[2023-06-13 21:08:17,887] [INFO] DFAST_QC pipeline started.
[2023-06-13 21:08:17,889] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 21:08:17,889] [INFO] DQC Reference Directory: /var/lib/cwl/stgdeba593c-4b8c-4c07-9e11-ae73bc251926/dqc_reference
[2023-06-13 21:08:19,049] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 21:08:19,055] [INFO] Task started: Prodigal
[2023-06-13 21:08:19,055] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ce5ad16-902e-471e-baee-d32c94e117dc/GCA_938041545.1_ERR589515_bin.13_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938041545.1_ERR589515_bin.13_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938041545.1_ERR589515_bin.13_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 21:08:24,585] [INFO] Task succeeded: Prodigal
[2023-06-13 21:08:24,585] [INFO] Task started: HMMsearch
[2023-06-13 21:08:24,585] [INFO] Running command: hmmsearch --tblout GCA_938041545.1_ERR589515_bin.13_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdeba593c-4b8c-4c07-9e11-ae73bc251926/dqc_reference/reference_markers.hmm GCA_938041545.1_ERR589515_bin.13_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 21:08:24,817] [INFO] Task succeeded: HMMsearch
[2023-06-13 21:08:24,818] [INFO] Found 6/6 markers.
[2023-06-13 21:08:24,842] [INFO] Query marker FASTA was written to GCA_938041545.1_ERR589515_bin.13_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 21:08:24,842] [INFO] Task started: Blastn
[2023-06-13 21:08:24,843] [INFO] Running command: blastn -query GCA_938041545.1_ERR589515_bin.13_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgdeba593c-4b8c-4c07-9e11-ae73bc251926/dqc_reference/reference_markers.fasta -out GCA_938041545.1_ERR589515_bin.13_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:08:25,679] [INFO] Task succeeded: Blastn
[2023-06-13 21:08:25,683] [INFO] Selected 17 target genomes.
[2023-06-13 21:08:25,683] [INFO] Target genome list was writen to GCA_938041545.1_ERR589515_bin.13_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 21:08:25,686] [INFO] Task started: fastANI
[2023-06-13 21:08:25,686] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ce5ad16-902e-471e-baee-d32c94e117dc/GCA_938041545.1_ERR589515_bin.13_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938041545.1_ERR589515_bin.13_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938041545.1_ERR589515_bin.13_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 21:08:33,932] [INFO] Task succeeded: fastANI
[2023-06-13 21:08:33,933] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdeba593c-4b8c-4c07-9e11-ae73bc251926/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 21:08:33,933] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdeba593c-4b8c-4c07-9e11-ae73bc251926/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 21:08:33,943] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 21:08:33,943] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 21:08:33,943] [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
Rothia mucilaginosa	strain=ATCC 25296	GCA_000175615.1	43675	43675	suspected-type	True	94.314	681	746	95	below_threshold
Rothia aeria	strain=FDAARGOS_1137	GCA_016726365.1	172042	172042	type	True	79.0221	264	746	95	below_threshold
Rothia dentocariosa	strain=NCTC10917	GCA_900455895.1	2047	2047	type	True	79.0135	219	746	95	below_threshold
Rothia dentocariosa	strain=ATCC 17931	GCA_000164695.2	2047	2047	type	True	79.0135	222	746	95	below_threshold
Rothia aerolata	strain=CCM 8669	GCA_014635585.1	1812262	1812262	type	True	78.3183	189	746	95	below_threshold
Rothia terrae	strain=LMG 23708	GCA_012396615.1	396015	396015	type	True	78.2606	136	746	95	below_threshold
Glutamicibacter mysorens	strain=NBRC 103060	GCA_001552115.1	257984	257984	type	True	77.3555	73	746	95	below_threshold
Arthrobacter luteolus	strain=DSM 13067	GCA_008973725.1	98672	98672	type	True	77.3125	83	746	95	below_threshold
Rothia koreensis	strain=JCM 15915	GCA_004136575.1	592378	592378	type	True	77.1662	85	746	95	below_threshold
Kocuria rhizophila	strain=TA68	GCA_003667225.1	72000	72000	type	True	77.1034	104	746	95	below_threshold
Glutamicibacter mishrai	strain=S5-52	GCA_012221945.1	1775880	1775880	type	True	77.0545	76	746	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	77.0115	53	746	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	76.1731	55	746	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	75.9193	57	746	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 21:08:33,945] [INFO] DFAST Taxonomy check result was written to GCA_938041545.1_ERR589515_bin.13_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 21:08:33,945] [INFO] ===== Taxonomy check completed =====
[2023-06-13 21:08:33,946] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 21:08:33,946] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdeba593c-4b8c-4c07-9e11-ae73bc251926/dqc_reference/checkm_data
[2023-06-13 21:08:33,947] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 21:08:33,972] [INFO] Task started: CheckM
[2023-06-13 21:08:33,972] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938041545.1_ERR589515_bin.13_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938041545.1_ERR589515_bin.13_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938041545.1_ERR589515_bin.13_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 21:08:54,791] [INFO] Task succeeded: CheckM
[2023-06-13 21:08:54,792] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 21:08:54,811] [INFO] ===== Completeness check finished =====
[2023-06-13 21:08:54,811] [INFO] ===== Start GTDB Search =====
[2023-06-13 21:08:54,811] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938041545.1_ERR589515_bin.13_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 21:08:54,812] [INFO] Task started: Blastn
[2023-06-13 21:08:54,812] [INFO] Running command: blastn -query GCA_938041545.1_ERR589515_bin.13_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgdeba593c-4b8c-4c07-9e11-ae73bc251926/dqc_reference/reference_markers_gtdb.fasta -out GCA_938041545.1_ERR589515_bin.13_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:08:56,017] [INFO] Task succeeded: Blastn
[2023-06-13 21:08:56,020] [INFO] Selected 6 target genomes.
[2023-06-13 21:08:56,020] [INFO] Target genome list was writen to GCA_938041545.1_ERR589515_bin.13_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 21:08:56,024] [INFO] Task started: fastANI
[2023-06-13 21:08:56,024] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ce5ad16-902e-471e-baee-d32c94e117dc/GCA_938041545.1_ERR589515_bin.13_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938041545.1_ERR589515_bin.13_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938041545.1_ERR589515_bin.13_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 21:08:59,550] [INFO] Task succeeded: fastANI
[2023-06-13 21:08:59,560] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 21:08:59,561] [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_001548235.1	s__Rothia mucilaginosa_B	95.4314	695	746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	95.72	95.51	0.97	0.96	3	conclusive
GCF_000175615.1	s__Rothia mucilaginosa	94.314	681	746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	95.99	95.33	0.94	0.89	44	-
GCF_001808955.1	s__Rothia sp001808955	94.093	698	746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	96.04	95.53	0.94	0.90	20	-
GCA_015265375.1	s__Rothia sp015265375	93.6503	620	746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	95.30	95.30	0.97	0.97	2	-
GCF_001061665.1	s__Rothia mucilaginosa_A	88.7724	625	746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	97.28	96.59	0.94	0.92	10	-
GCF_901875305.1	s__Rothia sp902373285	87.8269	636	746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	97.53	97.34	0.97	0.96	6	-
--------------------------------------------------------------------------------
[2023-06-13 21:08:59,563] [INFO] GTDB search result was written to GCA_938041545.1_ERR589515_bin.13_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 21:08:59,564] [INFO] ===== GTDB Search completed =====
[2023-06-13 21:08:59,567] [INFO] DFAST_QC result json was written to GCA_938041545.1_ERR589515_bin.13_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 21:08:59,567] [INFO] DFAST_QC completed!
[2023-06-13 21:08:59,567] [INFO] Total running time: 0h0m42s