[2024-01-24 11:48:21,286] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:48:21,287] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:48:21,287] [INFO] DQC Reference Directory: /var/lib/cwl/stg0947139c-464c-4a38-a36f-7b98a3d8d774/dqc_reference
[2024-01-24 11:48:24,564] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:48:24,566] [INFO] Task started: Prodigal
[2024-01-24 11:48:24,566] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ec99ed1-26c5-4fec-ae1e-eebd4c3245fe/GCF_003725335.1_ASM372533v1_genomic.fna.gz | prodigal -d GCF_003725335.1_ASM372533v1_genomic.fna/cds.fna -a GCF_003725335.1_ASM372533v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:48:32,603] [INFO] Task succeeded: Prodigal
[2024-01-24 11:48:32,603] [INFO] Task started: HMMsearch
[2024-01-24 11:48:32,603] [INFO] Running command: hmmsearch --tblout GCF_003725335.1_ASM372533v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0947139c-464c-4a38-a36f-7b98a3d8d774/dqc_reference/reference_markers.hmm GCF_003725335.1_ASM372533v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:48:32,833] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:48:32,835] [INFO] Found 6/6 markers.
[2024-01-24 11:48:32,860] [INFO] Query marker FASTA was written to GCF_003725335.1_ASM372533v1_genomic.fna/markers.fasta
[2024-01-24 11:48:32,860] [INFO] Task started: Blastn
[2024-01-24 11:48:32,861] [INFO] Running command: blastn -query GCF_003725335.1_ASM372533v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0947139c-464c-4a38-a36f-7b98a3d8d774/dqc_reference/reference_markers.fasta -out GCF_003725335.1_ASM372533v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:48:33,515] [INFO] Task succeeded: Blastn
[2024-01-24 11:48:33,518] [INFO] Selected 13 target genomes.
[2024-01-24 11:48:33,518] [INFO] Target genome list was writen to GCF_003725335.1_ASM372533v1_genomic.fna/target_genomes.txt
[2024-01-24 11:48:33,602] [INFO] Task started: fastANI
[2024-01-24 11:48:33,602] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ec99ed1-26c5-4fec-ae1e-eebd4c3245fe/GCF_003725335.1_ASM372533v1_genomic.fna.gz --refList GCF_003725335.1_ASM372533v1_genomic.fna/target_genomes.txt --output GCF_003725335.1_ASM372533v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:48:40,673] [INFO] Task succeeded: fastANI
[2024-01-24 11:48:40,674] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0947139c-464c-4a38-a36f-7b98a3d8d774/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:48:40,674] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0947139c-464c-4a38-a36f-7b98a3d8d774/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:48:40,692] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:48:40,693] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:48:40,693] [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
Parvibacter caecicola	strain=DSM 22242	GCA_003725335.1	747645	747645	type	True	100.0	802	802	95	conclusive
Parvibacter caecicola	strain=DSM 22242	GCA_024623225.1	747645	747645	type	True	99.9962	802	802	95	conclusive
Parvibacter caecicola	strain=DSM 22242	GCA_014192485.1	747645	747645	type	True	99.9733	787	802	95	conclusive
Adlercreutzia mucosicola	strain=DSM 19490	GCA_024623255.1	580026	580026	type	True	80.8065	299	802	95	below_threshold
Adlercreutzia caecimuris	strain=B7	GCA_000403355.2	671266	671266	type	True	80.712	324	802	95	below_threshold
Adlercreutzia caecimuris	strain=DSM 21839	GCA_024623275.1	671266	671266	type	True	80.2853	329	802	95	below_threshold
Adlercreutzia muris	strain=DSM 29508	GCA_024623245.1	1796610	1796610	type	True	80.2228	323	802	95	below_threshold
Adlercreutzia muris	strain=DSM 29508	GCA_008831045.1	1796610	1796610	type	True	80.0804	324	802	95	below_threshold
Gordonibacter pamelaeae	strain=7-10-1-bT	GCA_000210055.1	471189	471189	type	True	78.8511	254	802	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003725965.1	242230	242230	type	True	78.4751	243	802	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003339815.1	242230	242230	type	True	78.4112	255	802	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	78.3083	254	802	95	below_threshold
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	76.2389	68	802	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:48:40,695] [INFO] DFAST Taxonomy check result was written to GCF_003725335.1_ASM372533v1_genomic.fna/tc_result.tsv
[2024-01-24 11:48:40,695] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:48:40,696] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:48:40,696] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0947139c-464c-4a38-a36f-7b98a3d8d774/dqc_reference/checkm_data
[2024-01-24 11:48:40,697] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:48:40,724] [INFO] Task started: CheckM
[2024-01-24 11:48:40,725] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003725335.1_ASM372533v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003725335.1_ASM372533v1_genomic.fna/checkm_input GCF_003725335.1_ASM372533v1_genomic.fna/checkm_result
[2024-01-24 11:49:08,241] [INFO] Task succeeded: CheckM
[2024-01-24 11:49:08,242] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:49:08,259] [INFO] ===== Completeness check finished =====
[2024-01-24 11:49:08,260] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:49:08,260] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003725335.1_ASM372533v1_genomic.fna/markers.fasta)
[2024-01-24 11:49:08,261] [INFO] Task started: Blastn
[2024-01-24 11:49:08,261] [INFO] Running command: blastn -query GCF_003725335.1_ASM372533v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0947139c-464c-4a38-a36f-7b98a3d8d774/dqc_reference/reference_markers_gtdb.fasta -out GCF_003725335.1_ASM372533v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:49:09,318] [INFO] Task succeeded: Blastn
[2024-01-24 11:49:09,322] [INFO] Selected 18 target genomes.
[2024-01-24 11:49:09,322] [INFO] Target genome list was writen to GCF_003725335.1_ASM372533v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:49:09,337] [INFO] Task started: fastANI
[2024-01-24 11:49:09,337] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ec99ed1-26c5-4fec-ae1e-eebd4c3245fe/GCF_003725335.1_ASM372533v1_genomic.fna.gz --refList GCF_003725335.1_ASM372533v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003725335.1_ASM372533v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:49:18,061] [INFO] Task succeeded: fastANI
[2024-01-24 11:49:18,080] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:49:18,080] [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
GCF_003725335.1	s__Parvibacter caecicola	100.0	802	802	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Parvibacter	95.0	98.71	98.43	0.93	0.91	7	conclusive
GCA_910588725.1	s__Parvibacter sp910588725	82.8654	375	802	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Parvibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422625.1	s__Adlercreutzia mucosicola	80.6751	312	802	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	97.91	97.91	0.87	0.87	2	-
GCF_000403355.2	s__Adlercreutzia caecimuris	80.6729	326	802	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	97.41	97.35	0.86	0.85	5	-
GCA_003612475.1	s__D16-63 sp003612475	80.1499	239	802	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__D16-63	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008831045.1	s__Adlercreutzia muris	80.127	321	802	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	97.80	97.69	0.87	0.84	7	-
GCF_009911695.1	s__QWKK01 sp009911695	79.7725	293	802	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__QWKK01	95.0	98.01	97.98	0.92	0.92	3	-
GCA_910589165.1	s__Adlercreutzia sp910589165	79.6201	315	802	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910589695.1	s__QWKK01 sp910589695	79.5344	279	802	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__QWKK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018710945.1	s__Aphodovivens avistercoris	79.2018	215	802	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Aphodovivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013185065.1	s__CAAEEV01 sp013185065	79.1852	251	802	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAAEEV01	95.0	97.04	97.04	0.76	0.76	2	-
GCF_011038975.1	s__CAAEEV01 sp011038975	78.8292	278	802	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAAEEV01	95.0	99.99	99.99	0.98	0.98	2	-
GCF_000210055.1	s__Gordonibacter pamelaeae	78.8254	257	802	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	98.65	97.59	0.89	0.82	6	-
GCF_003339815.1	s__Eggerthella sinensis	78.3943	256	802	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	99.07	98.15	0.94	0.88	3	-
GCA_900754955.1	s__CAAEEV01 sp900754955	78.3217	154	802	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAAEEV01	95.0	99.85	99.85	0.86	0.86	2	-
GCA_904420215.1	s__CAJFUR01 sp904420215	77.823	194	802	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAJFUR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018715725.1	s__Aveggerthella excrementigallinarum	77.6928	166	802	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Aveggerthella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001486445.1	s__RUG013 sp001486445	77.2449	122	802	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__RUG013	95.0	98.36	97.63	0.92	0.89	7	-
--------------------------------------------------------------------------------
[2024-01-24 11:49:18,081] [INFO] GTDB search result was written to GCF_003725335.1_ASM372533v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:49:18,082] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:49:18,086] [INFO] DFAST_QC result json was written to GCF_003725335.1_ASM372533v1_genomic.fna/dqc_result.json
[2024-01-24 11:49:18,086] [INFO] DFAST_QC completed!
[2024-01-24 11:49:18,086] [INFO] Total running time: 0h0m57s