[2024-01-24 13:24:48,207] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:24:48,208] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:24:48,208] [INFO] DQC Reference Directory: /var/lib/cwl/stg89d6e20e-4fd4-4dea-8d81-82ef314c4909/dqc_reference
[2024-01-24 13:24:49,591] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:24:49,592] [INFO] Task started: Prodigal
[2024-01-24 13:24:49,592] [INFO] Running command: gunzip -c /var/lib/cwl/stgf17d16a9-15f3-4f20-a9d8-25877ae6c61b/GCF_020686965.1_ASM2068696v1_genomic.fna.gz | prodigal -d GCF_020686965.1_ASM2068696v1_genomic.fna/cds.fna -a GCF_020686965.1_ASM2068696v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:24:58,589] [INFO] Task succeeded: Prodigal
[2024-01-24 13:24:58,589] [INFO] Task started: HMMsearch
[2024-01-24 13:24:58,590] [INFO] Running command: hmmsearch --tblout GCF_020686965.1_ASM2068696v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89d6e20e-4fd4-4dea-8d81-82ef314c4909/dqc_reference/reference_markers.hmm GCF_020686965.1_ASM2068696v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:24:58,934] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:24:58,935] [INFO] Found 6/6 markers.
[2024-01-24 13:24:58,966] [INFO] Query marker FASTA was written to GCF_020686965.1_ASM2068696v1_genomic.fna/markers.fasta
[2024-01-24 13:24:58,967] [INFO] Task started: Blastn
[2024-01-24 13:24:58,967] [INFO] Running command: blastn -query GCF_020686965.1_ASM2068696v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89d6e20e-4fd4-4dea-8d81-82ef314c4909/dqc_reference/reference_markers.fasta -out GCF_020686965.1_ASM2068696v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:59,720] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:59,723] [INFO] Selected 29 target genomes.
[2024-01-24 13:24:59,724] [INFO] Target genome list was writen to GCF_020686965.1_ASM2068696v1_genomic.fna/target_genomes.txt
[2024-01-24 13:24:59,749] [INFO] Task started: fastANI
[2024-01-24 13:24:59,749] [INFO] Running command: fastANI --query /var/lib/cwl/stgf17d16a9-15f3-4f20-a9d8-25877ae6c61b/GCF_020686965.1_ASM2068696v1_genomic.fna.gz --refList GCF_020686965.1_ASM2068696v1_genomic.fna/target_genomes.txt --output GCF_020686965.1_ASM2068696v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:18,774] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:18,775] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89d6e20e-4fd4-4dea-8d81-82ef314c4909/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:18,775] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89d6e20e-4fd4-4dea-8d81-82ef314c4909/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:18,814] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:25:18,814] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:25:18,815] [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
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	81.7021	90	1134	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	81.289	95	1134	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	80.4314	142	1134	95	below_threshold
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	79.6372	91	1134	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_025147655.1	1322	1322	type	True	79.6316	71	1134	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	79.4576	99	1134	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	79.4508	85	1134	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	79.2466	100	1134	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	79.2316	98	1134	95	below_threshold
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	79.2002	66	1134	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	78.3183	122	1134	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	77.7927	80	1134	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	77.6256	79	1134	95	below_threshold
Sellimonas caecigallum	strain=SW451	GCA_019754295.1	2592333	2592333	type	True	77.1714	53	1134	95	below_threshold
Merdimonas faecis	strain=BR31	GCA_001754075.1	1653435	1653435	type	True	77.1314	72	1134	95	below_threshold
Blautia coccoides	strain=DSM 935	GCA_004340925.1	1532	1532	type	True	77.1205	73	1134	95	below_threshold
Blautia coccoides	strain=NCTC11035	GCA_900461125.1	1532	1532	type	True	77.0995	73	1134	95	below_threshold
Blautia producta	strain=ATCC 27340	GCA_000373885.1	33035	33035	suspected-type	True	77.0125	75	1134	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	76.9616	69	1134	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	76.5657	60	1134	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_000160095.1	154046	154046	suspected-type	True	76.4476	56	1134	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	76.2091	69	1134	95	below_threshold
Hungatella effluvii	strain=DSM 24995	GCA_003201875.1	1096246	1096246	type	True	76.1864	65	1134	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:18,819] [INFO] DFAST Taxonomy check result was written to GCF_020686965.1_ASM2068696v1_genomic.fna/tc_result.tsv
[2024-01-24 13:25:18,820] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:18,821] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:18,821] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89d6e20e-4fd4-4dea-8d81-82ef314c4909/dqc_reference/checkm_data
[2024-01-24 13:25:18,823] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:18,868] [INFO] Task started: CheckM
[2024-01-24 13:25:18,868] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020686965.1_ASM2068696v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020686965.1_ASM2068696v1_genomic.fna/checkm_input GCF_020686965.1_ASM2068696v1_genomic.fna/checkm_result
[2024-01-24 13:25:50,687] [INFO] Task succeeded: CheckM
[2024-01-24 13:25:50,689] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:25:50,717] [INFO] ===== Completeness check finished =====
[2024-01-24 13:25:50,718] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:25:50,718] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020686965.1_ASM2068696v1_genomic.fna/markers.fasta)
[2024-01-24 13:25:50,719] [INFO] Task started: Blastn
[2024-01-24 13:25:50,719] [INFO] Running command: blastn -query GCF_020686965.1_ASM2068696v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89d6e20e-4fd4-4dea-8d81-82ef314c4909/dqc_reference/reference_markers_gtdb.fasta -out GCF_020686965.1_ASM2068696v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:51,802] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:51,806] [INFO] Selected 17 target genomes.
[2024-01-24 13:25:51,806] [INFO] Target genome list was writen to GCF_020686965.1_ASM2068696v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:25:51,860] [INFO] Task started: fastANI
[2024-01-24 13:25:51,860] [INFO] Running command: fastANI --query /var/lib/cwl/stgf17d16a9-15f3-4f20-a9d8-25877ae6c61b/GCF_020686965.1_ASM2068696v1_genomic.fna.gz --refList GCF_020686965.1_ASM2068696v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020686965.1_ASM2068696v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:01,354] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:01,371] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:01,371] [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_018228645.1	s__Choladocola sp003481535	97.7532	825	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	97.90	97.68	0.80	0.76	5	conclusive
GCA_018223365.1	s__Choladocola sp018223365	92.7863	727	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003480725.1	s__Choladocola sp003480725	82.2172	448	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	97.99	97.12	0.84	0.75	9	-
GCF_000225345.1	s__Roseburia hominis	81.7021	90	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.94	95.20	0.88	0.81	15	-
GCF_900104635.1	s__Faecalimonas phoceensis	79.2739	65	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	98.10	95.01	0.81	0.60	21	-
GCA_018376135.1	s__Choladocola sp018376135	78.6701	274	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017558865.1	s__Choladocola sp017558865	78.4422	199	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002160135.1	s__Choladocola avistercoris	77.7038	207	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	98.18	97.96	0.88	0.84	7	-
GCA_009774145.1	s__Choladocola sp009774145	77.4898	213	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	98.49	98.49	0.80	0.80	2	-
GCA_009774155.1	s__Choladocola sp009774155	77.3907	167	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	98.91	98.91	0.77	0.77	2	-
GCA_910583895.1	s__Choladocola sp910583895	77.3895	175	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910583615.1	s__Choladocola sp910583615	77.351	191	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910575445.1	s__Choladocola sp910575445	77.3446	148	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	99.04	98.55	0.92	0.85	5	-
GCF_016899975.1	s__Fusicatenibacter sp900543115	77.1789	77	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Fusicatenibacter	95.0	98.27	97.10	0.88	0.78	8	-
GCA_012520645.1	s__JAAYNV01 sp012520645	76.1662	67	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__JAAYNV01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:01,373] [INFO] GTDB search result was written to GCF_020686965.1_ASM2068696v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:01,374] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:01,378] [INFO] DFAST_QC result json was written to GCF_020686965.1_ASM2068696v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:01,378] [INFO] DFAST_QC completed!
[2024-01-24 13:26:01,378] [INFO] Total running time: 0h1m13s