[2024-01-24 13:48:58,124] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:58,126] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:58,126] [INFO] DQC Reference Directory: /var/lib/cwl/stg36a3d263-0212-436a-8e66-83a708ac7dc1/dqc_reference
[2024-01-24 13:48:59,505] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:48:59,507] [INFO] Task started: Prodigal
[2024-01-24 13:48:59,507] [INFO] Running command: gunzip -c /var/lib/cwl/stg73eb2108-3b4d-4f91-b5d7-d85c471e6984/GCF_009696275.1_ASM969627v1_genomic.fna.gz | prodigal -d GCF_009696275.1_ASM969627v1_genomic.fna/cds.fna -a GCF_009696275.1_ASM969627v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:15,036] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:15,037] [INFO] Task started: HMMsearch
[2024-01-24 13:49:15,037] [INFO] Running command: hmmsearch --tblout GCF_009696275.1_ASM969627v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36a3d263-0212-436a-8e66-83a708ac7dc1/dqc_reference/reference_markers.hmm GCF_009696275.1_ASM969627v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:15,409] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:15,410] [INFO] Found 6/6 markers.
[2024-01-24 13:49:15,465] [INFO] Query marker FASTA was written to GCF_009696275.1_ASM969627v1_genomic.fna/markers.fasta
[2024-01-24 13:49:15,466] [INFO] Task started: Blastn
[2024-01-24 13:49:15,466] [INFO] Running command: blastn -query GCF_009696275.1_ASM969627v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36a3d263-0212-436a-8e66-83a708ac7dc1/dqc_reference/reference_markers.fasta -out GCF_009696275.1_ASM969627v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:16,167] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:16,170] [INFO] Selected 20 target genomes.
[2024-01-24 13:49:16,170] [INFO] Target genome list was writen to GCF_009696275.1_ASM969627v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:16,177] [INFO] Task started: fastANI
[2024-01-24 13:49:16,177] [INFO] Running command: fastANI --query /var/lib/cwl/stg73eb2108-3b4d-4f91-b5d7-d85c471e6984/GCF_009696275.1_ASM969627v1_genomic.fna.gz --refList GCF_009696275.1_ASM969627v1_genomic.fna/target_genomes.txt --output GCF_009696275.1_ASM969627v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:37,048] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:37,049] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36a3d263-0212-436a-8e66-83a708ac7dc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:37,049] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36a3d263-0212-436a-8e66-83a708ac7dc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:37,065] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:49:37,065] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:49:37,066] [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
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	100.0	1956	1963	95	inconclusive
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	96.5351	1496	1963	95	inconclusive
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	80.4428	901	1963	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_000154365.1	208479	208479	type	True	80.2833	126	1963	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	80.233	80	1963	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002959675.1	208479	208479	type	True	80.1693	125	1963	95	below_threshold
Ruminococcus gauvreauii	strain=DSM 19829	GCA_025151995.1	438033	438033	type	True	79.6385	64	1963	95	below_threshold
Acetatifactor muris	strain=DSM 23669	GCA_024623325.1	879566	879566	type	True	78.4091	140	1963	95	below_threshold
Blautia producta	strain=DSM 2950	GCA_000439125.1	33035	33035	suspected-type	True	78.3309	82	1963	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	78.3219	89	1963	95	below_threshold
Blautia producta	strain=ATCC 27340	GCA_000373885.1	33035	33035	suspected-type	True	78.3121	80	1963	95	below_threshold
Diplocloster modestus	strain=ASD4241	GCA_019042245.1	2850322	2850322	type	True	77.7536	80	1963	95	below_threshold
Blautia coccoides	strain=DSM 935	GCA_004340925.1	1532	1532	type	True	77.5408	79	1963	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	77.0677	94	1963	95	below_threshold
Kineothrix alysoides	strain=KNHs209	GCA_000732725.1	1469948	1469948	type	True	76.7598	81	1963	95	below_threshold
Hespellia stercorisuis	strain=DSM 15480	GCA_900142165.1	180311	180311	type	True	76.6744	53	1963	95	below_threshold
Cuneatibacter caecimuris	strain=DSM 29486	GCA_004216775.1	1796618	1796618	type	True	76.5865	73	1963	95	below_threshold
Kineothrix alysoides	strain=DSM 100556	GCA_004345255.1	1469948	1469948	type	True	76.4872	80	1963	95	below_threshold
Anaerocolumna xylanovorans	strain=DSM 12503	GCA_900143645.1	100134	100134	type	True	76.1801	51	1963	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:37,068] [INFO] DFAST Taxonomy check result was written to GCF_009696275.1_ASM969627v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:37,068] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:37,068] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:37,069] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36a3d263-0212-436a-8e66-83a708ac7dc1/dqc_reference/checkm_data
[2024-01-24 13:49:37,070] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:37,127] [INFO] Task started: CheckM
[2024-01-24 13:49:37,128] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009696275.1_ASM969627v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009696275.1_ASM969627v1_genomic.fna/checkm_input GCF_009696275.1_ASM969627v1_genomic.fna/checkm_result
[2024-01-24 13:50:25,120] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:25,122] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:25,155] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:25,156] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:25,157] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009696275.1_ASM969627v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:25,157] [INFO] Task started: Blastn
[2024-01-24 13:50:25,157] [INFO] Running command: blastn -query GCF_009696275.1_ASM969627v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36a3d263-0212-436a-8e66-83a708ac7dc1/dqc_reference/reference_markers_gtdb.fasta -out GCF_009696275.1_ASM969627v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:26,275] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:26,279] [INFO] Selected 13 target genomes.
[2024-01-24 13:50:26,279] [INFO] Target genome list was writen to GCF_009696275.1_ASM969627v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:26,305] [INFO] Task started: fastANI
[2024-01-24 13:50:26,306] [INFO] Running command: fastANI --query /var/lib/cwl/stg73eb2108-3b4d-4f91-b5d7-d85c471e6984/GCF_009696275.1_ASM969627v1_genomic.fna.gz --refList GCF_009696275.1_ASM969627v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009696275.1_ASM969627v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:38,182] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:38,197] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:38,197] [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_009696275.1	s__Eisenbergiella porci	100.0	1956	1963	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	97.00	96.55	0.75	0.70	10	conclusive
GCF_003478505.1	s__Ventrimonas sp003478505	82.6264	83	1963	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.07	97.61	0.91	0.78	6	-
GCF_003478085.1	s__Eisenbergiella sp003478085	80.7191	935	1963	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	99.95	99.91	0.98	0.96	6	-
GCF_001881565.1	s__Eisenbergiella tayi	80.4546	900	1963	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	97.85	97.22	0.85	0.80	21	-
GCA_900548905.1	s__Eisenbergiella sp900548905	80.1663	832	1963	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119595.1	s__Eisenbergiella merdavium	78.0812	383	1963	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	98.10	98.10	0.87	0.87	2	-
GCA_019113175.1	s__Eisenbergiella stercoravium	77.7833	359	1963	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	97.74	96.88	0.81	0.75	3	-
GCA_900544445.1	s__Eisenbergiella intestinigallinarum	77.6932	344	1963	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	98.26	98.01	0.85	0.82	4	-
GCA_019115665.1	s__Eisenbergiella pullistercoris	77.6177	322	1963	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118445.1	s__Eisenbergiella merdipullorum	77.3403	293	1963	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	99.80	99.80	0.86	0.86	2	-
GCA_904392525.1	s__Eisenbergiella sp904392525	77.0143	272	1963	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017621975.1	s__VSOB01 sp017621975	76.4665	81	1963	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__VSOB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018385425.1	s__Acetatifactor sp018385425	76.3312	74	1963	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	99.11	99.11	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:38,199] [INFO] GTDB search result was written to GCF_009696275.1_ASM969627v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:38,200] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:38,203] [INFO] DFAST_QC result json was written to GCF_009696275.1_ASM969627v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:38,203] [INFO] DFAST_QC completed!
[2024-01-24 13:50:38,204] [INFO] Total running time: 0h1m40s