[2024-01-24 13:49:30,745] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:30,747] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:30,747] [INFO] DQC Reference Directory: /var/lib/cwl/stg18eb396f-0e08-4c53-b516-7ae687aef9df/dqc_reference
[2024-01-24 13:49:32,112] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:32,113] [INFO] Task started: Prodigal
[2024-01-24 13:49:32,113] [INFO] Running command: gunzip -c /var/lib/cwl/stg185e8f0f-c74c-40e9-ba66-ad56b9075aae/GCF_002042885.1_ASM204288v1_genomic.fna.gz | prodigal -d GCF_002042885.1_ASM204288v1_genomic.fna/cds.fna -a GCF_002042885.1_ASM204288v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:45,434] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:45,435] [INFO] Task started: HMMsearch
[2024-01-24 13:49:45,435] [INFO] Running command: hmmsearch --tblout GCF_002042885.1_ASM204288v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18eb396f-0e08-4c53-b516-7ae687aef9df/dqc_reference/reference_markers.hmm GCF_002042885.1_ASM204288v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:45,817] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:45,819] [INFO] Found 6/6 markers.
[2024-01-24 13:49:45,870] [INFO] Query marker FASTA was written to GCF_002042885.1_ASM204288v1_genomic.fna/markers.fasta
[2024-01-24 13:49:45,871] [INFO] Task started: Blastn
[2024-01-24 13:49:45,871] [INFO] Running command: blastn -query GCF_002042885.1_ASM204288v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18eb396f-0e08-4c53-b516-7ae687aef9df/dqc_reference/reference_markers.fasta -out GCF_002042885.1_ASM204288v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:46,754] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:46,759] [INFO] Selected 16 target genomes.
[2024-01-24 13:49:46,759] [INFO] Target genome list was writen to GCF_002042885.1_ASM204288v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:46,766] [INFO] Task started: fastANI
[2024-01-24 13:49:46,767] [INFO] Running command: fastANI --query /var/lib/cwl/stg185e8f0f-c74c-40e9-ba66-ad56b9075aae/GCF_002042885.1_ASM204288v1_genomic.fna.gz --refList GCF_002042885.1_ASM204288v1_genomic.fna/target_genomes.txt --output GCF_002042885.1_ASM204288v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:03,643] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:03,643] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18eb396f-0e08-4c53-b516-7ae687aef9df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:03,644] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18eb396f-0e08-4c53-b516-7ae687aef9df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:03,657] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:03,657] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:03,657] [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 portucalensis	strain=A60	GCA_002042885.1	1639133	1639133	type	True	100.0	1616	1618	95	conclusive
Citrobacter freundii	strain=MTCC 1658	GCA_000312465.1	546	546	type	True	94.7349	1394	1618	95	below_threshold
Citrobacter freundii	strain=ATCC 8090	GCA_011064845.1	546	546	type	True	94.7197	1385	1618	95	below_threshold
Citrobacter freundii	strain=NBRC 12681	GCA_000759735.1	546	546	type	True	94.7036	1393	1618	95	below_threshold
Citrobacter freundii	strain=ATCC 8090	GCA_000734905.1	546	546	type	True	94.6864	1339	1618	95	below_threshold
Citrobacter arsenatis	strain=LY-1	GCA_004353845.1	2546350	2546350	type	True	92.8155	1411	1618	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	82.9472	995	1618	95	below_threshold
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	82.9278	986	1618	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	81.7388	832	1618	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.6345	852	1618	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.5753	853	1618	95	below_threshold
Cedecea lapagei	strain=NCTC11466	GCA_900635955.1	158823	158823	type	True	80.0326	620	1618	95	below_threshold
Serratia odorifera	strain=DSM 4582	GCA_000163595.1	618	618	type	True	78.4649	418	1618	95	below_threshold
Serratia odorifera	strain=NCTC11214	GCA_900635445.1	618	618	type	True	78.4555	432	1618	95	below_threshold
Rouxiella chamberiensis	strain=130333	GCA_000951135.1	1513468	1513468	type	True	78.3495	311	1618	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:03,659] [INFO] DFAST Taxonomy check result was written to GCF_002042885.1_ASM204288v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:03,659] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:03,659] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:03,660] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18eb396f-0e08-4c53-b516-7ae687aef9df/dqc_reference/checkm_data
[2024-01-24 13:50:03,660] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:03,712] [INFO] Task started: CheckM
[2024-01-24 13:50:03,712] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002042885.1_ASM204288v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002042885.1_ASM204288v1_genomic.fna/checkm_input GCF_002042885.1_ASM204288v1_genomic.fna/checkm_result
[2024-01-24 13:50:46,984] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:46,986] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:47,016] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:47,016] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:47,017] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002042885.1_ASM204288v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:47,017] [INFO] Task started: Blastn
[2024-01-24 13:50:47,018] [INFO] Running command: blastn -query GCF_002042885.1_ASM204288v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18eb396f-0e08-4c53-b516-7ae687aef9df/dqc_reference/reference_markers_gtdb.fasta -out GCF_002042885.1_ASM204288v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:48,215] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:48,219] [INFO] Selected 13 target genomes.
[2024-01-24 13:50:48,219] [INFO] Target genome list was writen to GCF_002042885.1_ASM204288v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:48,230] [INFO] Task started: fastANI
[2024-01-24 13:50:48,231] [INFO] Running command: fastANI --query /var/lib/cwl/stg185e8f0f-c74c-40e9-ba66-ad56b9075aae/GCF_002042885.1_ASM204288v1_genomic.fna.gz --refList GCF_002042885.1_ASM204288v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002042885.1_ASM204288v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:02,433] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:02,448] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:02,448] [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_002042885.1	s__Citrobacter portucalensis	100.0	1616	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	98.01	95.95	0.89	0.83	128	conclusive
GCF_011064845.1	s__Citrobacter freundii	94.7342	1384	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	98.70	97.40	0.89	0.80	446	-
GCF_900079995.3	s__Citrobacter europaeus	93.0103	1405	1618	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	92.8155	1411	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	99.27	99.27	0.92	0.92	2	-
GCF_002075345.1	s__Citrobacter braakii	92.4722	1338	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	98.63	96.30	0.86	0.77	154	-
GCF_018035235.1	s__Citrobacter freundii_A	91.2516	1347	1618	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	90.9363	1333	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003818115.1	s__Citrobacter youngae	90.4936	1301	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	97.80	95.31	0.91	0.87	45	-
GCA_900759445.1	s__Klebsiella sp900759445	86.6403	720	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005843885.1	s__Escherichia sp005843885	82.3478	929	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	96.83	95.39	0.87	0.80	37	-
GCF_001598695.1	s__Klebsiella oxytoca	81.4128	817	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	99.31	98.97	0.94	0.89	181	-
GCA_901456055.1	s__Phytobacter ursingii	80.9323	778	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Phytobacter	95.0	97.10	96.01	0.86	0.80	7	-
GCF_900111105.1	s__Rosenbergiella nectarea	79.11	106	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rosenbergiella	95.0	96.23	96.23	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:02,450] [INFO] GTDB search result was written to GCF_002042885.1_ASM204288v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:02,451] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:02,454] [INFO] DFAST_QC result json was written to GCF_002042885.1_ASM204288v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:02,455] [INFO] DFAST_QC completed!
[2024-01-24 13:51:02,455] [INFO] Total running time: 0h1m32s