[2023-06-29 00:37:18,584] [INFO] DFAST_QC pipeline started.
[2023-06-29 00:37:18,594] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 00:37:18,594] [INFO] DQC Reference Directory: /var/lib/cwl/stg6bebfad5-5526-48ae-b1ea-d148604421d2/dqc_reference
[2023-06-29 00:37:19,857] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 00:37:19,858] [INFO] Task started: Prodigal
[2023-06-29 00:37:19,858] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ff71c94-0123-4033-a163-3ffae90c0270/GCA_913041545.1_ERR599044_bin.14_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913041545.1_ERR599044_bin.14_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913041545.1_ERR599044_bin.14_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 00:37:27,671] [INFO] Task succeeded: Prodigal
[2023-06-29 00:37:27,672] [INFO] Task started: HMMsearch
[2023-06-29 00:37:27,672] [INFO] Running command: hmmsearch --tblout GCA_913041545.1_ERR599044_bin.14_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6bebfad5-5526-48ae-b1ea-d148604421d2/dqc_reference/reference_markers.hmm GCA_913041545.1_ERR599044_bin.14_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 00:37:27,964] [INFO] Task succeeded: HMMsearch
[2023-06-29 00:37:27,965] [INFO] Found 6/6 markers.
[2023-06-29 00:37:27,995] [INFO] Query marker FASTA was written to GCA_913041545.1_ERR599044_bin.14_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-29 00:37:27,996] [INFO] Task started: Blastn
[2023-06-29 00:37:27,996] [INFO] Running command: blastn -query GCA_913041545.1_ERR599044_bin.14_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bebfad5-5526-48ae-b1ea-d148604421d2/dqc_reference/reference_markers.fasta -out GCA_913041545.1_ERR599044_bin.14_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:37:28,700] [INFO] Task succeeded: Blastn
[2023-06-29 00:37:28,704] [INFO] Selected 19 target genomes.
[2023-06-29 00:37:28,704] [INFO] Target genome list was writen to GCA_913041545.1_ERR599044_bin.14_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 00:37:28,708] [INFO] Task started: fastANI
[2023-06-29 00:37:28,708] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ff71c94-0123-4033-a163-3ffae90c0270/GCA_913041545.1_ERR599044_bin.14_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913041545.1_ERR599044_bin.14_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913041545.1_ERR599044_bin.14_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 00:37:42,445] [INFO] Task succeeded: fastANI
[2023-06-29 00:37:42,445] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6bebfad5-5526-48ae-b1ea-d148604421d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 00:37:42,446] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6bebfad5-5526-48ae-b1ea-d148604421d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 00:37:42,455] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 00:37:42,455] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 00:37:42,455] [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
Methylophaga sulfidovorans	strain=DSM 11578	GCA_900114205.1	45496	45496	type	True	84.2862	733	1040	95	below_threshold
Methylophaga aminisulfidivorans	strain=MP	GCA_000214595.2	230105	230105	type	True	84.1958	760	1040	95	below_threshold
Methylophaga nitratireducenticrescens	strain=JAM1	GCA_000260985.3	754476	754476	type	True	78.1901	114	1040	95	below_threshold
Methylophaga pinxianii	strain=TMB456	GCA_020447225.1	2881052	2881052	type	True	78.1052	135	1040	95	below_threshold
Methylophaga thiooxydans	strain=DMS010	GCA_000156355.1	392484	392484	type	True	77.9805	230	1040	95	below_threshold
Methylophaga lonarensis	strain=MPL	GCA_000349205.1	999151	999151	type	True	77.0356	91	1040	95	below_threshold
Methylophaga frappieri	strain=JAM7	GCA_000260965.1	754477	754477	type	True	76.6752	83	1040	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 00:37:42,458] [INFO] DFAST Taxonomy check result was written to GCA_913041545.1_ERR599044_bin.14_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 00:37:42,458] [INFO] ===== Taxonomy check completed =====
[2023-06-29 00:37:42,459] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 00:37:42,459] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6bebfad5-5526-48ae-b1ea-d148604421d2/dqc_reference/checkm_data
[2023-06-29 00:37:42,460] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 00:37:42,501] [INFO] Task started: CheckM
[2023-06-29 00:37:42,501] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913041545.1_ERR599044_bin.14_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913041545.1_ERR599044_bin.14_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913041545.1_ERR599044_bin.14_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-29 00:38:12,809] [INFO] Task succeeded: CheckM
[2023-06-29 00:38:12,811] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 00:38:12,835] [INFO] ===== Completeness check finished =====
[2023-06-29 00:38:12,836] [INFO] ===== Start GTDB Search =====
[2023-06-29 00:38:12,836] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913041545.1_ERR599044_bin.14_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 00:38:12,836] [INFO] Task started: Blastn
[2023-06-29 00:38:12,837] [INFO] Running command: blastn -query GCA_913041545.1_ERR599044_bin.14_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bebfad5-5526-48ae-b1ea-d148604421d2/dqc_reference/reference_markers_gtdb.fasta -out GCA_913041545.1_ERR599044_bin.14_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:38:13,935] [INFO] Task succeeded: Blastn
[2023-06-29 00:38:13,940] [INFO] Selected 14 target genomes.
[2023-06-29 00:38:13,940] [INFO] Target genome list was writen to GCA_913041545.1_ERR599044_bin.14_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 00:38:14,018] [INFO] Task started: fastANI
[2023-06-29 00:38:14,018] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ff71c94-0123-4033-a163-3ffae90c0270/GCA_913041545.1_ERR599044_bin.14_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913041545.1_ERR599044_bin.14_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913041545.1_ERR599044_bin.14_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 00:38:22,025] [INFO] Task succeeded: fastANI
[2023-06-29 00:38:22,040] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 00:38:22,040] [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_002706095.1	s__Methylophaga sp002706095	99.9907	997	1040	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	98.12	97.28	0.92	0.89	8	conclusive
GCF_900114205.1	s__Methylophaga sulfidovorans	84.283	733	1040	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000214595.1	s__Methylophaga aminisulfidivorans	84.1958	760	1040	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	97.12	97.07	0.93	0.92	4	-
GCA_011052985.1	s__Methylophaga aminisulfidivorans_A	80.5692	231	1040	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002696735.1	s__Methylophaga sp002696735	80.0172	151	1040	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	98.51	97.89	0.93	0.90	20	-
GCA_002354555.1	s__Methylophaga sp002354555	78.1564	138	1040	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	98.87	98.17	0.91	0.88	3	-
GCA_009711715.1	s__Methylophaga sp009711715	77.9833	175	1040	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000156355.1	s__Methylophaga thiooxydans	77.9802	230	1040	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	96.48	96.37	0.89	0.88	3	-
GCA_002363955.1	s__Methylophaga sp002363955	77.6076	127	1040	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	98.95	98.64	0.94	0.91	14	-
GCA_013215825.1	s__GCA-002733105 sp013215825	76.2166	65	1040	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 00:38:22,042] [INFO] GTDB search result was written to GCA_913041545.1_ERR599044_bin.14_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 00:38:22,043] [INFO] ===== GTDB Search completed =====
[2023-06-29 00:38:22,046] [INFO] DFAST_QC result json was written to GCA_913041545.1_ERR599044_bin.14_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 00:38:22,046] [INFO] DFAST_QC completed!
[2023-06-29 00:38:22,046] [INFO] Total running time: 0h1m3s