[2023-06-18 18:31:19,818] [INFO] DFAST_QC pipeline started.
[2023-06-18 18:31:19,823] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 18:31:19,823] [INFO] DQC Reference Directory: /var/lib/cwl/stg69c0026c-2521-4e96-8b18-429d382a2dc0/dqc_reference
[2023-06-18 18:31:21,139] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 18:31:21,140] [INFO] Task started: Prodigal
[2023-06-18 18:31:21,140] [INFO] Running command: gunzip -c /var/lib/cwl/stg780c1db0-daf5-41f8-b62c-7f14e2533946/GCA_937945085.1_SRR2047620_bin.39_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937945085.1_SRR2047620_bin.39_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937945085.1_SRR2047620_bin.39_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 18:31:33,201] [INFO] Task succeeded: Prodigal
[2023-06-18 18:31:33,202] [INFO] Task started: HMMsearch
[2023-06-18 18:31:33,202] [INFO] Running command: hmmsearch --tblout GCA_937945085.1_SRR2047620_bin.39_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69c0026c-2521-4e96-8b18-429d382a2dc0/dqc_reference/reference_markers.hmm GCA_937945085.1_SRR2047620_bin.39_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-18 18:31:33,532] [INFO] Task succeeded: HMMsearch
[2023-06-18 18:31:33,533] [INFO] Found 6/6 markers.
[2023-06-18 18:31:33,572] [INFO] Query marker FASTA was written to GCA_937945085.1_SRR2047620_bin.39_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-18 18:31:33,573] [INFO] Task started: Blastn
[2023-06-18 18:31:33,573] [INFO] Running command: blastn -query GCA_937945085.1_SRR2047620_bin.39_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg69c0026c-2521-4e96-8b18-429d382a2dc0/dqc_reference/reference_markers.fasta -out GCA_937945085.1_SRR2047620_bin.39_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:31:34,504] [INFO] Task succeeded: Blastn
[2023-06-18 18:31:34,508] [INFO] Selected 15 target genomes.
[2023-06-18 18:31:34,508] [INFO] Target genome list was writen to GCA_937945085.1_SRR2047620_bin.39_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-18 18:31:34,514] [INFO] Task started: fastANI
[2023-06-18 18:31:34,515] [INFO] Running command: fastANI --query /var/lib/cwl/stg780c1db0-daf5-41f8-b62c-7f14e2533946/GCA_937945085.1_SRR2047620_bin.39_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937945085.1_SRR2047620_bin.39_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937945085.1_SRR2047620_bin.39_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 18:31:50,161] [INFO] Task succeeded: fastANI
[2023-06-18 18:31:50,162] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69c0026c-2521-4e96-8b18-429d382a2dc0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 18:31:50,162] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69c0026c-2521-4e96-8b18-429d382a2dc0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 18:31:50,175] [INFO] Found 15 fastANI hits (4 hits with ANI > threshold)
[2023-06-18 18:31:50,175] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-18 18:31:50,175] [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
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	97.8905	1186	1506	95	conclusive
Cronobacter sakazakii	strain=NBRC 102416	GCA_000684935.1	28141	28141	type	True	97.8859	1273	1506	95	conclusive
Cronobacter sakazakii	strain=FDAARGOS_927	GCA_016103025.1	28141	28141	type	True	97.8176	1304	1506	95	conclusive
Cronobacter sakazakii	strain=ATCC 29544	GCA_000982825.1	28141	28141	type	True	97.7861	1304	1506	95	conclusive
Cronobacter malonaticus	strain=LMG 23826	GCA_001277215.2	413503	413503	type	True	94.7944	1284	1506	95	below_threshold
Cronobacter malonaticus	strain=LMG 23826	GCA_000409305.1	413503	413503	type	True	94.7746	1253	1506	95	below_threshold
Klebsiella quasipneumoniae subsp. quasipneumoniae	strain=01A030T	GCA_020525925.1	1667327	1463165	type	True	81.6505	757	1506	95	below_threshold
Klebsiella quasipneumoniae	strain=FDAARGOS_1503	GCA_020099175.1	1463165	1463165	type	True	81.6363	763	1506	95	below_threshold
Klebsiella quasipneumoniae	strain=DSM 28211	GCA_020115515.1	1463165	1463165	type	True	81.5978	749	1506	95	below_threshold
Klebsiella quasipneumoniae subsp. similipneumoniae	strain=07A044T	GCA_020525685.1	1463164	1463165	type	True	81.5258	763	1506	95	below_threshold
Klebsiella quasipneumoniae subsp. similipneumoniae	strain=07A044	GCA_000613225.1	1463164	1463165	type	True	81.4959	754	1506	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.3666	820	1506	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.0448	802	1506	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	80.9182	809	1506	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	80.8671	827	1506	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 18:31:50,177] [INFO] DFAST Taxonomy check result was written to GCA_937945085.1_SRR2047620_bin.39_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-18 18:31:50,178] [INFO] ===== Taxonomy check completed =====
[2023-06-18 18:31:50,178] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 18:31:50,178] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69c0026c-2521-4e96-8b18-429d382a2dc0/dqc_reference/checkm_data
[2023-06-18 18:31:50,179] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 18:31:50,223] [INFO] Task started: CheckM
[2023-06-18 18:31:50,224] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937945085.1_SRR2047620_bin.39_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937945085.1_SRR2047620_bin.39_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937945085.1_SRR2047620_bin.39_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-18 18:32:28,576] [INFO] Task succeeded: CheckM
[2023-06-18 18:32:28,578] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.68%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 18:32:28,600] [INFO] ===== Completeness check finished =====
[2023-06-18 18:32:28,600] [INFO] ===== Start GTDB Search =====
[2023-06-18 18:32:28,601] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937945085.1_SRR2047620_bin.39_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-18 18:32:28,601] [INFO] Task started: Blastn
[2023-06-18 18:32:28,601] [INFO] Running command: blastn -query GCA_937945085.1_SRR2047620_bin.39_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg69c0026c-2521-4e96-8b18-429d382a2dc0/dqc_reference/reference_markers_gtdb.fasta -out GCA_937945085.1_SRR2047620_bin.39_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:32:29,863] [INFO] Task succeeded: Blastn
[2023-06-18 18:32:29,868] [INFO] Selected 14 target genomes.
[2023-06-18 18:32:29,868] [INFO] Target genome list was writen to GCA_937945085.1_SRR2047620_bin.39_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 18:32:29,901] [INFO] Task started: fastANI
[2023-06-18 18:32:29,902] [INFO] Running command: fastANI --query /var/lib/cwl/stg780c1db0-daf5-41f8-b62c-7f14e2533946/GCA_937945085.1_SRR2047620_bin.39_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937945085.1_SRR2047620_bin.39_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937945085.1_SRR2047620_bin.39_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 18:32:44,066] [INFO] Task succeeded: fastANI
[2023-06-18 18:32:44,083] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 18:32:44,083] [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_000982825.1	s__Cronobacter sakazakii	97.8009	1303	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	98.00	97.39	0.92	0.86	440	conclusive
GCF_001277215.2	s__Cronobacter malonaticus	94.7944	1284	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	98.86	98.11	0.94	0.89	62	-
GCF_001277175.1	s__Cronobacter universalis	93.648	1258	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	99.87	99.62	0.99	0.98	4	-
GCA_000027065.2	s__Cronobacter turicensis	92.1504	1274	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	97.17	96.06	0.93	0.89	18	-
GCF_001277195.1	s__Cronobacter muytjensii	89.3017	1202	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	99.13	98.83	0.94	0.91	9	-
GCF_001277235.1	s__Cronobacter dublinensis	89.301	1220	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	97.74	96.92	0.93	0.89	42	-
GCF_000751755.1	s__Klebsiella quasipneumoniae	81.521	776	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	97.20	95.71	0.90	0.83	644	-
GCF_000742135.1	s__Klebsiella pneumoniae	81.2304	746	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.216	98.97	95.97	0.88	0.77	11294	-
GCF_000828055.2	s__Klebsiella variicola	81.2003	746	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.94	96.87	0.93	0.84	528	-
GCF_900978845.1	s__Klebsiella africana	81.0027	726	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.216	95.65	95.27	0.93	0.90	27	-
GCF_000215745.1	s__Klebsiella aerogenes	80.5078	746	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.40	95.78	0.92	0.85	341	-
GCF_001656035.1	s__Yersinia entomophaga	77.6159	266	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.84	99.69	0.97	0.94	3	-
GCF_001112925.1	s__Yersinia nurmii	77.5118	271	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001152565.1	s__Yersinia pekkanenii	77.2485	197	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.90	99.90	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-06-18 18:32:44,085] [INFO] GTDB search result was written to GCA_937945085.1_SRR2047620_bin.39_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-18 18:32:44,086] [INFO] ===== GTDB Search completed =====
[2023-06-18 18:32:44,091] [INFO] DFAST_QC result json was written to GCA_937945085.1_SRR2047620_bin.39_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-18 18:32:44,091] [INFO] DFAST_QC completed!
[2023-06-18 18:32:44,091] [INFO] Total running time: 0h1m24s