[2024-01-24 13:45:45,213] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:45,215] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:45,215] [INFO] DQC Reference Directory: /var/lib/cwl/stg457f2844-e301-44a5-8039-dc07d83febc4/dqc_reference
[2024-01-24 13:45:46,486] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:46,487] [INFO] Task started: Prodigal
[2024-01-24 13:45:46,487] [INFO] Running command: gunzip -c /var/lib/cwl/stge3e455a9-3c62-40df-a1a6-1ac66cae7f17/GCF_013394855.1_ASM1339485v1_genomic.fna.gz | prodigal -d GCF_013394855.1_ASM1339485v1_genomic.fna/cds.fna -a GCF_013394855.1_ASM1339485v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:45:57,576] [INFO] Task succeeded: Prodigal
[2024-01-24 13:45:57,577] [INFO] Task started: HMMsearch
[2024-01-24 13:45:57,577] [INFO] Running command: hmmsearch --tblout GCF_013394855.1_ASM1339485v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg457f2844-e301-44a5-8039-dc07d83febc4/dqc_reference/reference_markers.hmm GCF_013394855.1_ASM1339485v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:45:58,000] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:45:58,001] [INFO] Found 6/6 markers.
[2024-01-24 13:45:58,058] [INFO] Query marker FASTA was written to GCF_013394855.1_ASM1339485v1_genomic.fna/markers.fasta
[2024-01-24 13:45:58,058] [INFO] Task started: Blastn
[2024-01-24 13:45:58,058] [INFO] Running command: blastn -query GCF_013394855.1_ASM1339485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg457f2844-e301-44a5-8039-dc07d83febc4/dqc_reference/reference_markers.fasta -out GCF_013394855.1_ASM1339485v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:45:58,856] [INFO] Task succeeded: Blastn
[2024-01-24 13:45:58,859] [INFO] Selected 13 target genomes.
[2024-01-24 13:45:58,860] [INFO] Target genome list was writen to GCF_013394855.1_ASM1339485v1_genomic.fna/target_genomes.txt
[2024-01-24 13:45:58,866] [INFO] Task started: fastANI
[2024-01-24 13:45:58,866] [INFO] Running command: fastANI --query /var/lib/cwl/stge3e455a9-3c62-40df-a1a6-1ac66cae7f17/GCF_013394855.1_ASM1339485v1_genomic.fna.gz --refList GCF_013394855.1_ASM1339485v1_genomic.fna/target_genomes.txt --output GCF_013394855.1_ASM1339485v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:10,331] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:10,332] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg457f2844-e301-44a5-8039-dc07d83febc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:10,332] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg457f2844-e301-44a5-8039-dc07d83febc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:10,344] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:46:10,344] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:46:10,344] [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
Jinshanibacter zhutongyuii	strain=CF-458	GCA_004295645.1	2498113	2498113	type	True	91.0095	1330	1586	95	below_threshold
Jinshanibacter allomyrinae	strain=BWR-B9	GCA_016649425.1	2791986	2791986	type	True	89.583	1242	1586	95	below_threshold
Pragia fontium	strain=DSM 5563	GCA_900112475.1	82985	82985	type	True	80.6161	602	1586	95	below_threshold
Pragia fontium	strain=DSM 5563	GCA_004959795.1	82985	82985	type	True	80.6026	597	1586	95	below_threshold
Budvicia aquatica	strain=NCTC12282	GCA_900706715.1	82979	82979	type	True	79.933	566	1586	95	below_threshold
Budvicia aquatica	strain=DSM 5075	GCA_000427805.1	82979	82979	type	True	79.5012	567	1586	95	below_threshold
Budvicia diplopodorum	strain=D9	GCA_009800925.1	1119056	1119056	type	True	79.4049	459	1586	95	below_threshold
Pectobacterium quasiaquaticum	strain=A477-S1-J17	GCA_014946775.2	2774015	2774015	type	True	78.9435	162	1586	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	78.8145	134	1586	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	78.6606	175	1586	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	77.8723	143	1586	95	below_threshold
Buttiauxella massiliensis	strain=Marseille-P9829	GCA_902500225.1	2831590	2831590	type	True	77.6324	161	1586	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:10,346] [INFO] DFAST Taxonomy check result was written to GCF_013394855.1_ASM1339485v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:10,347] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:10,347] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:10,347] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg457f2844-e301-44a5-8039-dc07d83febc4/dqc_reference/checkm_data
[2024-01-24 13:46:10,348] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:10,396] [INFO] Task started: CheckM
[2024-01-24 13:46:10,397] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013394855.1_ASM1339485v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013394855.1_ASM1339485v1_genomic.fna/checkm_input GCF_013394855.1_ASM1339485v1_genomic.fna/checkm_result
[2024-01-24 13:46:50,066] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:50,068] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:50,089] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:50,089] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:50,090] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013394855.1_ASM1339485v1_genomic.fna/markers.fasta)
[2024-01-24 13:46:50,090] [INFO] Task started: Blastn
[2024-01-24 13:46:50,090] [INFO] Running command: blastn -query GCF_013394855.1_ASM1339485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg457f2844-e301-44a5-8039-dc07d83febc4/dqc_reference/reference_markers_gtdb.fasta -out GCF_013394855.1_ASM1339485v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:51,093] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:51,097] [INFO] Selected 8 target genomes.
[2024-01-24 13:46:51,097] [INFO] Target genome list was writen to GCF_013394855.1_ASM1339485v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:51,120] [INFO] Task started: fastANI
[2024-01-24 13:46:51,120] [INFO] Running command: fastANI --query /var/lib/cwl/stge3e455a9-3c62-40df-a1a6-1ac66cae7f17/GCF_013394855.1_ASM1339485v1_genomic.fna.gz --refList GCF_013394855.1_ASM1339485v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013394855.1_ASM1339485v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:00,385] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:00,393] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:00,393] [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_013394855.1	s__Limnobaculum xujianqingii	100.0	1580	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Limnobaculum	95.0	98.42	97.65	0.92	0.89	4	conclusive
GCF_004295645.1	s__Limnobaculum zhutongyuii	91.011	1330	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Limnobaculum	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016649425.1	s__Limnobaculum allomyrinae	89.583	1242	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Limnobaculum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003096015.2	s__Limnobaculum parvum	87.5624	1017	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Limnobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112475.1	s__Pragia fontium	80.6181	600	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pragia	95.0	99.20	98.63	0.97	0.95	5	-
GCF_000427805.1	s__Budvicia aquatica	79.5067	565	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Budvicia	95.0	99.94	99.91	1.00	1.00	3	-
GCF_009800925.1	s__Budvicia diplopodorum	79.4046	461	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Budvicia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:00,395] [INFO] GTDB search result was written to GCF_013394855.1_ASM1339485v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:00,395] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:00,398] [INFO] DFAST_QC result json was written to GCF_013394855.1_ASM1339485v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:00,399] [INFO] DFAST_QC completed!
[2024-01-24 13:47:00,399] [INFO] Total running time: 0h1m15s