[2024-01-24 12:22:04,956] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:04,957] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:04,958] [INFO] DQC Reference Directory: /var/lib/cwl/stg69f24785-eac1-44be-9c6e-b9b9df82bc5d/dqc_reference
[2024-01-24 12:22:06,185] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:06,186] [INFO] Task started: Prodigal
[2024-01-24 12:22:06,186] [INFO] Running command: gunzip -c /var/lib/cwl/stgb567b12d-1d7b-44f3-909a-2d4cf60b2701/GCF_000439085.1_ASM43908v1_genomic.fna.gz | prodigal -d GCF_000439085.1_ASM43908v1_genomic.fna/cds.fna -a GCF_000439085.1_ASM43908v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:16,351] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:16,351] [INFO] Task started: HMMsearch
[2024-01-24 12:22:16,351] [INFO] Running command: hmmsearch --tblout GCF_000439085.1_ASM43908v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69f24785-eac1-44be-9c6e-b9b9df82bc5d/dqc_reference/reference_markers.hmm GCF_000439085.1_ASM43908v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:16,686] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:16,687] [INFO] Found 6/6 markers.
[2024-01-24 12:22:16,729] [INFO] Query marker FASTA was written to GCF_000439085.1_ASM43908v1_genomic.fna/markers.fasta
[2024-01-24 12:22:16,730] [INFO] Task started: Blastn
[2024-01-24 12:22:16,730] [INFO] Running command: blastn -query GCF_000439085.1_ASM43908v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69f24785-eac1-44be-9c6e-b9b9df82bc5d/dqc_reference/reference_markers.fasta -out GCF_000439085.1_ASM43908v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:17,563] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:17,572] [INFO] Selected 10 target genomes.
[2024-01-24 12:22:17,573] [INFO] Target genome list was writen to GCF_000439085.1_ASM43908v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:17,582] [INFO] Task started: fastANI
[2024-01-24 12:22:17,582] [INFO] Running command: fastANI --query /var/lib/cwl/stgb567b12d-1d7b-44f3-909a-2d4cf60b2701/GCF_000439085.1_ASM43908v1_genomic.fna.gz --refList GCF_000439085.1_ASM43908v1_genomic.fna/target_genomes.txt --output GCF_000439085.1_ASM43908v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:27,618] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:27,619] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69f24785-eac1-44be-9c6e-b9b9df82bc5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:27,619] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69f24785-eac1-44be-9c6e-b9b9df82bc5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:27,629] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 12:22:27,629] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:27,629] [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
Leminorella grimontii	strain=DSM 5078	GCA_000439085.1	82981	82981	type	True	100.0	1385	1386	95	conclusive
Leminorella grimontii	strain=JCM 5902	GCA_024343555.1	82981	82981	type	True	99.9943	1376	1386	95	conclusive
Leminorella grimontii	strain=ATCC 33999	GCA_000735425.1	82981	82981	type	True	99.9851	1375	1386	95	conclusive
Leminorella grimontii	strain=NCTC12152	GCA_900706845.1	82981	82981	type	True	99.9784	1386	1386	95	conclusive
Leminorella richardii	strain=NCTC12151	GCA_900478135.1	158841	158841	type	True	82.7968	944	1386	95	below_threshold
Jinshanibacter zhutongyuii	strain=CF-458	GCA_004295645.1	2498113	2498113	type	True	78.2647	368	1386	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.2535	352	1386	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	78.2165	337	1386	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.1767	323	1386	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	77.6695	233	1386	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:27,631] [INFO] DFAST Taxonomy check result was written to GCF_000439085.1_ASM43908v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:27,631] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:27,632] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:27,632] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69f24785-eac1-44be-9c6e-b9b9df82bc5d/dqc_reference/checkm_data
[2024-01-24 12:22:27,633] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:27,677] [INFO] Task started: CheckM
[2024-01-24 12:22:27,677] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000439085.1_ASM43908v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000439085.1_ASM43908v1_genomic.fna/checkm_input GCF_000439085.1_ASM43908v1_genomic.fna/checkm_result
[2024-01-24 12:23:02,456] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:02,457] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:02,480] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:02,480] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:02,481] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000439085.1_ASM43908v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:02,481] [INFO] Task started: Blastn
[2024-01-24 12:23:02,481] [INFO] Running command: blastn -query GCF_000439085.1_ASM43908v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69f24785-eac1-44be-9c6e-b9b9df82bc5d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000439085.1_ASM43908v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:03,718] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:03,722] [INFO] Selected 21 target genomes.
[2024-01-24 12:23:03,722] [INFO] Target genome list was writen to GCF_000439085.1_ASM43908v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:03,769] [INFO] Task started: fastANI
[2024-01-24 12:23:03,769] [INFO] Running command: fastANI --query /var/lib/cwl/stgb567b12d-1d7b-44f3-909a-2d4cf60b2701/GCF_000439085.1_ASM43908v1_genomic.fna.gz --refList GCF_000439085.1_ASM43908v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000439085.1_ASM43908v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:20,929] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:20,945] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:20,945] [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_000439085.1	s__Leminorella grimontii	100.0	1385	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leminorella	95.0	99.99	99.98	1.00	0.99	4	conclusive
GCF_900478135.1	s__Leminorella richardii	82.809	942	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leminorella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016649425.1	s__Limnobaculum allomyrinae	78.4693	338	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Limnobaculum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000513215.1	s__Serratia bockelmannii	78.3307	322	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.0065	98.98	98.60	0.94	0.92	42	-
GCF_900187015.1	s__Serratia ficaria	78.297	378	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	99.70	99.56	0.95	0.92	5	-
GCF_002220655.1	s__Serratia marcescens_K	78.2962	347	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.0833	98.79	98.10	0.94	0.88	411	-
GCF_003096015.2	s__Limnobaculum parvum	78.2858	319	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Limnobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013394855.1	s__Limnobaculum xujianqingii	78.2741	355	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Limnobaculum	95.0	98.42	97.65	0.92	0.89	4	-
GCF_016742975.1	s__Serratia nevei	78.2734	314	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.1913	97.82	96.26	0.83	0.75	139	-
GCF_004295645.1	s__Limnobaculum zhutongyuii	78.2546	369	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Limnobaculum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900112475.1	s__Pragia fontium	78.2185	331	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pragia	95.0	99.20	98.63	0.97	0.95	5	-
GCF_001642805.2	s__Serratia surfactantfaciens	78.156	341	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	98.81	97.95	0.93	0.91	10	-
GCF_006715005.1	s__Serratia marcescens_J	78.147	339	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.1913	98.92	98.92	0.95	0.95	2	-
GCF_001902635.1	s__Serratia marcescens_F	78.1068	331	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013375155.1	s__Serratia ureilytica	78.0819	341	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.3985	98.73	97.62	0.94	0.88	142	-
GCF_001598855.1	s__Pluralibacter gergoviae	78.0605	322	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pluralibacter	95.0	98.81	98.03	0.90	0.85	23	-
GCF_009800925.1	s__Budvicia diplopodorum	77.7748	312	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Budvicia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342285.1	s__Klebsiella sp004342285	77.7456	251	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427805.1	s__Budvicia aquatica	77.6447	278	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Budvicia	95.0	99.94	99.91	1.00	1.00	3	-
GCF_003612015.1	s__Pantoea piersonii	77.5374	266	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.15	96.25	0.97	0.92	11	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:20,947] [INFO] GTDB search result was written to GCF_000439085.1_ASM43908v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:20,947] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:20,952] [INFO] DFAST_QC result json was written to GCF_000439085.1_ASM43908v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:20,952] [INFO] DFAST_QC completed!
[2024-01-24 12:23:20,952] [INFO] Total running time: 0h1m16s