[2023-06-16 22:13:21,928] [INFO] DFAST_QC pipeline started.
[2023-06-16 22:13:21,932] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 22:13:21,932] [INFO] DQC Reference Directory: /var/lib/cwl/stg7004c2c4-6f84-48d7-b885-34690162139b/dqc_reference
[2023-06-16 22:13:23,226] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 22:13:23,227] [INFO] Task started: Prodigal
[2023-06-16 22:13:23,227] [INFO] Running command: gunzip -c /var/lib/cwl/stg2c7d3a51-8547-4af0-a237-793cb3bdbfa4/GCA_905216045.1_SRR5558281-mag-bin.11_genomic.fna.gz | prodigal -d GCA_905216045.1_SRR5558281-mag-bin.11_genomic.fna/cds.fna -a GCA_905216045.1_SRR5558281-mag-bin.11_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 22:13:28,625] [INFO] Task succeeded: Prodigal
[2023-06-16 22:13:28,626] [INFO] Task started: HMMsearch
[2023-06-16 22:13:28,626] [INFO] Running command: hmmsearch --tblout GCA_905216045.1_SRR5558281-mag-bin.11_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7004c2c4-6f84-48d7-b885-34690162139b/dqc_reference/reference_markers.hmm GCA_905216045.1_SRR5558281-mag-bin.11_genomic.fna/protein.faa > /dev/null
[2023-06-16 22:13:28,846] [INFO] Task succeeded: HMMsearch
[2023-06-16 22:13:28,847] [INFO] Found 6/6 markers.
[2023-06-16 22:13:28,868] [INFO] Query marker FASTA was written to GCA_905216045.1_SRR5558281-mag-bin.11_genomic.fna/markers.fasta
[2023-06-16 22:13:28,869] [INFO] Task started: Blastn
[2023-06-16 22:13:28,869] [INFO] Running command: blastn -query GCA_905216045.1_SRR5558281-mag-bin.11_genomic.fna/markers.fasta -db /var/lib/cwl/stg7004c2c4-6f84-48d7-b885-34690162139b/dqc_reference/reference_markers.fasta -out GCA_905216045.1_SRR5558281-mag-bin.11_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 22:13:29,628] [INFO] Task succeeded: Blastn
[2023-06-16 22:13:29,633] [INFO] Selected 13 target genomes.
[2023-06-16 22:13:29,634] [INFO] Target genome list was writen to GCA_905216045.1_SRR5558281-mag-bin.11_genomic.fna/target_genomes.txt
[2023-06-16 22:13:29,635] [INFO] Task started: fastANI
[2023-06-16 22:13:29,635] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c7d3a51-8547-4af0-a237-793cb3bdbfa4/GCA_905216045.1_SRR5558281-mag-bin.11_genomic.fna.gz --refList GCA_905216045.1_SRR5558281-mag-bin.11_genomic.fna/target_genomes.txt --output GCA_905216045.1_SRR5558281-mag-bin.11_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 22:13:35,918] [INFO] Task succeeded: fastANI
[2023-06-16 22:13:35,919] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7004c2c4-6f84-48d7-b885-34690162139b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 22:13:35,920] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7004c2c4-6f84-48d7-b885-34690162139b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 22:13:35,937] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 22:13:35,937] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 22:13:35,937] [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
Collinsella aerofaciens	strain=ATCC 25986	GCA_000169035.1	74426	74426	type	True	94.8159	501	556	95	below_threshold
Collinsella aerofaciens	strain=NCTC11838	GCA_900461335.1	74426	74426	type	True	94.7673	506	556	95	below_threshold
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	94.7521	512	556	95	below_threshold
Collinsella bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	80.273	197	556	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	79.9662	225	556	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	79.8583	229	556	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	79.8175	216	556	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.3348	188	556	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	78.9867	168	556	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	78.8886	210	556	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	78.588	126	556	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 22:13:35,941] [INFO] DFAST Taxonomy check result was written to GCA_905216045.1_SRR5558281-mag-bin.11_genomic.fna/tc_result.tsv
[2023-06-16 22:13:35,942] [INFO] ===== Taxonomy check completed =====
[2023-06-16 22:13:35,943] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 22:13:35,943] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7004c2c4-6f84-48d7-b885-34690162139b/dqc_reference/checkm_data
[2023-06-16 22:13:35,945] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 22:13:35,979] [INFO] Task started: CheckM
[2023-06-16 22:13:35,979] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905216045.1_SRR5558281-mag-bin.11_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905216045.1_SRR5558281-mag-bin.11_genomic.fna/checkm_input GCA_905216045.1_SRR5558281-mag-bin.11_genomic.fna/checkm_result
[2023-06-16 22:13:58,432] [INFO] Task succeeded: CheckM
[2023-06-16 22:13:58,433] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.04%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 22:13:58,454] [INFO] ===== Completeness check finished =====
[2023-06-16 22:13:58,454] [INFO] ===== Start GTDB Search =====
[2023-06-16 22:13:58,455] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905216045.1_SRR5558281-mag-bin.11_genomic.fna/markers.fasta)
[2023-06-16 22:13:58,455] [INFO] Task started: Blastn
[2023-06-16 22:13:58,455] [INFO] Running command: blastn -query GCA_905216045.1_SRR5558281-mag-bin.11_genomic.fna/markers.fasta -db /var/lib/cwl/stg7004c2c4-6f84-48d7-b885-34690162139b/dqc_reference/reference_markers_gtdb.fasta -out GCA_905216045.1_SRR5558281-mag-bin.11_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 22:13:59,795] [INFO] Task succeeded: Blastn
[2023-06-16 22:13:59,801] [INFO] Selected 27 target genomes.
[2023-06-16 22:13:59,801] [INFO] Target genome list was writen to GCA_905216045.1_SRR5558281-mag-bin.11_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 22:13:59,858] [INFO] Task started: fastANI
[2023-06-16 22:13:59,858] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c7d3a51-8547-4af0-a237-793cb3bdbfa4/GCA_905216045.1_SRR5558281-mag-bin.11_genomic.fna.gz --refList GCA_905216045.1_SRR5558281-mag-bin.11_genomic.fna/target_genomes_gtdb.txt --output GCA_905216045.1_SRR5558281-mag-bin.11_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 22:14:10,959] [INFO] Task succeeded: fastANI
[2023-06-16 22:14:10,984] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 22:14:10,984] [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_905216045.1	s__Collinsella sp905216045	99.9999	541	556	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1904	95.27	95.27	0.89	0.89	2	conclusive
GCA_900545665.1	s__Collinsella sp900545665	94.8492	484	556	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1787	95.41	95.41	0.86	0.86	2	-
GCA_900752015.1	s__Collinsella sp900752015	94.7835	472	556	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1642	99.95	99.95	0.93	0.93	2	-
GCA_900540985.1	s__Collinsella sp900540985	94.7722	475	556	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0011	97.54	95.11	0.88	0.81	3	-
GCA_900552185.1	s__Collinsella sp900552185	94.7535	367	556	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1905	N/A	N/A	N/A	N/A	1	-
GCA_900550195.1	s__Collinsella sp900550195	94.7514	465	556	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1628	N/A	N/A	N/A	N/A	1	-
GCA_900547345.1	s__Collinsella sp900547345	94.7499	429	556	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0188	95.15	95.15	0.87	0.87	2	-
GCA_900541065.1	s__Collinsella sp900541065	94.7319	487	556	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0334	N/A	N/A	N/A	N/A	1	-
GCA_900754525.1	s__Collinsella sp900754525	94.7009	447	556	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0709	95.23	95.09	0.81	0.78	4	-
GCA_900549065.1	s__Collinsella sp900549065	94.6141	419	556	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1036	N/A	N/A	N/A	N/A	1	-
GCA_900762015.1	s__Collinsella sp900762015	94.5397	440	556	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1172	N/A	N/A	N/A	N/A	1	-
GCF_019131995.1	s__Collinsella aerofaciens_S	94.4977	504	556	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.99	99.99	0.99	0.99	2	-
GCA_900543605.1	s__Collinsella sp900543605	94.4966	448	556	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008671285.1	s__Collinsella sp003487125	94.4644	362	556	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.69	95.69	0.82	0.82	2	-
GCA_900553475.1	s__Collinsella sp900553475	94.4436	361	556	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0051	N/A	N/A	N/A	N/A	1	-
GCA_900541725.1	s__Collinsella sp900541725	94.4212	489	556	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900548815.1	s__Collinsella sp900548815	94.4031	456	556	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900751755.1	s__Collinsella sp900751755	94.3978	454	556	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.91	99.91	0.92	0.92	2	-
GCA_900552145.1	s__Collinsella sp900552145	94.3865	446	556	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.82	98.82	0.84	0.84	2	-
GCA_900761615.1	s__Collinsella sp900761615	94.3419	406	556	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.16	95.16	0.89	0.89	2	-
GCA_900540905.1	s__Collinsella sp900540905	94.3233	477	556	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.98	99.98	0.97	0.97	2	-
GCA_905215195.1	s__Collinsella sp905215195	94.309	370	556	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555815.1	s__Collinsella sp900555815	94.1197	260	556	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554905.1	s__Collinsella sp900554905	94.1014	306	556	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0183	N/A	N/A	N/A	N/A	1	-
GCA_900551635.1	s__Collinsella sp900551635	93.8943	322	556	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.56	99.56	0.78	0.78	2	-
GCA_900545905.1	s__Collinsella sp900545905	93.6123	349	556	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900759045.1	s__Collinsella sp900759045	93.1007	448	556	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 22:14:10,987] [INFO] GTDB search result was written to GCA_905216045.1_SRR5558281-mag-bin.11_genomic.fna/result_gtdb.tsv
[2023-06-16 22:14:10,987] [INFO] ===== GTDB Search completed =====
[2023-06-16 22:14:10,992] [INFO] DFAST_QC result json was written to GCA_905216045.1_SRR5558281-mag-bin.11_genomic.fna/dqc_result.json
[2023-06-16 22:14:10,992] [INFO] DFAST_QC completed!
[2023-06-16 22:14:10,992] [INFO] Total running time: 0h0m49s