[2023-06-17 12:24:49,346] [INFO] DFAST_QC pipeline started.
[2023-06-17 12:24:49,366] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 12:24:49,367] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f1d061c-fd72-47fd-8999-f6e10ba24896/dqc_reference
[2023-06-17 12:24:50,698] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 12:24:50,699] [INFO] Task started: Prodigal
[2023-06-17 12:24:50,699] [INFO] Running command: gunzip -c /var/lib/cwl/stge7afd608-a93c-42b4-a29e-ea01bffbbf8f/GCA_003486355.1_ASM348635v1_genomic.fna.gz | prodigal -d GCA_003486355.1_ASM348635v1_genomic.fna/cds.fna -a GCA_003486355.1_ASM348635v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 12:24:57,137] [INFO] Task succeeded: Prodigal
[2023-06-17 12:24:57,138] [INFO] Task started: HMMsearch
[2023-06-17 12:24:57,138] [INFO] Running command: hmmsearch --tblout GCA_003486355.1_ASM348635v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f1d061c-fd72-47fd-8999-f6e10ba24896/dqc_reference/reference_markers.hmm GCA_003486355.1_ASM348635v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 12:24:57,422] [INFO] Task succeeded: HMMsearch
[2023-06-17 12:24:57,423] [INFO] Found 6/6 markers.
[2023-06-17 12:24:57,456] [INFO] Query marker FASTA was written to GCA_003486355.1_ASM348635v1_genomic.fna/markers.fasta
[2023-06-17 12:24:57,456] [INFO] Task started: Blastn
[2023-06-17 12:24:57,456] [INFO] Running command: blastn -query GCA_003486355.1_ASM348635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f1d061c-fd72-47fd-8999-f6e10ba24896/dqc_reference/reference_markers.fasta -out GCA_003486355.1_ASM348635v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 12:24:58,137] [INFO] Task succeeded: Blastn
[2023-06-17 12:24:58,141] [INFO] Selected 30 target genomes.
[2023-06-17 12:24:58,141] [INFO] Target genome list was writen to GCA_003486355.1_ASM348635v1_genomic.fna/target_genomes.txt
[2023-06-17 12:24:58,148] [INFO] Task started: fastANI
[2023-06-17 12:24:58,148] [INFO] Running command: fastANI --query /var/lib/cwl/stge7afd608-a93c-42b4-a29e-ea01bffbbf8f/GCA_003486355.1_ASM348635v1_genomic.fna.gz --refList GCA_003486355.1_ASM348635v1_genomic.fna/target_genomes.txt --output GCA_003486355.1_ASM348635v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 12:25:13,562] [INFO] Task succeeded: fastANI
[2023-06-17 12:25:13,562] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f1d061c-fd72-47fd-8999-f6e10ba24896/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 12:25:13,563] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f1d061c-fd72-47fd-8999-f6e10ba24896/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 12:25:13,577] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 12:25:13,577] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 12:25:13,577] [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 faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	79.5336	149	859	95	below_threshold
Lachnospira eligens	strain=ATCC 27750	GCA_000146185.1	39485	39485	suspected-type	True	78.5912	75	859	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	78.1672	111	859	95	below_threshold
Roseburia porci	strain=MUC/MUC-530-WT-4D	GCA_009695765.1	2605790	2605790	type	True	78.1089	119	859	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	78.0669	109	859	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	78.0599	104	859	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	77.986	108	859	95	below_threshold
Agathobacter ruminis	strain=JK623	GCA_002735305.1	1712665	1712665	type	True	77.9751	83	859	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	77.1685	63	859	95	below_threshold
Anaerobutyricum hallii	strain=DSM 3353	GCA_000173975.1	39488	39488	type	True	76.9983	52	859	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_000154065.1	88431	88431	type	True	76.9799	53	859	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	76.9711	53	859	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 12:25:13,579] [INFO] DFAST Taxonomy check result was written to GCA_003486355.1_ASM348635v1_genomic.fna/tc_result.tsv
[2023-06-17 12:25:13,580] [INFO] ===== Taxonomy check completed =====
[2023-06-17 12:25:13,580] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 12:25:13,580] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f1d061c-fd72-47fd-8999-f6e10ba24896/dqc_reference/checkm_data
[2023-06-17 12:25:13,581] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 12:25:13,613] [INFO] Task started: CheckM
[2023-06-17 12:25:13,613] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003486355.1_ASM348635v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003486355.1_ASM348635v1_genomic.fna/checkm_input GCA_003486355.1_ASM348635v1_genomic.fna/checkm_result
[2023-06-17 12:25:39,967] [INFO] Task succeeded: CheckM
[2023-06-17 12:25:39,969] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 12:25:39,991] [INFO] ===== Completeness check finished =====
[2023-06-17 12:25:39,992] [INFO] ===== Start GTDB Search =====
[2023-06-17 12:25:39,992] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003486355.1_ASM348635v1_genomic.fna/markers.fasta)
[2023-06-17 12:25:39,993] [INFO] Task started: Blastn
[2023-06-17 12:25:39,993] [INFO] Running command: blastn -query GCA_003486355.1_ASM348635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f1d061c-fd72-47fd-8999-f6e10ba24896/dqc_reference/reference_markers_gtdb.fasta -out GCA_003486355.1_ASM348635v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 12:25:41,023] [INFO] Task succeeded: Blastn
[2023-06-17 12:25:41,028] [INFO] Selected 14 target genomes.
[2023-06-17 12:25:41,028] [INFO] Target genome list was writen to GCA_003486355.1_ASM348635v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 12:25:41,031] [INFO] Task started: fastANI
[2023-06-17 12:25:41,031] [INFO] Running command: fastANI --query /var/lib/cwl/stge7afd608-a93c-42b4-a29e-ea01bffbbf8f/GCA_003486355.1_ASM348635v1_genomic.fna.gz --refList GCA_003486355.1_ASM348635v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003486355.1_ASM348635v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 12:25:48,849] [INFO] Task succeeded: fastANI
[2023-06-17 12:25:48,864] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 12:25:48,865] [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_000020605.1	s__Agathobacter rectalis	96.5873	753	859	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	97.37	96.06	0.82	0.65	151	conclusive
GCA_900546625.1	s__Agathobacter sp900546625	94.5805	725	859	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	96.96	96.96	0.86	0.86	2	-
GCA_900317585.1	s__Agathobacter sp900317585	94.0508	616	859	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.18	95.52	0.87	0.83	5	-
GCA_905209075.1	s__Agathobacter sp905209075	81.3255	302	859	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.22	97.67	0.80	0.73	5	-
GCA_900549895.1	s__Agathobacter sp900549895	78.8604	86	859	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548765.1	s__Agathobacter sp900548765	78.7003	170	859	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	97.03	97.03	0.78	0.78	2	-
GCA_900552085.1	s__Agathobacter sp900552085	78.6898	119	859	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	97.03	95.54	0.78	0.69	7	-
GCA_015057085.1	s__Agathobacter sp015057085	78.0128	83	859	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015057035.1	s__Agathobacter sp015057035	77.7494	68	859	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587655.1	s__Agathobacter sp910587655	77.3506	73	859	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017937095.1	s__Roseburia sp017937095	77.1634	73	859	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014804775.1	s__Roseburia sp014804775	76.9859	52	859	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002299665.1	s__CAG-45 sp002299665	76.8312	52	859	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-45	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 12:25:48,867] [INFO] GTDB search result was written to GCA_003486355.1_ASM348635v1_genomic.fna/result_gtdb.tsv
[2023-06-17 12:25:48,868] [INFO] ===== GTDB Search completed =====
[2023-06-17 12:25:48,871] [INFO] DFAST_QC result json was written to GCA_003486355.1_ASM348635v1_genomic.fna/dqc_result.json
[2023-06-17 12:25:48,872] [INFO] DFAST_QC completed!
[2023-06-17 12:25:48,872] [INFO] Total running time: 0h0m60s