[2023-06-08 20:36:16,595] [INFO] DFAST_QC pipeline started.
[2023-06-08 20:36:16,598] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 20:36:16,598] [INFO] DQC Reference Directory: /var/lib/cwl/stgf41926c3-f7b1-4e8f-958d-986a29e9a84b/dqc_reference
[2023-06-08 20:36:17,848] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 20:36:17,849] [INFO] Task started: Prodigal
[2023-06-08 20:36:17,849] [INFO] Running command: gunzip -c /var/lib/cwl/stg04a53429-23f3-476f-ae79-cdc3e6150923/GCA_947367265.1_SRR15429272_bin.10_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947367265.1_SRR15429272_bin.10_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947367265.1_SRR15429272_bin.10_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 20:36:21,782] [INFO] Task succeeded: Prodigal
[2023-06-08 20:36:21,782] [INFO] Task started: HMMsearch
[2023-06-08 20:36:21,782] [INFO] Running command: hmmsearch --tblout GCA_947367265.1_SRR15429272_bin.10_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf41926c3-f7b1-4e8f-958d-986a29e9a84b/dqc_reference/reference_markers.hmm GCA_947367265.1_SRR15429272_bin.10_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 20:36:21,978] [INFO] Task succeeded: HMMsearch
[2023-06-08 20:36:21,979] [INFO] Found 6/6 markers.
[2023-06-08 20:36:21,998] [INFO] Query marker FASTA was written to GCA_947367265.1_SRR15429272_bin.10_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 20:36:21,998] [INFO] Task started: Blastn
[2023-06-08 20:36:21,998] [INFO] Running command: blastn -query GCA_947367265.1_SRR15429272_bin.10_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf41926c3-f7b1-4e8f-958d-986a29e9a84b/dqc_reference/reference_markers.fasta -out GCA_947367265.1_SRR15429272_bin.10_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:36:22,833] [INFO] Task succeeded: Blastn
[2023-06-08 20:36:22,837] [INFO] Selected 17 target genomes.
[2023-06-08 20:36:22,837] [INFO] Target genome list was writen to GCA_947367265.1_SRR15429272_bin.10_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 20:36:22,839] [INFO] Task started: fastANI
[2023-06-08 20:36:22,839] [INFO] Running command: fastANI --query /var/lib/cwl/stg04a53429-23f3-476f-ae79-cdc3e6150923/GCA_947367265.1_SRR15429272_bin.10_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947367265.1_SRR15429272_bin.10_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947367265.1_SRR15429272_bin.10_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 20:36:30,307] [INFO] Task succeeded: fastANI
[2023-06-08 20:36:30,308] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf41926c3-f7b1-4e8f-958d-986a29e9a84b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 20:36:30,308] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf41926c3-f7b1-4e8f-958d-986a29e9a84b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 20:36:30,325] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 20:36:30,325] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 20:36:30,325] [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
Adlercreutzia caecimuris	strain=B7	GCA_000403355.2	671266	671266	type	True	82.0482	181	370	95	below_threshold
Adlercreutzia caecimuris	strain=DSM 21839	GCA_024623275.1	671266	671266	type	True	82.033	181	370	95	below_threshold
Adlercreutzia muris	strain=DSM 29508	GCA_024623245.1	1796610	1796610	type	True	81.72	188	370	95	below_threshold
Adlercreutzia muris	strain=DSM 29508	GCA_008831045.1	1796610	1796610	type	True	81.6543	188	370	95	below_threshold
Adlercreutzia equolifaciens subsp. celatus	strain=DSM 18785	GCA_024171685.1	394340	446660	type	True	81.1535	182	370	95	below_threshold
Adlercreutzia equolifaciens subsp. celatus	strain=JCM 14811	GCA_016865385.1	394340	446660	type	True	81.1054	182	370	95	below_threshold
Adlercreutzia equolifaciens subsp. equolifaciens	strain=DSM 19450	GCA_000478885.1	2864143	446660	type	True	81.0237	181	370	95	below_threshold
Adlercreutzia equolifaciens subsp. celatus	strain=DSM 18785	GCA_003726015.1	394340	446660	type	True	81.0169	183	370	95	below_threshold
Gordonibacter urolithinfaciens	strain=DSM 27213T	GCA_900199375.1	1335613	1335613	type	True	80.7639	191	370	95	below_threshold
Gordonibacter urolithinfaciens	strain=DSM 27213	GCA_003788975.1	1335613	1335613	type	True	80.7549	190	370	95	below_threshold
Gordonibacter pamelaeae	strain=7-10-1-bT	GCA_000210055.1	471189	471189	type	True	80.6002	197	370	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_000024265.1	84112	84112	type	True	80.4527	156	370	95	below_threshold
Eggerthella lenta	strain=UCSF2243	GCA_003339945.1	84112	84112	type	True	80.3713	155	370	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	80.2827	153	370	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_003339975.1	84112	84112	type	True	80.2469	162	370	95	below_threshold
Eggerthella timonensis	strain=Marseille-P3135	GCA_900184265.1	1871008	1871008	type	True	80.165	166	370	95	below_threshold
Eggerthella guodeyinii	strain=HF-1101	GCA_009834925.2	2690837	2690837	type	True	80.0548	181	370	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 20:36:30,328] [INFO] DFAST Taxonomy check result was written to GCA_947367265.1_SRR15429272_bin.10_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 20:36:30,328] [INFO] ===== Taxonomy check completed =====
[2023-06-08 20:36:30,329] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 20:36:30,329] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf41926c3-f7b1-4e8f-958d-986a29e9a84b/dqc_reference/checkm_data
[2023-06-08 20:36:30,330] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 20:36:30,352] [INFO] Task started: CheckM
[2023-06-08 20:36:30,352] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947367265.1_SRR15429272_bin.10_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947367265.1_SRR15429272_bin.10_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947367265.1_SRR15429272_bin.10_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 20:36:49,287] [INFO] Task succeeded: CheckM
[2023-06-08 20:36:49,289] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.22%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 20:36:49,309] [INFO] ===== Completeness check finished =====
[2023-06-08 20:36:49,309] [INFO] ===== Start GTDB Search =====
[2023-06-08 20:36:49,310] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947367265.1_SRR15429272_bin.10_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 20:36:49,310] [INFO] Task started: Blastn
[2023-06-08 20:36:49,310] [INFO] Running command: blastn -query GCA_947367265.1_SRR15429272_bin.10_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf41926c3-f7b1-4e8f-958d-986a29e9a84b/dqc_reference/reference_markers_gtdb.fasta -out GCA_947367265.1_SRR15429272_bin.10_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:36:50,705] [INFO] Task succeeded: Blastn
[2023-06-08 20:36:50,709] [INFO] Selected 16 target genomes.
[2023-06-08 20:36:50,709] [INFO] Target genome list was writen to GCA_947367265.1_SRR15429272_bin.10_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 20:36:50,714] [INFO] Task started: fastANI
[2023-06-08 20:36:50,714] [INFO] Running command: fastANI --query /var/lib/cwl/stg04a53429-23f3-476f-ae79-cdc3e6150923/GCA_947367265.1_SRR15429272_bin.10_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947367265.1_SRR15429272_bin.10_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947367265.1_SRR15429272_bin.10_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 20:36:58,563] [INFO] Task succeeded: fastANI
[2023-06-08 20:36:58,583] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 20:36:58,583] [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_003612475.1	s__D16-63 sp003612475	98.1061	333	370	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__D16-63	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910588095.1	s__D16-63 sp910588095	87.497	254	370	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_009911695.1	s__QWKK01 sp009911695	82.5358	191	370	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__QWKK01	95.0	98.01	97.98	0.92	0.92	3	-
GCF_000403355.2	s__Adlercreutzia caecimuris	82.062	181	370	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	97.41	97.35	0.86	0.85	5	-
GCA_910589695.1	s__QWKK01 sp910589695	81.989	192	370	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__QWKK01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422625.1	s__Adlercreutzia mucosicola	81.7657	191	370	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	97.91	97.91	0.87	0.87	2	-
GCF_013185065.1	s__CAAEEV01 sp013185065	81.7648	193	370	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	81.7544	195	370	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAAEEV01	95.0	99.99	99.99	0.98	0.98	2	-
GCF_008831045.1	s__Adlercreutzia muris	81.58	190	370	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	97.80	97.69	0.87	0.84	7	-
GCA_910589165.1	s__Adlercreutzia sp910589165	81.0761	177	370	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000478885.1	s__Adlercreutzia equolifaciens	81.0237	181	370	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	97.05	95.56	0.84	0.79	7	-
GCA_018710945.1	s__Aphodovivens avistercoris	80.8648	152	370	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Aphodovivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900199375.1	s__Gordonibacter urolithinfaciens	80.7962	190	370	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	98.27	97.45	0.89	0.82	14	-
GCF_000024265.1	s__Eggerthella lenta	80.4915	155	370	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	98.39	97.51	0.89	0.82	72	-
GCF_009834925.2	s__Eggerthella sp014287365	80.0548	181	370	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	97.74	96.91	0.89	0.85	3	-
GCA_910588725.1	s__Parvibacter sp910588725	79.3725	121	370	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Parvibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 20:36:58,586] [INFO] GTDB search result was written to GCA_947367265.1_SRR15429272_bin.10_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 20:36:58,586] [INFO] ===== GTDB Search completed =====
[2023-06-08 20:36:58,591] [INFO] DFAST_QC result json was written to GCA_947367265.1_SRR15429272_bin.10_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 20:36:58,591] [INFO] DFAST_QC completed!
[2023-06-08 20:36:58,591] [INFO] Total running time: 0h0m42s