[2024-01-25 18:09:50,728] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:09:50,730] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:09:50,730] [INFO] DQC Reference Directory: /var/lib/cwl/stg0bfef197-564b-48ef-9a50-571b3d00afab/dqc_reference
[2024-01-25 18:09:51,914] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:09:51,915] [INFO] Task started: Prodigal
[2024-01-25 18:09:51,915] [INFO] Running command: gunzip -c /var/lib/cwl/stg07df93c7-f42e-4e84-ba2a-54a97e0b3e00/GCF_016632365.1_ASM1663236v1_genomic.fna.gz | prodigal -d GCF_016632365.1_ASM1663236v1_genomic.fna/cds.fna -a GCF_016632365.1_ASM1663236v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:10:00,569] [INFO] Task succeeded: Prodigal
[2024-01-25 18:10:00,570] [INFO] Task started: HMMsearch
[2024-01-25 18:10:00,570] [INFO] Running command: hmmsearch --tblout GCF_016632365.1_ASM1663236v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0bfef197-564b-48ef-9a50-571b3d00afab/dqc_reference/reference_markers.hmm GCF_016632365.1_ASM1663236v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:10:00,922] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:10:00,923] [INFO] Found 6/6 markers.
[2024-01-25 18:10:00,967] [INFO] Query marker FASTA was written to GCF_016632365.1_ASM1663236v1_genomic.fna/markers.fasta
[2024-01-25 18:10:00,967] [INFO] Task started: Blastn
[2024-01-25 18:10:00,967] [INFO] Running command: blastn -query GCF_016632365.1_ASM1663236v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0bfef197-564b-48ef-9a50-571b3d00afab/dqc_reference/reference_markers.fasta -out GCF_016632365.1_ASM1663236v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:01,834] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:01,837] [INFO] Selected 31 target genomes.
[2024-01-25 18:10:01,837] [INFO] Target genome list was writen to GCF_016632365.1_ASM1663236v1_genomic.fna/target_genomes.txt
[2024-01-25 18:10:01,863] [INFO] Task started: fastANI
[2024-01-25 18:10:01,863] [INFO] Running command: fastANI --query /var/lib/cwl/stg07df93c7-f42e-4e84-ba2a-54a97e0b3e00/GCF_016632365.1_ASM1663236v1_genomic.fna.gz --refList GCF_016632365.1_ASM1663236v1_genomic.fna/target_genomes.txt --output GCF_016632365.1_ASM1663236v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:10:27,164] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:27,164] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0bfef197-564b-48ef-9a50-571b3d00afab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:10:27,165] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0bfef197-564b-48ef-9a50-571b3d00afab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:10:27,181] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:10:27,182] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:10:27,182] [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
Cronobacter dublinensis subsp. lausannensis	strain=LMG 23824	GCA_000409365.1	413500	413497	type	True	79.4908	526	1244	95	below_threshold
Cronobacter dublinensis subsp. lactaridi	strain=LMG 23825	GCA_000409345.1	413499	413497	type	True	79.4697	528	1244	95	below_threshold
Cronobacter dublinensis subsp. dublinensis	strain=LMG 23823	GCA_000409225.1	413498	413497	type	True	79.4381	487	1244	95	below_threshold
Cronobacter muytjensii	strain=ATCC 51329	GCA_000409285.1	413501	413501	type	True	79.3959	496	1244	95	below_threshold
Cronobacter muytjensii	strain=ATCC 51329	GCA_001277195.1	413501	413501	type	True	79.3858	506	1244	95	below_threshold
Cronobacter malonaticus	strain=LMG 23826	GCA_000409305.1	413503	413503	type	True	79.284	514	1244	95	below_threshold
Cronobacter universalis	strain=NCTC 9529	GCA_000319325.1	535744	535744	type	True	79.2595	517	1244	95	below_threshold
Cronobacter malonaticus	strain=LMG 23826	GCA_001277215.2	413503	413503	type	True	79.1785	536	1244	95	below_threshold
Franconibacter helveticus	strain=513	GCA_000485945.1	357240	357240	type	True	79.0744	488	1244	95	below_threshold
Franconibacter helveticus	strain=LMG 23732	GCA_000463115.2	357240	357240	type	True	79.0596	514	1244	95	below_threshold
Atlantibacter hermannii	strain=FDAARGOS_888	GCA_016027855.1	565	565	type	True	79.0221	469	1244	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	79.0206	410	1244	95	below_threshold
Atlantibacter hermannii	strain=NBRC 105704	GCA_000248015.2	565	565	type	True	78.9174	464	1244	95	below_threshold
Raoultella electrica	strain=DSM 102253	GCA_006711645.1	1259973	1259973	type	True	78.8956	459	1244	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	78.8642	448	1244	95	below_threshold
Klebsiella quasipneumoniae	strain=FDAARGOS_1503	GCA_020099175.1	1463165	1463165	type	True	78.757	500	1244	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	78.7502	468	1244	95	below_threshold
Raoultella planticola	strain=ATCC 33531	GCA_000735435.1	575	575	type	True	78.7392	453	1244	95	below_threshold
Klebsiella quasipneumoniae subsp. quasipneumoniae	strain=01A030T	GCA_020525925.1	1667327	1463165	type	True	78.7349	501	1244	95	below_threshold
Klebsiella quasipneumoniae subsp. quasipneumoniae	strain=01A030	GCA_000751755.1	1667327	1463165	type	True	78.7252	493	1244	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	78.7061	465	1244	95	below_threshold
Yokenella regensburgei	strain=NCTC11966	GCA_900460805.1	158877	158877	type	True	78.7052	437	1244	95	below_threshold
Klebsiella quasipneumoniae	strain=DSM 28211	GCA_020115515.1	1463165	1463165	type	True	78.671	494	1244	95	below_threshold
Pseudocitrobacter vendiensis	strain=type strain: CPO20170097	GCA_943590815.1	2488306	2488306	type	True	78.6584	435	1244	95	below_threshold
Klebsiella variicola	strain=type strain: F2R9	GCA_900978195.1	244366	244366	type	True	78.5835	484	1244	95	below_threshold
Yokenella regensburgei	strain=ATCC 49455	GCA_000735455.1	158877	158877	type	True	78.5774	435	1244	95	below_threshold
Kluyvera georgiana	strain=ATCC 51603	GCA_001654985.1	73098	73098	type	True	78.5742	450	1244	95	below_threshold
Citrobacter youngae	strain=NCTC13709	GCA_900638065.1	133448	133448	type	True	78.5346	400	1244	95	below_threshold
Klebsiella variicola	strain=DSM 15968	GCA_000828055.2	244366	244366	type	True	78.5318	500	1244	95	below_threshold
Mixta gaviniae	strain=DSM 22758	GCA_002953195.1	665914	665914	type	True	78.4465	385	1244	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	78.4397	479	1244	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:10:27,183] [INFO] DFAST Taxonomy check result was written to GCF_016632365.1_ASM1663236v1_genomic.fna/tc_result.tsv
[2024-01-25 18:10:27,184] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:10:27,184] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:10:27,184] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0bfef197-564b-48ef-9a50-571b3d00afab/dqc_reference/checkm_data
[2024-01-25 18:10:27,185] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:10:27,226] [INFO] Task started: CheckM
[2024-01-25 18:10:27,226] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016632365.1_ASM1663236v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016632365.1_ASM1663236v1_genomic.fna/checkm_input GCF_016632365.1_ASM1663236v1_genomic.fna/checkm_result
[2024-01-25 18:10:55,312] [INFO] Task succeeded: CheckM
[2024-01-25 18:10:55,313] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:10:55,332] [INFO] ===== Completeness check finished =====
[2024-01-25 18:10:55,332] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:10:55,333] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016632365.1_ASM1663236v1_genomic.fna/markers.fasta)
[2024-01-25 18:10:55,333] [INFO] Task started: Blastn
[2024-01-25 18:10:55,333] [INFO] Running command: blastn -query GCF_016632365.1_ASM1663236v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0bfef197-564b-48ef-9a50-571b3d00afab/dqc_reference/reference_markers_gtdb.fasta -out GCF_016632365.1_ASM1663236v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:56,705] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:56,710] [INFO] Selected 14 target genomes.
[2024-01-25 18:10:56,710] [INFO] Target genome list was writen to GCF_016632365.1_ASM1663236v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:10:56,727] [INFO] Task started: fastANI
[2024-01-25 18:10:56,727] [INFO] Running command: fastANI --query /var/lib/cwl/stg07df93c7-f42e-4e84-ba2a-54a97e0b3e00/GCF_016632365.1_ASM1663236v1_genomic.fna.gz --refList GCF_016632365.1_ASM1663236v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016632365.1_ASM1663236v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:11:09,110] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:09,120] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:11:09,121] [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
GCA_019140855.1	s__Jejubacter sp019140855	99.1465	1134	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Jejubacter	95.0	99.14	99.12	0.91	0.91	3	conclusive
GCA_000302695.1	s__Jejubacter sp000302695	81.2542	779	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Jejubacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010092695.1	s__Jejubacter sp010092695	81.2435	783	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Jejubacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001277235.1	s__Cronobacter dublinensis	79.4141	501	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	97.74	96.92	0.93	0.89	42	-
GCF_001277175.1	s__Cronobacter universalis	79.2934	522	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	99.87	99.62	0.99	0.98	4	-
GCA_000621185.1	s__Franconibacter pulveris	79.2729	499	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Franconibacter	95.0	98.43	96.71	0.95	0.93	7	-
GCF_001277215.2	s__Cronobacter malonaticus	79.1963	534	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	98.86	98.11	0.94	0.89	62	-
GCF_005671395.1	s__Jejubacter calystegiae	79.0979	595	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Jejubacter	95.0	98.55	98.55	0.90	0.90	2	-
GCF_000463115.2	s__Franconibacter helveticus	79.0576	513	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Franconibacter	95.0	99.42	99.04	0.94	0.92	6	-
GCA_900635495.1	s__Atlantibacter hermannii	79.0516	473	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	98.95	98.59	0.96	0.90	28	-
GCA_019237635.1	s__Enterobacter_B sp019237635	79.0442	448	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000164865.1	s__Enterobacter_B lignolyticus	78.9247	526	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_B	95.0	98.80	98.80	0.94	0.94	2	-
GCF_900021175.1	s__Enterobacter_A timonensis	78.9188	476	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002953215.1	s__Mixta calida	78.2279	398	1244	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta	95.0	99.65	99.42	0.96	0.92	22	-
--------------------------------------------------------------------------------
[2024-01-25 18:11:09,122] [INFO] GTDB search result was written to GCF_016632365.1_ASM1663236v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:11:09,122] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:11:09,126] [INFO] DFAST_QC result json was written to GCF_016632365.1_ASM1663236v1_genomic.fna/dqc_result.json
[2024-01-25 18:11:09,126] [INFO] DFAST_QC completed!
[2024-01-25 18:11:09,126] [INFO] Total running time: 0h1m18s