[2024-01-24 11:34:54,481] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:54,483] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:54,483] [INFO] DQC Reference Directory: /var/lib/cwl/stg036efe0d-155a-4d42-98c4-0c956b5b9c5e/dqc_reference
[2024-01-24 11:34:56,317] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:56,318] [INFO] Task started: Prodigal
[2024-01-24 11:34:56,318] [INFO] Running command: gunzip -c /var/lib/cwl/stgf7e3d3d5-8fe4-46e9-b54c-109f067578f7/GCF_024622195.1_ASM2462219v1_genomic.fna.gz | prodigal -d GCF_024622195.1_ASM2462219v1_genomic.fna/cds.fna -a GCF_024622195.1_ASM2462219v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:10,368] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:10,368] [INFO] Task started: HMMsearch
[2024-01-24 11:35:10,368] [INFO] Running command: hmmsearch --tblout GCF_024622195.1_ASM2462219v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg036efe0d-155a-4d42-98c4-0c956b5b9c5e/dqc_reference/reference_markers.hmm GCF_024622195.1_ASM2462219v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:10,702] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:10,703] [INFO] Found 6/6 markers.
[2024-01-24 11:35:10,754] [INFO] Query marker FASTA was written to GCF_024622195.1_ASM2462219v1_genomic.fna/markers.fasta
[2024-01-24 11:35:10,754] [INFO] Task started: Blastn
[2024-01-24 11:35:10,755] [INFO] Running command: blastn -query GCF_024622195.1_ASM2462219v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg036efe0d-155a-4d42-98c4-0c956b5b9c5e/dqc_reference/reference_markers.fasta -out GCF_024622195.1_ASM2462219v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:11,428] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:11,432] [INFO] Selected 29 target genomes.
[2024-01-24 11:35:11,433] [INFO] Target genome list was writen to GCF_024622195.1_ASM2462219v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:11,446] [INFO] Task started: fastANI
[2024-01-24 11:35:11,446] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7e3d3d5-8fe4-46e9-b54c-109f067578f7/GCF_024622195.1_ASM2462219v1_genomic.fna.gz --refList GCF_024622195.1_ASM2462219v1_genomic.fna/target_genomes.txt --output GCF_024622195.1_ASM2462219v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:31,550] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:31,550] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg036efe0d-155a-4d42-98c4-0c956b5b9c5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:31,551] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg036efe0d-155a-4d42-98c4-0c956b5b9c5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:31,568] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:31,568] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:31,569] [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
Murimonas intestini	strain=DSM 26524	GCA_024622195.1	1337051	1337051	type	True	100.0	1891	1891	95	conclusive
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	79.8052	79	1891	95	below_threshold
Coprococcus catus	strain=ATCC 27761	GCA_025289135.1	116085	116085	suspected-type	True	79.4938	59	1891	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	79.3602	71	1891	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	78.9861	65	1891	95	below_threshold
Blautia coccoides	strain=NCTC11035	GCA_900461125.1	1532	1532	type	True	78.1289	155	1891	95	below_threshold
Blautia coccoides	strain=DSM 935	GCA_004340925.1	1532	1532	type	True	78.0048	150	1891	95	below_threshold
[Clostridium] hylemonae	strain=DSM 15053	GCA_008281175.1	89153	89153	type	True	77.3966	67	1891	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	77.3157	89	1891	95	below_threshold
[Clostridium] hylemonae	strain=DSM 15053	GCA_000156515.1	89153	89153	type	True	77.2726	69	1891	95	below_threshold
Lactonifactor longoviformis	strain=DSM 17459	GCA_900129135.1	341220	341220	suspected-type	True	77.239	91	1891	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_025147655.1	1322	1322	type	True	77.0916	66	1891	95	below_threshold
Faecalicatena faecalis	strain=AGMB00832	GCA_012524165.2	2726362	2726362	type	True	77.0083	88	1891	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	76.9345	69	1891	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	76.9077	71	1891	95	below_threshold
Diplocloster agilis	strain=ASD5720	GCA_019042275.1	2850323	2850323	type	True	76.7806	82	1891	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	76.7474	66	1891	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	76.6906	63	1891	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	76.6564	65	1891	95	below_threshold
Lachnotalea glycerini	strain=DSM 28816	GCA_003201285.1	1763509	1763509	type	True	76.6496	51	1891	95	below_threshold
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	76.5538	84	1891	95	below_threshold
Anaerostipes hominis	strain=BG01	GCA_002270485.1	2025494	2025494	type	True	76.4529	51	1891	95	below_threshold
Diplocloster modestus	strain=ASD4241	GCA_019042245.1	2850322	2850322	type	True	76.3093	85	1891	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:31,570] [INFO] DFAST Taxonomy check result was written to GCF_024622195.1_ASM2462219v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:31,571] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:31,571] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:31,571] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg036efe0d-155a-4d42-98c4-0c956b5b9c5e/dqc_reference/checkm_data
[2024-01-24 11:35:31,572] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:31,630] [INFO] Task started: CheckM
[2024-01-24 11:35:31,630] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024622195.1_ASM2462219v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024622195.1_ASM2462219v1_genomic.fna/checkm_input GCF_024622195.1_ASM2462219v1_genomic.fna/checkm_result
[2024-01-24 11:36:15,852] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:15,853] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:15,876] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:15,876] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:15,876] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024622195.1_ASM2462219v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:15,877] [INFO] Task started: Blastn
[2024-01-24 11:36:15,877] [INFO] Running command: blastn -query GCF_024622195.1_ASM2462219v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg036efe0d-155a-4d42-98c4-0c956b5b9c5e/dqc_reference/reference_markers_gtdb.fasta -out GCF_024622195.1_ASM2462219v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:16,905] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:16,908] [INFO] Selected 26 target genomes.
[2024-01-24 11:36:16,908] [INFO] Target genome list was writen to GCF_024622195.1_ASM2462219v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:16,942] [INFO] Task started: fastANI
[2024-01-24 11:36:16,942] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7e3d3d5-8fe4-46e9-b54c-109f067578f7/GCF_024622195.1_ASM2462219v1_genomic.fna.gz --refList GCF_024622195.1_ASM2462219v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024622195.1_ASM2462219v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:35,731] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:35,752] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:35,752] [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_003148945.1	s__Murimonas intestini	99.9988	1885	1891	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Murimonas	95.0	98.81	98.81	0.92	0.92	2	conclusive
GCA_900549995.1	s__UMGS1251 sp900549995	78.0625	87	1891	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UMGS1251	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900539655.1	s__Robinsoniella sp900539655	77.5219	155	1891	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Robinsoniella	95.0	99.96	99.96	0.92	0.92	2	-
GCF_000797495.1	s__Robinsoniella peoriensis	77.5102	169	1891	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Robinsoniella	95.0	98.88	98.73	0.91	0.88	7	-
GCA_900762665.1	s__CAG-56 sp900762665	76.9512	140	1891	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-56	95.0	99.95	99.95	0.93	0.93	2	-
GCF_003463065.1	s__Limivivens sp900066135	76.9312	107	1891	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Limivivens	95.0	98.47	97.63	0.91	0.79	5	-
GCA_004557975.1	s__Choladousia sp004557975	76.7654	83	1891	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900539525.1	s__CAG-56 sp900539525	76.6863	113	1891	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-56	95.0	99.91	99.91	0.93	0.93	2	-
GCA_910575835.1	s__Sporofaciens sp910575835	76.635	60	1891	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009911175.1	s__Schaedlerella sp009911175	76.6161	72	1891	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	98.09	98.08	0.79	0.79	3	-
GCA_900757145.1	s__Choladousia sp900757145	76.5742	59	1891	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	99.16	99.16	0.96	0.96	2	-
GCA_900551235.1	s__UMGS1375 sp900551235	76.4862	86	1891	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UMGS1375	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019112785.1	s__Blautia stercorigallinarum	76.479	77	1891	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.88	99.88	0.94	0.94	2	-
GCA_910589075.1	s__VSOB01 sp910589075	76.353	51	1891	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_905214675.1	s__UMGS1375 sp905214675	76.2164	54	1891	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UMGS1375	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017621815.1	s__CAG-95 sp017621815	76.1439	52	1891	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910575605.1	s__UBA7109 sp910575605	76.143	55	1891	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA7109	95.0	99.27	99.27	0.93	0.93	2	-
GCA_019114545.1	s__Blautia pullistercoris	76.0943	74	1891	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.87	98.79	0.80	0.76	4	-
GCA_900543715.1	s__Blautia merdigallinarum	76.0846	95	1891	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.67	98.67	0.84	0.84	2	-
GCA_019115125.1	s__Blautia_A faecipullorum	76.0569	79	1891	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.90	97.90	0.82	0.82	2	-
GCA_910575105.1	s__MD308 sp910575105	75.8912	62	1891	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__MD308	95.0	99.99	99.99	0.99	0.99	2	-
GCA_910580075.1	s__Eubacterium_J sp910580075	75.8602	54	1891	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_J	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019120545.1	s__Blautia stercoripullorum	75.4231	64	1891	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:35,754] [INFO] GTDB search result was written to GCF_024622195.1_ASM2462219v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:35,754] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:35,759] [INFO] DFAST_QC result json was written to GCF_024622195.1_ASM2462219v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:35,759] [INFO] DFAST_QC completed!
[2024-01-24 11:36:35,759] [INFO] Total running time: 0h1m41s