[2024-01-24 14:06:29,826] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:29,829] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:29,829] [INFO] DQC Reference Directory: /var/lib/cwl/stg9846483a-9960-4d88-b537-45d1c2c5b396/dqc_reference
[2024-01-24 14:06:31,134] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:31,135] [INFO] Task started: Prodigal
[2024-01-24 14:06:31,135] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b5de09d-9cc5-4cb4-bd2d-f28a289e01cc/GCF_003363015.1_ASM336301v1_genomic.fna.gz | prodigal -d GCF_003363015.1_ASM336301v1_genomic.fna/cds.fna -a GCF_003363015.1_ASM336301v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:44,571] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:44,571] [INFO] Task started: HMMsearch
[2024-01-24 14:06:44,571] [INFO] Running command: hmmsearch --tblout GCF_003363015.1_ASM336301v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9846483a-9960-4d88-b537-45d1c2c5b396/dqc_reference/reference_markers.hmm GCF_003363015.1_ASM336301v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:44,818] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:44,819] [INFO] Found 6/6 markers.
[2024-01-24 14:06:44,857] [INFO] Query marker FASTA was written to GCF_003363015.1_ASM336301v1_genomic.fna/markers.fasta
[2024-01-24 14:06:44,858] [INFO] Task started: Blastn
[2024-01-24 14:06:44,858] [INFO] Running command: blastn -query GCF_003363015.1_ASM336301v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9846483a-9960-4d88-b537-45d1c2c5b396/dqc_reference/reference_markers.fasta -out GCF_003363015.1_ASM336301v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:45,774] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:45,778] [INFO] Selected 20 target genomes.
[2024-01-24 14:06:45,778] [INFO] Target genome list was writen to GCF_003363015.1_ASM336301v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:45,786] [INFO] Task started: fastANI
[2024-01-24 14:06:45,786] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b5de09d-9cc5-4cb4-bd2d-f28a289e01cc/GCF_003363015.1_ASM336301v1_genomic.fna.gz --refList GCF_003363015.1_ASM336301v1_genomic.fna/target_genomes.txt --output GCF_003363015.1_ASM336301v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:02,425] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:02,426] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9846483a-9960-4d88-b537-45d1c2c5b396/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:02,426] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9846483a-9960-4d88-b537-45d1c2c5b396/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:02,442] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:07:02,442] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:02,443] [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
Enterobacillus tribolii	strain=DSM 103736	GCA_003363015.1	1487935	1487935	type	True	100.0	1621	1623	95	conclusive
Enterobacillus tribolii	strain=IG-V01	GCA_019739135.1	1487935	1487935	type	True	99.9945	1612	1623	95	conclusive
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	80.0014	655	1623	95	below_threshold
Serratia ficaria	strain=NCTC12148	GCA_900187015.1	61651	61651	type	True	79.9573	674	1623	95	below_threshold
Serratia ficaria	strain=NBRC 102596	GCA_001590885.1	61651	61651	type	True	79.9179	663	1623	95	below_threshold
Serratia marcescens	strain=ATCC 13880 substr. Sm_S65_jyu2015	GCA_017298975.1	615	615	suspected-type	True	79.9147	674	1623	95	below_threshold
Serratia marcescens	strain=ATCC 13880	GCA_017654245.1	615	615	suspected-type	True	79.9056	668	1623	95	below_threshold
Serratia nematodiphila	strain=DSM 21420	GCA_000738675.1	458197	458197	suspected-type	True	79.8824	669	1623	95	below_threshold
Serratia nematodiphila	strain=CGMCC 1.6853	GCA_900101535.1	458197	458197	suspected-type	True	79.8585	663	1623	95	below_threshold
Serratia ureilytica	strain=CCUG:50595	GCA_013375155.1	300181	300181	type	True	79.8583	659	1623	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	79.788	622	1623	95	below_threshold
Edwardsiella anguillarum	strain=ET080813	GCA_000264765.2	1821960	1821960	type	True	79.4182	501	1623	95	below_threshold
Edwardsiella anguillarum	strain=CCUG 64215	GCA_008801815.1	1821960	1821960	type	True	79.3754	505	1623	95	below_threshold
Edwardsiella tarda	strain=FDAARGOS_1473	GCA_019933175.1	636	636	type	True	78.9929	406	1623	95	below_threshold
Edwardsiella tarda	strain=NBRC 105688	GCA_000341505.1	636	636	type	True	78.8475	402	1623	95	below_threshold
Edwardsiella tarda	strain=ATCC 15947	GCA_000264805.1	636	636	type	True	78.8062	377	1623	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	78.6867	533	1623	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	78.5604	455	1623	95	below_threshold
Hafnia paralvei	strain=ATCC 29927	GCA_001655005.1	546367	546367	type	True	78.4354	381	1623	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	78.2512	354	1623	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:02,444] [INFO] DFAST Taxonomy check result was written to GCF_003363015.1_ASM336301v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:02,445] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:02,445] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:02,445] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9846483a-9960-4d88-b537-45d1c2c5b396/dqc_reference/checkm_data
[2024-01-24 14:07:02,446] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:02,493] [INFO] Task started: CheckM
[2024-01-24 14:07:02,493] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003363015.1_ASM336301v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003363015.1_ASM336301v1_genomic.fna/checkm_input GCF_003363015.1_ASM336301v1_genomic.fna/checkm_result
[2024-01-24 14:07:43,314] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:43,315] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:43,337] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:43,337] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:43,337] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003363015.1_ASM336301v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:43,337] [INFO] Task started: Blastn
[2024-01-24 14:07:43,338] [INFO] Running command: blastn -query GCF_003363015.1_ASM336301v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9846483a-9960-4d88-b537-45d1c2c5b396/dqc_reference/reference_markers_gtdb.fasta -out GCF_003363015.1_ASM336301v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:44,867] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:44,871] [INFO] Selected 19 target genomes.
[2024-01-24 14:07:44,871] [INFO] Target genome list was writen to GCF_003363015.1_ASM336301v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:44,889] [INFO] Task started: fastANI
[2024-01-24 14:07:44,889] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b5de09d-9cc5-4cb4-bd2d-f28a289e01cc/GCF_003363015.1_ASM336301v1_genomic.fna.gz --refList GCF_003363015.1_ASM336301v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003363015.1_ASM336301v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:02,978] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:02,993] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:02,994] [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_003363015.1	s__Enterobacillus tribolii	100.0	1621	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002220655.1	s__Serratia marcescens_K	79.9886	680	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.0833	98.79	98.10	0.94	0.88	411	-
GCF_900187015.1	s__Serratia ficaria	79.9533	675	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	99.70	99.56	0.95	0.92	5	-
GCF_006715005.1	s__Serratia marcescens_J	79.9382	637	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.1913	98.92	98.92	0.95	0.95	2	-
GCF_017299535.1	s__Serratia marcescens	79.9174	674	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.8494	99.42	98.47	0.97	0.85	72	-
GCF_016742975.1	s__Serratia nevei	79.9111	581	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.1913	97.82	96.26	0.83	0.75	139	-
GCF_000738675.1	s__Serratia nematodiphila	79.8941	667	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.8494	98.32	97.66	0.93	0.88	85	-
GCF_001642805.2	s__Serratia surfactantfaciens	79.8732	660	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	98.81	97.95	0.93	0.91	10	-
GCF_013375155.1	s__Serratia ureilytica	79.8621	658	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.3985	98.73	97.62	0.94	0.88	142	-
GCF_000513215.1	s__Serratia bockelmannii	79.8603	641	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.0065	98.98	98.60	0.94	0.92	42	-
GCF_001896205.1	s__Edwardsiella piscicida	79.6256	503	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Edwardsiella	95.0	99.37	99.20	0.95	0.93	23	-
GCF_000264765.2	s__Edwardsiella anguillarum	79.428	500	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Edwardsiella	95.0	99.86	99.66	0.99	0.97	9	-
GCF_018336935.1	s__Serratia plymuthica_B	79.2821	587	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341505.1	s__Edwardsiella tarda	78.8475	402	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Edwardsiella	95.0	99.01	97.25	0.94	0.84	19	-
GCF_000474215.1	s__Edwardsiella hoshinae	78.6968	392	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Edwardsiella	95.0	99.86	99.58	0.98	0.94	4	-
GCF_000828055.2	s__Klebsiella variicola	78.6669	487	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.94	96.87	0.93	0.84	528	-
GCF_900095695.1	s__Hafnia alvei_B	78.5903	430	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Hafnia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001586165.1	s__Hafnia proteus	78.4409	462	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Hafnia	95.0	98.09	96.49	0.93	0.89	5	-
GCF_001655005.1	s__Hafnia paralvei	78.4317	382	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Hafnia	95.0	98.49	95.65	0.88	0.84	34	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:02,995] [INFO] GTDB search result was written to GCF_003363015.1_ASM336301v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:02,996] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:03,000] [INFO] DFAST_QC result json was written to GCF_003363015.1_ASM336301v1_genomic.fna/dqc_result.json
[2024-01-24 14:08:03,000] [INFO] DFAST_QC completed!
[2024-01-24 14:08:03,000] [INFO] Total running time: 0h1m33s