[2023-06-08 17:09:19,075] [INFO] DFAST_QC pipeline started.
[2023-06-08 17:09:19,077] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 17:09:19,078] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa606909-c570-406b-a6a7-8bf837af5514/dqc_reference
[2023-06-08 17:09:20,357] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 17:09:20,359] [INFO] Task started: Prodigal
[2023-06-08 17:09:20,360] [INFO] Running command: gunzip -c /var/lib/cwl/stg697decd1-f28b-4433-871b-a78da80b9058/GCA_902461505.1_UHGG-TPA_MGYG-HGUT-00337_genomic.fna.gz | prodigal -d GCA_902461505.1_UHGG-TPA_MGYG-HGUT-00337_genomic.fna/cds.fna -a GCA_902461505.1_UHGG-TPA_MGYG-HGUT-00337_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 17:09:28,551] [INFO] Task succeeded: Prodigal
[2023-06-08 17:09:28,551] [INFO] Task started: HMMsearch
[2023-06-08 17:09:28,551] [INFO] Running command: hmmsearch --tblout GCA_902461505.1_UHGG-TPA_MGYG-HGUT-00337_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa606909-c570-406b-a6a7-8bf837af5514/dqc_reference/reference_markers.hmm GCA_902461505.1_UHGG-TPA_MGYG-HGUT-00337_genomic.fna/protein.faa > /dev/null
[2023-06-08 17:09:28,836] [INFO] Task succeeded: HMMsearch
[2023-06-08 17:09:28,837] [INFO] Found 6/6 markers.
[2023-06-08 17:09:28,878] [INFO] Query marker FASTA was written to GCA_902461505.1_UHGG-TPA_MGYG-HGUT-00337_genomic.fna/markers.fasta
[2023-06-08 17:09:28,878] [INFO] Task started: Blastn
[2023-06-08 17:09:28,879] [INFO] Running command: blastn -query GCA_902461505.1_UHGG-TPA_MGYG-HGUT-00337_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa606909-c570-406b-a6a7-8bf837af5514/dqc_reference/reference_markers.fasta -out GCA_902461505.1_UHGG-TPA_MGYG-HGUT-00337_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:09:29,744] [INFO] Task succeeded: Blastn
[2023-06-08 17:09:29,751] [INFO] Selected 20 target genomes.
[2023-06-08 17:09:29,751] [INFO] Target genome list was writen to GCA_902461505.1_UHGG-TPA_MGYG-HGUT-00337_genomic.fna/target_genomes.txt
[2023-06-08 17:09:29,756] [INFO] Task started: fastANI
[2023-06-08 17:09:29,756] [INFO] Running command: fastANI --query /var/lib/cwl/stg697decd1-f28b-4433-871b-a78da80b9058/GCA_902461505.1_UHGG-TPA_MGYG-HGUT-00337_genomic.fna.gz --refList GCA_902461505.1_UHGG-TPA_MGYG-HGUT-00337_genomic.fna/target_genomes.txt --output GCA_902461505.1_UHGG-TPA_MGYG-HGUT-00337_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 17:09:45,687] [INFO] Task succeeded: fastANI
[2023-06-08 17:09:45,688] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa606909-c570-406b-a6a7-8bf837af5514/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 17:09:45,689] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa606909-c570-406b-a6a7-8bf837af5514/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 17:09:45,709] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 17:09:45,710] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 17:09:45,710] [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
Morganella morganii subsp. morganii	strain=NBRC 3848	GCA_001598895.1	180434	582	type	True	93.7207	905	1078	95	below_threshold
Morganella morganii subsp. morganii	strain=ATCC 25830	GCA_006094455.1	180434	582	type	True	93.648	925	1078	95	below_threshold
Morganella morganii	strain=DSM 30164	GCA_019243775.1	582	582	type	True	93.5834	919	1078	95	below_threshold
Morganella psychrotolerans	strain=GCSL-P101	GCA_001676155.1	368603	368603	type	True	83.6386	794	1078	95	below_threshold
Serratia rhizosphaerae	strain=KUDC3025	GCA_009817885.1	2597702	2597702	type	True	77.7892	242	1078	95	below_threshold
Shimwellia blattae	strain=NCTC12127	GCA_900636035.1	563	563	type	True	77.7026	215	1078	95	below_threshold
Shimwellia blattae	strain=DSM 4481	GCA_000262305.1	563	563	type	True	77.6646	218	1078	95	below_threshold
Shimwellia blattae	strain=NBRC 105725	GCA_000327265.1	563	563	type	True	77.663	216	1078	95	below_threshold
Klebsiella huaxiensis	strain=WCHKl090001	GCA_003261575.2	2153354	2153354	type	True	77.5824	204	1078	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	77.5239	221	1078	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	77.5213	238	1078	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	77.4929	211	1078	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	77.4524	199	1078	95	below_threshold
Pectobacterium carotovorum	strain=DSM 30168	GCA_900129615.1	554	554	type	True	77.4027	155	1078	95	below_threshold
Pantoea eucrina	strain=LMG 5346	GCA_002095385.1	472693	472693	type	True	77.3362	160	1078	95	below_threshold
Klebsiella indica	strain=TOUT106	GCA_005860775.1	2582917	2582917	type	True	77.3153	217	1078	95	below_threshold
Rahnella perminowiae	strain=SL6	GCA_019049755.1	2816244	2816244	type	True	77.2615	188	1078	95	below_threshold
Dickeya undicola	strain=2B12	GCA_000784735.1	1577887	1577887	type	True	77.2209	194	1078	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 17:09:45,712] [INFO] DFAST Taxonomy check result was written to GCA_902461505.1_UHGG-TPA_MGYG-HGUT-00337_genomic.fna/tc_result.tsv
[2023-06-08 17:09:45,713] [INFO] ===== Taxonomy check completed =====
[2023-06-08 17:09:45,714] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 17:09:45,714] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa606909-c570-406b-a6a7-8bf837af5514/dqc_reference/checkm_data
[2023-06-08 17:09:45,716] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 17:09:45,769] [INFO] Task started: CheckM
[2023-06-08 17:09:45,769] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902461505.1_UHGG-TPA_MGYG-HGUT-00337_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902461505.1_UHGG-TPA_MGYG-HGUT-00337_genomic.fna/checkm_input GCA_902461505.1_UHGG-TPA_MGYG-HGUT-00337_genomic.fna/checkm_result
[2023-06-08 17:10:16,441] [INFO] Task succeeded: CheckM
[2023-06-08 17:10:16,442] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 17:10:16,465] [INFO] ===== Completeness check finished =====
[2023-06-08 17:10:16,466] [INFO] ===== Start GTDB Search =====
[2023-06-08 17:10:16,466] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902461505.1_UHGG-TPA_MGYG-HGUT-00337_genomic.fna/markers.fasta)
[2023-06-08 17:10:16,467] [INFO] Task started: Blastn
[2023-06-08 17:10:16,467] [INFO] Running command: blastn -query GCA_902461505.1_UHGG-TPA_MGYG-HGUT-00337_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa606909-c570-406b-a6a7-8bf837af5514/dqc_reference/reference_markers_gtdb.fasta -out GCA_902461505.1_UHGG-TPA_MGYG-HGUT-00337_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:10:17,718] [INFO] Task succeeded: Blastn
[2023-06-08 17:10:17,723] [INFO] Selected 11 target genomes.
[2023-06-08 17:10:17,723] [INFO] Target genome list was writen to GCA_902461505.1_UHGG-TPA_MGYG-HGUT-00337_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 17:10:17,728] [INFO] Task started: fastANI
[2023-06-08 17:10:17,729] [INFO] Running command: fastANI --query /var/lib/cwl/stg697decd1-f28b-4433-871b-a78da80b9058/GCA_902461505.1_UHGG-TPA_MGYG-HGUT-00337_genomic.fna.gz --refList GCA_902461505.1_UHGG-TPA_MGYG-HGUT-00337_genomic.fna/target_genomes_gtdb.txt --output GCA_902461505.1_UHGG-TPA_MGYG-HGUT-00337_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 17:10:27,063] [INFO] Task succeeded: fastANI
[2023-06-08 17:10:27,076] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 17:10:27,076] [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_000633515.1	s__Morganella morganii_B	95.7148	987	1078	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Morganella	95.0	96.84	95.81	0.92	0.90	4	conclusive
GCF_019243775.1	s__Morganella morganii	93.5834	919	1078	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Morganella	95.0	98.34	95.47	0.94	0.88	171	-
GCF_019242955.1	s__Morganella morganii_A	91.9684	956	1078	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Morganella	95.0	97.48	97.24	0.94	0.90	21	-
GCF_003996855.1	s__Morganella morganii_C	91.7742	873	1078	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Morganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001676055.1	s__Morganella psychrotolerans_B	83.6476	830	1078	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Morganella	95.0	95.92	95.92	0.88	0.88	2	-
GCF_001676155.1	s__Morganella psychrotolerans	83.6386	794	1078	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Morganella	95.0	97.64	95.31	0.94	0.87	3	-
GCF_001598695.1	s__Klebsiella oxytoca	77.5726	192	1078	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	99.31	98.97	0.94	0.89	181	-
GCF_009914055.1	s__Mixta intestinalis	77.523	175	1078	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_901456055.1	s__Phytobacter ursingii	77.357	192	1078	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Phytobacter	95.0	97.10	96.01	0.86	0.80	7	-
GCF_006517625.1	s__Mixta tenebrionis	77.1904	197	1078	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta	95.0	99.45	99.45	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-06-08 17:10:27,078] [INFO] GTDB search result was written to GCA_902461505.1_UHGG-TPA_MGYG-HGUT-00337_genomic.fna/result_gtdb.tsv
[2023-06-08 17:10:27,079] [INFO] ===== GTDB Search completed =====
[2023-06-08 17:10:27,083] [INFO] DFAST_QC result json was written to GCA_902461505.1_UHGG-TPA_MGYG-HGUT-00337_genomic.fna/dqc_result.json
[2023-06-08 17:10:27,083] [INFO] DFAST_QC completed!
[2023-06-08 17:10:27,083] [INFO] Total running time: 0h1m8s