[2024-01-25 17:44:50,269] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:44:50,271] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:44:50,271] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e7a7c8f-4c59-4cc1-b317-d6ac2d37780f/dqc_reference
[2024-01-25 17:44:51,384] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:44:51,385] [INFO] Task started: Prodigal
[2024-01-25 17:44:51,385] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ad05165-6121-4ac2-8688-22bc31632f89/GCF_002899365.1_ASM289936v1_genomic.fna.gz | prodigal -d GCF_002899365.1_ASM289936v1_genomic.fna/cds.fna -a GCF_002899365.1_ASM289936v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:45:04,546] [INFO] Task succeeded: Prodigal
[2024-01-25 17:45:04,547] [INFO] Task started: HMMsearch
[2024-01-25 17:45:04,547] [INFO] Running command: hmmsearch --tblout GCF_002899365.1_ASM289936v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e7a7c8f-4c59-4cc1-b317-d6ac2d37780f/dqc_reference/reference_markers.hmm GCF_002899365.1_ASM289936v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:45:04,817] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:45:04,818] [INFO] Found 6/6 markers.
[2024-01-25 17:45:04,858] [INFO] Query marker FASTA was written to GCF_002899365.1_ASM289936v1_genomic.fna/markers.fasta
[2024-01-25 17:45:04,858] [INFO] Task started: Blastn
[2024-01-25 17:45:04,858] [INFO] Running command: blastn -query GCF_002899365.1_ASM289936v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e7a7c8f-4c59-4cc1-b317-d6ac2d37780f/dqc_reference/reference_markers.fasta -out GCF_002899365.1_ASM289936v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:05,771] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:05,775] [INFO] Selected 15 target genomes.
[2024-01-25 17:45:05,775] [INFO] Target genome list was writen to GCF_002899365.1_ASM289936v1_genomic.fna/target_genomes.txt
[2024-01-25 17:45:05,789] [INFO] Task started: fastANI
[2024-01-25 17:45:05,789] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ad05165-6121-4ac2-8688-22bc31632f89/GCF_002899365.1_ASM289936v1_genomic.fna.gz --refList GCF_002899365.1_ASM289936v1_genomic.fna/target_genomes.txt --output GCF_002899365.1_ASM289936v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:45:22,210] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:22,210] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e7a7c8f-4c59-4cc1-b317-d6ac2d37780f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:45:22,210] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e7a7c8f-4c59-4cc1-b317-d6ac2d37780f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:45:22,221] [INFO] Found 15 fastANI hits (7 hits with ANI > threshold)
[2024-01-25 17:45:22,221] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 17:45:22,222] [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
Serratia marcescens	strain=ATCC 13880 substr. Sm_S65_jyu2015	GCA_017298975.1	615	615	suspected-type	True	99.9985	1678	1679	95	inconclusive
Serratia marcescens	strain=ATCC 13880 substr. Sm_S37_jyu2015	GCA_017301315.1	615	615	suspected-type	True	99.9985	1678	1679	95	inconclusive
Serratia marcescens	strain=ATCC 13880 substr. Sm_S81_jyu2015	GCA_017298875.1	615	615	suspected-type	True	99.9985	1678	1679	95	inconclusive
Serratia marcescens	strain=ATCC 13880 substr. Sm_S57_jyu2015	GCA_017301255.1	615	615	suspected-type	True	99.9985	1678	1679	95	inconclusive
Serratia marcescens	strain=ATCC 13880	GCA_017654245.1	615	615	suspected-type	True	99.9834	1666	1679	95	inconclusive
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	95.8132	1507	1679	95	inconclusive
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	95.1037	1488	1679	95	inconclusive
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	88.2803	1340	1679	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	79.2374	618	1679	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	78.6805	444	1679	95	below_threshold
Pseudomonas jinjuensis	strain=JCM 21621	GCA_900103845.1	198616	198616	type	True	76.6804	253	1679	95	below_threshold
Rhodanobacter denitrificans	strain=2APBS1	GCA_000230695.3	666685	666685	type	True	75.7333	144	1679	95	below_threshold
Rhodanobacter thiooxydans	strain=LCS2	GCA_000264375.1	416169	416169	type	True	75.729	140	1679	95	below_threshold
Cupriavidus malaysiensis	strain=USMAA1020	GCA_001854325.1	367825	367825	type	True	75.6634	239	1679	95	below_threshold
Rhodanobacter fulvus	strain=Jip2	GCA_000264315.1	219571	219571	type	True	75.5758	108	1679	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:45:22,223] [INFO] DFAST Taxonomy check result was written to GCF_002899365.1_ASM289936v1_genomic.fna/tc_result.tsv
[2024-01-25 17:45:22,224] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:45:22,224] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:45:22,224] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e7a7c8f-4c59-4cc1-b317-d6ac2d37780f/dqc_reference/checkm_data
[2024-01-25 17:45:22,225] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:45:22,275] [INFO] Task started: CheckM
[2024-01-25 17:45:22,275] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002899365.1_ASM289936v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002899365.1_ASM289936v1_genomic.fna/checkm_input GCF_002899365.1_ASM289936v1_genomic.fna/checkm_result
[2024-01-25 17:46:00,778] [INFO] Task succeeded: CheckM
[2024-01-25 17:46:00,779] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:46:00,800] [INFO] ===== Completeness check finished =====
[2024-01-25 17:46:00,801] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:46:00,801] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002899365.1_ASM289936v1_genomic.fna/markers.fasta)
[2024-01-25 17:46:00,801] [INFO] Task started: Blastn
[2024-01-25 17:46:00,801] [INFO] Running command: blastn -query GCF_002899365.1_ASM289936v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e7a7c8f-4c59-4cc1-b317-d6ac2d37780f/dqc_reference/reference_markers_gtdb.fasta -out GCF_002899365.1_ASM289936v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:02,258] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:02,262] [INFO] Selected 10 target genomes.
[2024-01-25 17:46:02,262] [INFO] Target genome list was writen to GCF_002899365.1_ASM289936v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:46:02,268] [INFO] Task started: fastANI
[2024-01-25 17:46:02,268] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ad05165-6121-4ac2-8688-22bc31632f89/GCF_002899365.1_ASM289936v1_genomic.fna.gz --refList GCF_002899365.1_ASM289936v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002899365.1_ASM289936v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:46:13,953] [INFO] Task succeeded: fastANI
[2024-01-25 17:46:13,961] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:46:13,961] [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_017299535.1	s__Serratia marcescens	99.9985	1678	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.8494	99.42	98.47	0.97	0.85	72	conclusive
GCF_000738675.1	s__Serratia nematodiphila	96.8108	1551	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.8494	98.32	97.66	0.93	0.88	85	-
GCF_000513215.1	s__Serratia bockelmannii	95.9795	1536	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.0065	98.98	98.60	0.94	0.92	42	-
GCF_002220655.1	s__Serratia marcescens_K	95.3045	1487	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.0833	98.79	98.10	0.94	0.88	411	-
GCF_013375155.1	s__Serratia ureilytica	95.2999	1499	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.3985	98.73	97.62	0.94	0.88	142	-
GCF_006715005.1	s__Serratia marcescens_J	95.0748	1496	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.1913	98.92	98.92	0.95	0.95	2	-
GCF_016742975.1	s__Serratia nevei	94.9719	1312	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.1913	97.82	96.26	0.83	0.75	139	-
GCF_001642805.2	s__Serratia surfactantfaciens	94.1662	1503	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	98.81	97.95	0.93	0.91	10	-
GCF_000264375.1	s__Rhodanobacter thiooxydans	75.7377	139	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	99.24	99.24	0.91	0.91	2	-
GCA_016713125.1	s__SZAS-79 sp016713125	75.4608	113	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__SZAS-79	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:46:13,962] [INFO] GTDB search result was written to GCF_002899365.1_ASM289936v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:46:13,963] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:46:13,966] [INFO] DFAST_QC result json was written to GCF_002899365.1_ASM289936v1_genomic.fna/dqc_result.json
[2024-01-25 17:46:13,966] [INFO] DFAST_QC completed!
[2024-01-25 17:46:13,966] [INFO] Total running time: 0h1m24s