[2023-06-13 11:03:33,626] [INFO] DFAST_QC pipeline started.
[2023-06-13 11:03:33,630] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 11:03:33,630] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ea262e6-9888-4792-a8ef-d580ca98b927/dqc_reference
[2023-06-13 11:03:35,194] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 11:03:35,194] [INFO] Task started: Prodigal
[2023-06-13 11:03:35,195] [INFO] Running command: gunzip -c /var/lib/cwl/stg42211ea3-37ed-4655-a59e-7cae37ed688a/GCA_938045985.1_ERR589530_bin.78_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938045985.1_ERR589530_bin.78_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938045985.1_ERR589530_bin.78_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 11:03:48,184] [INFO] Task succeeded: Prodigal
[2023-06-13 11:03:48,184] [INFO] Task started: HMMsearch
[2023-06-13 11:03:48,184] [INFO] Running command: hmmsearch --tblout GCA_938045985.1_ERR589530_bin.78_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ea262e6-9888-4792-a8ef-d580ca98b927/dqc_reference/reference_markers.hmm GCA_938045985.1_ERR589530_bin.78_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 11:03:48,569] [INFO] Task succeeded: HMMsearch
[2023-06-13 11:03:48,572] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg42211ea3-37ed-4655-a59e-7cae37ed688a/GCA_938045985.1_ERR589530_bin.78_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-13 11:03:48,632] [INFO] Query marker FASTA was written to GCA_938045985.1_ERR589530_bin.78_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 11:03:48,632] [INFO] Task started: Blastn
[2023-06-13 11:03:48,632] [INFO] Running command: blastn -query GCA_938045985.1_ERR589530_bin.78_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ea262e6-9888-4792-a8ef-d580ca98b927/dqc_reference/reference_markers.fasta -out GCA_938045985.1_ERR589530_bin.78_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:03:49,417] [INFO] Task succeeded: Blastn
[2023-06-13 11:03:49,422] [INFO] Selected 16 target genomes.
[2023-06-13 11:03:49,423] [INFO] Target genome list was writen to GCA_938045985.1_ERR589530_bin.78_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 11:03:49,428] [INFO] Task started: fastANI
[2023-06-13 11:03:49,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg42211ea3-37ed-4655-a59e-7cae37ed688a/GCA_938045985.1_ERR589530_bin.78_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938045985.1_ERR589530_bin.78_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938045985.1_ERR589530_bin.78_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 11:04:07,256] [INFO] Task succeeded: fastANI
[2023-06-13 11:04:07,257] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ea262e6-9888-4792-a8ef-d580ca98b927/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 11:04:07,257] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ea262e6-9888-4792-a8ef-d580ca98b927/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 11:04:07,269] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2023-06-13 11:04:07,270] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 11:04:07,270] [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
Citrobacter braakii	strain=ATCC 51113	GCA_002075345.1	57706	57706	type	True	98.5402	1320	1581	95	conclusive
Citrobacter braakii	strain=FDAARGOS 1421	GCA_019048805.1	57706	57706	type	True	98.4952	1336	1581	95	conclusive
Citrobacter europaeus	strain=97/79	GCA_900079995.3	1914243	1914243	type	True	93.142	1292	1581	95	below_threshold
Citrobacter arsenatis	strain=LY-1	GCA_004353845.1	2546350	2546350	type	True	92.7078	1300	1581	95	below_threshold
Citrobacter portucalensis	strain=A60	GCA_002042885.1	1639133	1639133	type	True	92.2177	1218	1581	95	below_threshold
Citrobacter freundii	strain=ATCC 8090	GCA_011064845.1	546	546	type	True	92.0241	1267	1581	95	below_threshold
Citrobacter freundii	strain=NBRC 12681	GCA_000759735.1	546	546	type	True	92.0205	1243	1581	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	82.3282	938	1581	95	below_threshold
Enterobacter quasimori	strain=090044	GCA_003964905.1	2838947	2838947	type	True	82.1634	813	1581	95	below_threshold
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	82.1029	896	1581	95	below_threshold
Enterobacter mori	strain=LMG 25706	GCA_000211415.1	539813	539813	type	True	82.0903	779	1581	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.7644	770	1581	95	below_threshold
Enterobacter bugandensis		GCA_900324475.1	881260	881260	type	True	81.5487	782	1581	95	below_threshold
Enterobacter bugandensis	strain=FDAARGOS 1427	GCA_019046905.1	881260	881260	type	True	81.4988	797	1581	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.4784	792	1581	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.3461	785	1581	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 11:04:07,275] [INFO] DFAST Taxonomy check result was written to GCA_938045985.1_ERR589530_bin.78_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 11:04:07,276] [INFO] ===== Taxonomy check completed =====
[2023-06-13 11:04:07,276] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 11:04:07,276] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ea262e6-9888-4792-a8ef-d580ca98b927/dqc_reference/checkm_data
[2023-06-13 11:04:07,278] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 11:04:07,336] [INFO] Task started: CheckM
[2023-06-13 11:04:07,336] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938045985.1_ERR589530_bin.78_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938045985.1_ERR589530_bin.78_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938045985.1_ERR589530_bin.78_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 11:04:49,606] [INFO] Task succeeded: CheckM
[2023-06-13 11:04:49,608] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.11%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-13 11:04:49,635] [INFO] ===== Completeness check finished =====
[2023-06-13 11:04:49,636] [INFO] ===== Start GTDB Search =====
[2023-06-13 11:04:49,636] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938045985.1_ERR589530_bin.78_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 11:04:49,637] [INFO] Task started: Blastn
[2023-06-13 11:04:49,637] [INFO] Running command: blastn -query GCA_938045985.1_ERR589530_bin.78_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ea262e6-9888-4792-a8ef-d580ca98b927/dqc_reference/reference_markers_gtdb.fasta -out GCA_938045985.1_ERR589530_bin.78_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:04:50,687] [INFO] Task succeeded: Blastn
[2023-06-13 11:04:50,692] [INFO] Selected 13 target genomes.
[2023-06-13 11:04:50,692] [INFO] Target genome list was writen to GCA_938045985.1_ERR589530_bin.78_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 11:04:50,704] [INFO] Task started: fastANI
[2023-06-13 11:04:50,704] [INFO] Running command: fastANI --query /var/lib/cwl/stg42211ea3-37ed-4655-a59e-7cae37ed688a/GCA_938045985.1_ERR589530_bin.78_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938045985.1_ERR589530_bin.78_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938045985.1_ERR589530_bin.78_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 11:05:04,776] [INFO] Task succeeded: fastANI
[2023-06-13 11:05:04,792] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 11:05:04,792] [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_002075345.1	s__Citrobacter braakii	98.5402	1320	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	98.63	96.30	0.86	0.77	154	conclusive
GCF_900079995.3	s__Citrobacter europaeus	93.142	1292	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	99.13	99.04	0.92	0.90	21	-
GCF_004353845.1	s__Citrobacter freundii_E	92.6849	1302	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	99.27	99.27	0.92	0.92	2	-
GCF_002042885.1	s__Citrobacter portucalensis	92.2288	1217	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	98.01	95.95	0.89	0.83	128	-
GCF_011064845.1	s__Citrobacter freundii	91.9963	1269	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	98.70	97.40	0.89	0.80	446	-
GCF_018035235.1	s__Citrobacter freundii_A	91.7158	1227	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	99.33	99.24	0.91	0.90	6	-
GCF_000155975.1	s__Citrobacter portucalensis_A	90.7326	1210	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900759445.1	s__Klebsiella sp900759445	90.6681	705	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000211415.1	s__Enterobacter mori	82.1071	777	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	97.59	96.13	0.88	0.85	23	-
GCF_004331265.1	s__Enterobacter wuhouensis	81.7644	770	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003594915.1	s__Enterobacter chuandaensis	81.581	780	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.38	98.32	0.92	0.92	3	-
GCF_011754535.1	s__Enterobacter cloacae_N	81.4519	796	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.03	98.99	0.93	0.91	4	-
GCF_900322725.1	s__Enterobacter quasihormaechei	81.4397	758	1581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.46	97.61	0.96	0.89	41	-
--------------------------------------------------------------------------------
[2023-06-13 11:05:04,794] [INFO] GTDB search result was written to GCA_938045985.1_ERR589530_bin.78_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 11:05:04,796] [INFO] ===== GTDB Search completed =====
[2023-06-13 11:05:04,800] [INFO] DFAST_QC result json was written to GCA_938045985.1_ERR589530_bin.78_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 11:05:04,801] [INFO] DFAST_QC completed!
[2023-06-13 11:05:04,801] [INFO] Total running time: 0h1m31s