04 19:18:27,294] [INFO] Query marker FASTA was written to GCA_004555405.1_ASM455540v1_genomic.fna/markers.fasta
[2023-06-04 19:18:27,295] [INFO] Task started: Blastn
[2023-06-04 19:18:27,295] [INFO] Running command: blastn -query GCA_004555405.1_ASM455540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19f987bd-8e88-41c6-8e9f-a4ed2b4c7208/dqc_reference/reference_markers.fasta -out GCA_004555405.1_ASM455540v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 19:18:27,962] [INFO] Task succeeded: Blastn
[2023-06-04 19:18:27,967] [INFO] Selected 16 target genomes.
[2023-06-04 19:18:27,968] [INFO] Target genome list was writen to GCA_004555405.1_ASM455540v1_genomic.fna/target_genomes.txt
[2023-06-04 19:18:28,013] [INFO] Task started: fastANI
[2023-06-04 19:18:28,013] [INFO] Running command: fastANI --query /var/lib/cwl/stg085e6d32-ad5a-4c29-a133-81f1391b3025/GCA_004555405.1_ASM455540v1_genomic.fna.gz --refList GCA_004555405.1_ASM455540v1_genomic.fna/target_genomes.txt --output GCA_004555405.1_ASM455540v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 19:18:35,273] [INFO] Task succeeded: fastANI
[2023-06-04 19:18:35,274] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19f987bd-8e88-41c6-8e9f-a4ed2b4c7208/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 19:18:35,274] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19f987bd-8e88-41c6-8e9f-a4ed2b4c7208/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 19:18:35,285] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 19:18:35,285] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 19:18:35,285] [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
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	78.1807	123	687	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	78.1182	173	687	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	78.1064	173	687	95	below_threshold
Faecalibacterium prausnitzii	strain=ATCC 27768	GCA_003324185.1	853	853	suspected-type	True	77.7602	185	687	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_025152575.1	214851	214851	type	True	77.6517	129	687	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	77.5351	145	687	95	below_threshold
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	77.3768	169	687	95	below_threshold
Pygmaiobacter massiliensis	strain=Marseille-P3336	GCA_900199435.1	1917873	1917873	type	True	75.8519	58	687	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 19:18:35,287] [INFO] DFAST Taxonomy check result was written to GCA_004555405.1_ASM455540v1_genomic.fna/tc_result.tsv
[2023-06-04 19:18:35,288] [INFO] ===== Taxonomy check completed =====
[2023-06-04 19:18:35,288] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 19:18:35,288] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19f987bd-8e88-41c6-8e9f-a4ed2b4c7208/dqc_reference/checkm_data
[2023-06-04 19:18:35,290] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 19:18:35,314] [INFO] Task started: CheckM
[2023-06-04 19:18:35,314] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004555405.1_ASM455540v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004555405.1_ASM455540v1_genomic.fna/checkm_input GCA_004555405.1_ASM455540v1_genomic.fna/checkm_result
[2023-06-04 19:19:01,182] [INFO] Task succeeded: CheckM
[2023-06-04 19:19:01,184] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 19:19:01,204] [INFO] ===== Completeness check finished =====
[2023-06-04 19:19:01,205] [INFO] ===== Start GTDB Search =====
[2023-06-04 19:19:01,205] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004555405.1_ASM455540v1_genomic.fna/markers.fasta)
[2023-06-04 19:19:01,205] [INFO] Task started: Blastn
[2023-06-04 19:19:01,206] [INFO] Running command: blastn -query GCA_004555405.1_ASM455540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19f987bd-8e88-41c6-8e9f-a4ed2b4c7208/dqc_reference/reference_markers_gtdb.fasta -out GCA_004555405.1_ASM455540v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 19:19:02,350] [INFO] Task succeeded: Blastn
[2023-06-04 19:19:02,355] [INFO] Selected 26 target genomes.
[2023-06-04 19:19:02,355] [INFO] Target genome list was writen to GCA_004555405.1_ASM455540v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 19:19:02,365] [INFO] Task started: fastANI
[2023-06-04 19:19:02,365] [INFO] Running command: fastANI --query /var/lib/cwl/stg085e6d32-ad5a-4c29-a133-81f1391b3025/GCA_004555405.1_ASM455540v1_genomic.fna.gz --refList GCA_004555405.1_ASM455540v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004555405.1_ASM455540v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 19:19:12,537] [INFO] Task succeeded: fastANI
[2023-06-04 19:19:12,562] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 19:19:12,562] [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_004555405.1	s__Gemmiger sp004555405	100.0	682	687	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	97.36	97.23	0.85	0.84	4	conclusive
GCF_002549775.1	s__Faecalibacterium prausnitzii_F	78.3131	184	687	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.99	97.71	0.95	0.94	3	-
GCA_004555865.1	s__SFJ001 sp004555865	78.2806	209	687	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__SFJ001	95.0	98.44	98.34	0.90	0.89	3	-
GCF_003287405.1	s__Faecalibacterium prausnitzii_J	78.213	183	687	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.32	96.98	0.87	0.83	5	-
GCF_010509575.1	s__Faecalibacterium prausnitzii_C	78.1064	173	687	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.30	96.44	0.84	0.71	49	-
GCF_002550035.1	s__Faecalibacterium prausnitzii_E	77.9228	145	687	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.41	96.74	0.87	0.80	12	-
GCA_004552305.1	s__Gemmiger variabilis_A	77.9211	161	687	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	97.82	96.59	0.82	0.70	4	-
GCA_900772565.1	s__Faecalibacterium sp900772565	77.8315	163	687	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002161595.1	s__Fournierella sp002161595	77.745	159	687	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	98.81	98.81	0.92	0.92	2	-
GCF_003324185.1	s__Faecalibacterium prausnitzii	77.7341	186	687	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0612	96.64	96.12	0.86	0.79	47	-
GCF_002159185.1	s__Fournierella sp002159185	77.7334	161	687	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_002160915.1	s__Faecalibacterium avium	77.7203	130	687	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.16	97.86	0.90	0.86	4	-
GCA_019116585.1	s__Faecalibacterium gallistercoris	77.6659	131	687	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.23	98.17	0.89	0.87	6	-
GCA_905214345.1	s__Gemmiger sp905214345	77.6553	143	687	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_003449675.1	s__Faecalibacterium sp003449675	77.6361	117	687	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	96.56	96.55	0.80	0.74	3	-
GCA_900765105.1	s__Faecalibacterium sp900765105	77.5827	125	687	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.27	98.27	0.82	0.82	2	-
GCA_019119685.1	s__Faecalibacterium faecigallinarum	77.5036	120	687	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.44	97.44	0.75	0.75	2	-
GCF_002160955.1	s__Gemmiger_A avium	77.4469	159	687	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger_A	95.0	98.36	98.15	0.86	0.80	3	-
GCA_905215595.1	s__Faecalibacterium sp905215595	77.4284	121	687	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116705.1	s__Gemmiger avistercoris	77.4157	113	687	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	99.94	99.94	0.92	0.92	2	-
GCA_017472375.1	s__SFJ001 sp017472375	77.2728	109	687	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__SFJ001	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019115045.1	s__Gemmiger excrementipullorum	77.088	125	687	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_019119365.1	s__Gemmiger stercoripullorum	76.9451	127	687	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	98.12	98.12	0.82	0.82	2	-
GCA_905212515.1	s__Ruthenibacterium sp905212515	76.1955	81	687	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruthenibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 19:19:12,564] [INFO] GTDB search result was written to GCA_004555405.1_ASM455540v1_genomic.fna/result_gtdb.tsv
[2023-06-04 19:19:12,564] [INFO] ===== GTDB Search completed =====
[2023-06-04 19:19:12,568] [INFO] DFAST_QC result json was written to GCA_004555405.1_ASM455540v1_genomic.fna/dqc_result.json
[2023-06-04 19:19:12,569] [INFO] DFAST_QC completed!
[2023-06-04 19:19:12,569] [INFO] Total running time: 0h0m54s