[2023-06-28 21:02:27,047] [INFO] DFAST_QC pipeline started.
[2023-06-28 21:02:27,050] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 21:02:27,050] [INFO] DQC Reference Directory: /var/lib/cwl/stg9bd1c164-ee19-4d8d-a5ca-b7b86e25f46c/dqc_reference
[2023-06-28 21:02:28,319] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 21:02:28,320] [INFO] Task started: Prodigal
[2023-06-28 21:02:28,320] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f6d1138-86b9-423f-96bf-42e9cdef3028/GCA_913049765.1_ERR598965_bin.167_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913049765.1_ERR598965_bin.167_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913049765.1_ERR598965_bin.167_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 21:02:38,752] [INFO] Task succeeded: Prodigal
[2023-06-28 21:02:38,753] [INFO] Task started: HMMsearch
[2023-06-28 21:02:38,753] [INFO] Running command: hmmsearch --tblout GCA_913049765.1_ERR598965_bin.167_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9bd1c164-ee19-4d8d-a5ca-b7b86e25f46c/dqc_reference/reference_markers.hmm GCA_913049765.1_ERR598965_bin.167_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 21:02:39,024] [INFO] Task succeeded: HMMsearch
[2023-06-28 21:02:39,025] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg4f6d1138-86b9-423f-96bf-42e9cdef3028/GCA_913049765.1_ERR598965_bin.167_MetaBAT_v2.12.1_MAG_genomic.fna.gz]
[2023-06-28 21:02:39,066] [INFO] Query marker FASTA was written to GCA_913049765.1_ERR598965_bin.167_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-28 21:02:39,067] [INFO] Task started: Blastn
[2023-06-28 21:02:39,067] [INFO] Running command: blastn -query GCA_913049765.1_ERR598965_bin.167_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg9bd1c164-ee19-4d8d-a5ca-b7b86e25f46c/dqc_reference/reference_markers.fasta -out GCA_913049765.1_ERR598965_bin.167_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:02:39,639] [INFO] Task succeeded: Blastn
[2023-06-28 21:02:39,645] [INFO] Selected 17 target genomes.
[2023-06-28 21:02:39,645] [INFO] Target genome list was writen to GCA_913049765.1_ERR598965_bin.167_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-28 21:02:39,648] [INFO] Task started: fastANI
[2023-06-28 21:02:39,648] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f6d1138-86b9-423f-96bf-42e9cdef3028/GCA_913049765.1_ERR598965_bin.167_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913049765.1_ERR598965_bin.167_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913049765.1_ERR598965_bin.167_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 21:02:56,104] [INFO] Task succeeded: fastANI
[2023-06-28 21:02:56,105] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9bd1c164-ee19-4d8d-a5ca-b7b86e25f46c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 21:02:56,105] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9bd1c164-ee19-4d8d-a5ca-b7b86e25f46c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 21:02:56,122] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2023-06-28 21:02:56,123] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 21:02:56,123] [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
Pseudomonas marincola	strain=JCM 14761	GCA_900116605.1	437900	437900	type	True	97.4812	1042	1090	95	conclusive
Pseudomonas segetis	strain=CIP 108523	GCA_900188155.1	298908	298908	type	True	79.3828	526	1090	95	below_threshold
Pseudomonas tumuqii	strain=LAMW06	GCA_013184545.1	2715755	2715755	type	True	79.2048	516	1090	95	below_threshold
Pseudomonas borbori	strain=DSM 17834	GCA_900115555.1	289003	289003	type	True	79.0414	482	1090	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	78.9791	441	1090	95	below_threshold
Pseudomonas granadensis	strain=LMG 27940	GCA_900105485.1	1421430	1421430	suspected-type	True	78.5404	372	1090	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	78.4345	404	1090	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	78.3161	330	1090	95	below_threshold
Pseudomonas vancouverensis	strain=CCUG 49675	GCA_008801375.1	95300	95300	type	True	78.2441	380	1090	95	below_threshold
Pseudomonas vancouverensis	strain=Dha-51	GCA_004348895.1	95300	95300	type	True	78.2225	380	1090	95	below_threshold
[Pseudomonas] nosocomialis	strain=A31/70	GCA_005876855.1	1056496	1056496	type	True	77.8333	327	1090	95	below_threshold
Pseudomonas nitrititolerans	strain=GL14	GCA_003696285.1	2482751	2482751	type	True	77.8075	295	1090	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	77.7878	299	1090	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	77.7751	304	1090	95	below_threshold
Stutzerimonas xanthomarina	strain=DSM 18231	GCA_024328335.1	271420	271420	suspected-type	True	77.6691	256	1090	95	below_threshold
Stutzerimonas xanthomarina	strain=DSM 18231	GCA_900129835.1	271420	271420	suspected-type	True	77.62	266	1090	95	below_threshold
Stutzerimonas balearica	strain=DSM6083 (=SP1402)	GCA_000818015.1	74829	74829	type	True	77.5804	293	1090	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 21:02:56,125] [INFO] DFAST Taxonomy check result was written to GCA_913049765.1_ERR598965_bin.167_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-28 21:02:56,126] [INFO] ===== Taxonomy check completed =====
[2023-06-28 21:02:56,126] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 21:02:56,126] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9bd1c164-ee19-4d8d-a5ca-b7b86e25f46c/dqc_reference/checkm_data
[2023-06-28 21:02:56,128] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 21:02:56,173] [INFO] Task started: CheckM
[2023-06-28 21:02:56,173] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913049765.1_ERR598965_bin.167_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913049765.1_ERR598965_bin.167_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913049765.1_ERR598965_bin.167_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-28 21:03:31,096] [INFO] Task succeeded: CheckM
[2023-06-28 21:03:31,098] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 44.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 21:03:31,121] [INFO] ===== Completeness check finished =====
[2023-06-28 21:03:31,122] [INFO] ===== Start GTDB Search =====
[2023-06-28 21:03:31,122] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913049765.1_ERR598965_bin.167_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-28 21:03:31,123] [INFO] Task started: Blastn
[2023-06-28 21:03:31,123] [INFO] Running command: blastn -query GCA_913049765.1_ERR598965_bin.167_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg9bd1c164-ee19-4d8d-a5ca-b7b86e25f46c/dqc_reference/reference_markers_gtdb.fasta -out GCA_913049765.1_ERR598965_bin.167_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:03:31,743] [INFO] Task succeeded: Blastn
[2023-06-28 21:03:31,748] [INFO] Selected 17 target genomes.
[2023-06-28 21:03:31,748] [INFO] Target genome list was writen to GCA_913049765.1_ERR598965_bin.167_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 21:03:31,806] [INFO] Task started: fastANI
[2023-06-28 21:03:31,806] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f6d1138-86b9-423f-96bf-42e9cdef3028/GCA_913049765.1_ERR598965_bin.167_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913049765.1_ERR598965_bin.167_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913049765.1_ERR598965_bin.167_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 21:03:47,590] [INFO] Task succeeded: fastANI
[2023-06-28 21:03:47,608] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 21:03:47,608] [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_900116605.1	s__Pseudomonas_E marincola	97.4812	1042	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.48	97.31	0.90	0.86	9	conclusive
GCA_002840155.1	s__Pseudomonas_E sp002840155	79.4156	504	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013184545.1	s__Pseudomonas_E sp013184545	79.2138	515	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099645.1	s__Pseudomonas_E peli	79.0724	482	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.85	96.04	0.90	0.85	7	-
GCF_900115555.1	s__Pseudomonas_E borbori	79.0322	483	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018398425.1	s__Pseudomonas_E lalucatii	78.9791	441	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	99.28	0.97	0.92	4	-
GCF_003060885.1	s__Pseudomonas_E sp003060885	78.9292	442	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001567565.1	s__Pseudomonas_E composti_A	78.7386	457	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004327355.1	s__Pseudomonas_E dryadis	78.6402	441	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.58	99.16	0.96	0.92	3	-
GCF_900105485.1	s__Pseudomonas_E granadensis	78.5397	372	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.04	95.81	0.93	0.92	8	-
GCF_016901015.1	s__Pseudomonas_E sp016901015	78.4345	404	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902825215.1	s__Pseudomonas_E fluorescens_G	78.3995	394	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.46	97.46	0.85	0.85	2	-
GCF_002890895.1	s__Pseudomonas_A stutzeri_AB	77.7101	257	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.17	97.01	0.91	0.85	18	-
GCA_004010935.1	s__Pseudomonas_A sp004010935	77.6217	255	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	96.94	95.82	0.92	0.89	15	-
GCF_900129835.1	s__Pseudomonas_A xanthomarina	77.62	266	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002452485.1	s__Pseudomonas_A stutzeri_P	77.5745	248	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000235745.1	s__Pseudomonas_A stutzeri_H	77.3794	255	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 21:03:47,610] [INFO] GTDB search result was written to GCA_913049765.1_ERR598965_bin.167_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 21:03:47,611] [INFO] ===== GTDB Search completed =====
[2023-06-28 21:03:47,615] [INFO] DFAST_QC result json was written to GCA_913049765.1_ERR598965_bin.167_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-28 21:03:47,615] [INFO] DFAST_QC completed!
[2023-06-28 21:03:47,615] [INFO] Total running time: 0h1m21s