[2023-06-13 20:23:47,544] [INFO] DFAST_QC pipeline started.
[2023-06-13 20:23:47,546] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 20:23:47,547] [INFO] DQC Reference Directory: /var/lib/cwl/stg3191add5-a6e1-4b5d-9b5b-6edf975bc8d3/dqc_reference
[2023-06-13 20:23:49,365] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 20:23:49,366] [INFO] Task started: Prodigal
[2023-06-13 20:23:49,366] [INFO] Running command: gunzip -c /var/lib/cwl/stg8eef6713-6436-482e-bc2a-429657f92cb2/GCA_022730795.1_ASM2273079v1_genomic.fna.gz | prodigal -d GCA_022730795.1_ASM2273079v1_genomic.fna/cds.fna -a GCA_022730795.1_ASM2273079v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 20:23:55,985] [INFO] Task succeeded: Prodigal
[2023-06-13 20:23:55,985] [INFO] Task started: HMMsearch
[2023-06-13 20:23:55,985] [INFO] Running command: hmmsearch --tblout GCA_022730795.1_ASM2273079v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3191add5-a6e1-4b5d-9b5b-6edf975bc8d3/dqc_reference/reference_markers.hmm GCA_022730795.1_ASM2273079v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 20:23:56,249] [INFO] Task succeeded: HMMsearch
[2023-06-13 20:23:56,250] [INFO] Found 6/6 markers.
[2023-06-13 20:23:56,277] [INFO] Query marker FASTA was written to GCA_022730795.1_ASM2273079v1_genomic.fna/markers.fasta
[2023-06-13 20:23:56,277] [INFO] Task started: Blastn
[2023-06-13 20:23:56,277] [INFO] Running command: blastn -query GCA_022730795.1_ASM2273079v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3191add5-a6e1-4b5d-9b5b-6edf975bc8d3/dqc_reference/reference_markers.fasta -out GCA_022730795.1_ASM2273079v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 20:23:56,848] [INFO] Task succeeded: Blastn
[2023-06-13 20:23:56,851] [INFO] Selected 28 target genomes.
[2023-06-13 20:23:56,851] [INFO] Target genome list was writen to GCA_022730795.1_ASM2273079v1_genomic.fna/target_genomes.txt
[2023-06-13 20:23:56,853] [INFO] Task started: fastANI
[2023-06-13 20:23:56,853] [INFO] Running command: fastANI --query /var/lib/cwl/stg8eef6713-6436-482e-bc2a-429657f92cb2/GCA_022730795.1_ASM2273079v1_genomic.fna.gz --refList GCA_022730795.1_ASM2273079v1_genomic.fna/target_genomes.txt --output GCA_022730795.1_ASM2273079v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 20:24:10,705] [INFO] Task succeeded: fastANI
[2023-06-13 20:24:10,706] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3191add5-a6e1-4b5d-9b5b-6edf975bc8d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 20:24:10,706] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3191add5-a6e1-4b5d-9b5b-6edf975bc8d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 20:24:10,719] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 20:24:10,719] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 20:24:10,719] [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	81.2189	169	886	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	80.6157	114	886	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	80.4735	112	886	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	80.1762	111	886	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	79.5534	107	886	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	79.1316	128	886	95	below_threshold
Roseburia porci	strain=MUC/MUC-530-WT-4D	GCA_009695765.1	2605790	2605790	type	True	78.7718	119	886	95	below_threshold
Roseburia lenta	strain=NSJ-9	GCA_014287435.1	2763061	2763061	type	True	78.7298	68	886	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	78.3394	52	886	95	below_threshold
Agathobacter ruminis	strain=JK623	GCA_002735305.1	1712665	1712665	type	True	77.8456	77	886	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 20:24:10,724] [INFO] DFAST Taxonomy check result was written to GCA_022730795.1_ASM2273079v1_genomic.fna/tc_result.tsv
[2023-06-13 20:24:10,724] [INFO] ===== Taxonomy check completed =====
[2023-06-13 20:24:10,725] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 20:24:10,725] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3191add5-a6e1-4b5d-9b5b-6edf975bc8d3/dqc_reference/checkm_data
[2023-06-13 20:24:10,726] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 20:24:10,767] [INFO] Task started: CheckM
[2023-06-13 20:24:10,767] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022730795.1_ASM2273079v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022730795.1_ASM2273079v1_genomic.fna/checkm_input GCA_022730795.1_ASM2273079v1_genomic.fna/checkm_result
[2023-06-13 20:24:35,650] [INFO] Task succeeded: CheckM
[2023-06-13 20:24:35,651] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 12.22%
Strain heterogeneity: 42.86%
--------------------------------------------------------------------------------
[2023-06-13 20:24:35,671] [INFO] ===== Completeness check finished =====
[2023-06-13 20:24:35,671] [INFO] ===== Start GTDB Search =====
[2023-06-13 20:24:35,672] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022730795.1_ASM2273079v1_genomic.fna/markers.fasta)
[2023-06-13 20:24:35,673] [INFO] Task started: Blastn
[2023-06-13 20:24:35,673] [INFO] Running command: blastn -query GCA_022730795.1_ASM2273079v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3191add5-a6e1-4b5d-9b5b-6edf975bc8d3/dqc_reference/reference_markers_gtdb.fasta -out GCA_022730795.1_ASM2273079v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 20:24:36,611] [INFO] Task succeeded: Blastn
[2023-06-13 20:24:36,614] [INFO] Selected 14 target genomes.
[2023-06-13 20:24:36,614] [INFO] Target genome list was writen to GCA_022730795.1_ASM2273079v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 20:24:36,615] [INFO] Task started: fastANI
[2023-06-13 20:24:36,615] [INFO] Running command: fastANI --query /var/lib/cwl/stg8eef6713-6436-482e-bc2a-429657f92cb2/GCA_022730795.1_ASM2273079v1_genomic.fna.gz --refList GCA_022730795.1_ASM2273079v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022730795.1_ASM2273079v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 20:24:43,676] [INFO] Task succeeded: fastANI
[2023-06-13 20:24:43,684] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 20:24:43,684] [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	96.5263	693	886	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	94.6889	644	886	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	93.8561	578	886	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	81.2946	283	886	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	79.0223	78	886	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003470905.1	s__Roseburia sp003470905	78.7221	107	886	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.69	98.30	0.90	0.82	7	-
GCA_900552085.1	s__Agathobacter sp900552085	78.4601	106	886	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_900543445.1	s__Agathobacter sp900543445	78.2132	116	886	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.64	98.60	0.88	0.84	3	-
GCF_002735305.1	s__Agathobacter ruminis	77.8915	76	886	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.23	97.94	0.91	0.87	3	-
GCA_910587655.1	s__Agathobacter sp910587655	77.3306	70	886	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	77.1159	74	886	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 20:24:43,686] [INFO] GTDB search result was written to GCA_022730795.1_ASM2273079v1_genomic.fna/result_gtdb.tsv
[2023-06-13 20:24:43,686] [INFO] ===== GTDB Search completed =====
[2023-06-13 20:24:43,689] [INFO] DFAST_QC result json was written to GCA_022730795.1_ASM2273079v1_genomic.fna/dqc_result.json
[2023-06-13 20:24:43,689] [INFO] DFAST_QC completed!
[2023-06-13 20:24:43,689] [INFO] Total running time: 0h0m56s