[2023-06-13 17:11:54,315] [INFO] DFAST_QC pipeline started.
[2023-06-13 17:11:54,317] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 17:11:54,317] [INFO] DQC Reference Directory: /var/lib/cwl/stgaaa45739-5bb4-4d2e-ae6b-76207024ae1a/dqc_reference
[2023-06-13 17:11:55,598] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 17:11:55,599] [INFO] Task started: Prodigal
[2023-06-13 17:11:55,600] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d61f029-267d-405b-8991-4da6be6f26b8/GCA_022773965.1_ASM2277396v1_genomic.fna.gz | prodigal -d GCA_022773965.1_ASM2277396v1_genomic.fna/cds.fna -a GCA_022773965.1_ASM2277396v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 17:12:03,664] [INFO] Task succeeded: Prodigal
[2023-06-13 17:12:03,664] [INFO] Task started: HMMsearch
[2023-06-13 17:12:03,664] [INFO] Running command: hmmsearch --tblout GCA_022773965.1_ASM2277396v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaaa45739-5bb4-4d2e-ae6b-76207024ae1a/dqc_reference/reference_markers.hmm GCA_022773965.1_ASM2277396v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 17:12:03,938] [INFO] Task succeeded: HMMsearch
[2023-06-13 17:12:03,940] [INFO] Found 6/6 markers.
[2023-06-13 17:12:03,985] [INFO] Query marker FASTA was written to GCA_022773965.1_ASM2277396v1_genomic.fna/markers.fasta
[2023-06-13 17:12:03,985] [INFO] Task started: Blastn
[2023-06-13 17:12:03,985] [INFO] Running command: blastn -query GCA_022773965.1_ASM2277396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaaa45739-5bb4-4d2e-ae6b-76207024ae1a/dqc_reference/reference_markers.fasta -out GCA_022773965.1_ASM2277396v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:12:04,499] [INFO] Task succeeded: Blastn
[2023-06-13 17:12:04,503] [INFO] Selected 29 target genomes.
[2023-06-13 17:12:04,504] [INFO] Target genome list was writen to GCA_022773965.1_ASM2277396v1_genomic.fna/target_genomes.txt
[2023-06-13 17:12:04,510] [INFO] Task started: fastANI
[2023-06-13 17:12:04,510] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d61f029-267d-405b-8991-4da6be6f26b8/GCA_022773965.1_ASM2277396v1_genomic.fna.gz --refList GCA_022773965.1_ASM2277396v1_genomic.fna/target_genomes.txt --output GCA_022773965.1_ASM2277396v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 17:12:19,217] [INFO] Task succeeded: fastANI
[2023-06-13 17:12:19,217] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaaa45739-5bb4-4d2e-ae6b-76207024ae1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 17:12:19,218] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaaa45739-5bb4-4d2e-ae6b-76207024ae1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 17:12:19,233] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 17:12:19,234] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 17:12:19,234] [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	77.8623	113	1001	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	77.5903	111	1001	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	77.5809	109	1001	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	77.5721	111	1001	95	below_threshold
Roseburia porci	strain=MUC/MUC-530-WT-4D	GCA_009695765.1	2605790	2605790	type	True	77.0071	67	1001	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	76.8903	77	1001	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	76.8237	108	1001	95	below_threshold
Roseburia lenta	strain=NSJ-9	GCA_014287435.1	2763061	2763061	type	True	76.5864	61	1001	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	76.5255	65	1001	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	76.2547	50	1001	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 17:12:19,237] [INFO] DFAST Taxonomy check result was written to GCA_022773965.1_ASM2277396v1_genomic.fna/tc_result.tsv
[2023-06-13 17:12:19,238] [INFO] ===== Taxonomy check completed =====
[2023-06-13 17:12:19,238] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 17:12:19,239] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaaa45739-5bb4-4d2e-ae6b-76207024ae1a/dqc_reference/checkm_data
[2023-06-13 17:12:19,241] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 17:12:19,282] [INFO] Task started: CheckM
[2023-06-13 17:12:19,283] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022773965.1_ASM2277396v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022773965.1_ASM2277396v1_genomic.fna/checkm_input GCA_022773965.1_ASM2277396v1_genomic.fna/checkm_result
[2023-06-13 17:12:50,308] [INFO] Task succeeded: CheckM
[2023-06-13 17:12:50,310] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.98%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 17:12:50,334] [INFO] ===== Completeness check finished =====
[2023-06-13 17:12:50,334] [INFO] ===== Start GTDB Search =====
[2023-06-13 17:12:50,335] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022773965.1_ASM2277396v1_genomic.fna/markers.fasta)
[2023-06-13 17:12:50,336] [INFO] Task started: Blastn
[2023-06-13 17:12:50,336] [INFO] Running command: blastn -query GCA_022773965.1_ASM2277396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaaa45739-5bb4-4d2e-ae6b-76207024ae1a/dqc_reference/reference_markers_gtdb.fasta -out GCA_022773965.1_ASM2277396v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:12:50,833] [INFO] Task succeeded: Blastn
[2023-06-13 17:12:50,838] [INFO] Selected 23 target genomes.
[2023-06-13 17:12:50,838] [INFO] Target genome list was writen to GCA_022773965.1_ASM2277396v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 17:12:50,855] [INFO] Task started: fastANI
[2023-06-13 17:12:50,855] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d61f029-267d-405b-8991-4da6be6f26b8/GCA_022773965.1_ASM2277396v1_genomic.fna.gz --refList GCA_022773965.1_ASM2277396v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022773965.1_ASM2277396v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 17:13:02,584] [INFO] Task succeeded: fastANI
[2023-06-13 17:13:02,601] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 17:13:02,602] [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_004562765.1	s__W0P33-017 sp004562765	82.4223	609	1001	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__W0P33-017	95.0	97.98	97.98	0.87	0.87	2	-
GCA_017623885.1	s__W0P33-017 sp017623885	78.683	208	1001	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__W0P33-017	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910589045.1	s__W0P33-017 sp910589045	78.202	266	1001	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__W0P33-017	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001406815.1	s__Agathobacter faecis	77.8623	113	1001	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.10	97.07	0.85	0.62	43	-
GCF_900537995.1	s__Roseburia intestinalis	77.6011	110	1001	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.51	98.07	0.86	0.80	21	-
GCA_002474415.1	s__Agathobacter sp002474415	77.0217	70	1001	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_003478275.1	s__AM51-8 sp003478275	76.8613	58	1001	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__AM51-8	95.0	99.20	98.90	0.94	0.89	8	-
GCF_000225345.1	s__Roseburia hominis	76.8237	108	1001	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.94	95.20	0.88	0.81	15	-
GCA_902782995.1	s__RUG115 sp902782995	76.7126	75	1001	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316805.1	s__Agathobacter sp900316805	76.707	76	1001	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	99.85	99.74	0.94	0.92	3	-
GCA_015056815.1	s__SIG333 sp015056815	76.5994	58	1001	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__SIG333	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548205.1	s__Roseburia sp900548205	76.5268	52	1001	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	99.97	99.97	0.82	0.82	2	-
GCA_910578885.1	s__RUG115 sp910578885	76.4855	62	1001	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546495.1	s__Eubacterium_I sp900546495	76.042	61	1001	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_I	95.0	99.94	99.87	0.93	0.88	3	-
--------------------------------------------------------------------------------
[2023-06-13 17:13:02,603] [INFO] GTDB search result was written to GCA_022773965.1_ASM2277396v1_genomic.fna/result_gtdb.tsv
[2023-06-13 17:13:02,604] [INFO] ===== GTDB Search completed =====
[2023-06-13 17:13:02,608] [INFO] DFAST_QC result json was written to GCA_022773965.1_ASM2277396v1_genomic.fna/dqc_result.json
[2023-06-13 17:13:02,608] [INFO] DFAST_QC completed!
[2023-06-13 17:13:02,608] [INFO] Total running time: 0h1m8s