[2024-01-25 20:18:50,499] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:18:50,505] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:18:50,505] [INFO] DQC Reference Directory: /var/lib/cwl/stgb8895c7f-ef4c-4104-80a8-280c7b0c4adb/dqc_reference
[2024-01-25 20:18:51,683] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:18:51,684] [INFO] Task started: Prodigal
[2024-01-25 20:18:51,684] [INFO] Running command: gunzip -c /var/lib/cwl/stg3898a93c-f188-4bf6-8e96-5bcbb7eae3ee/GCF_003591175.1_ASM359117v1_genomic.fna.gz | prodigal -d GCF_003591175.1_ASM359117v1_genomic.fna/cds.fna -a GCF_003591175.1_ASM359117v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:19:06,824] [INFO] Task succeeded: Prodigal
[2024-01-25 20:19:06,824] [INFO] Task started: HMMsearch
[2024-01-25 20:19:06,824] [INFO] Running command: hmmsearch --tblout GCF_003591175.1_ASM359117v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb8895c7f-ef4c-4104-80a8-280c7b0c4adb/dqc_reference/reference_markers.hmm GCF_003591175.1_ASM359117v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:19:07,098] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:19:07,099] [INFO] Found 6/6 markers.
[2024-01-25 20:19:07,141] [INFO] Query marker FASTA was written to GCF_003591175.1_ASM359117v1_genomic.fna/markers.fasta
[2024-01-25 20:19:07,141] [INFO] Task started: Blastn
[2024-01-25 20:19:07,141] [INFO] Running command: blastn -query GCF_003591175.1_ASM359117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8895c7f-ef4c-4104-80a8-280c7b0c4adb/dqc_reference/reference_markers.fasta -out GCF_003591175.1_ASM359117v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:08,018] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:08,022] [INFO] Selected 13 target genomes.
[2024-01-25 20:19:08,023] [INFO] Target genome list was writen to GCF_003591175.1_ASM359117v1_genomic.fna/target_genomes.txt
[2024-01-25 20:19:08,033] [INFO] Task started: fastANI
[2024-01-25 20:19:08,033] [INFO] Running command: fastANI --query /var/lib/cwl/stg3898a93c-f188-4bf6-8e96-5bcbb7eae3ee/GCF_003591175.1_ASM359117v1_genomic.fna.gz --refList GCF_003591175.1_ASM359117v1_genomic.fna/target_genomes.txt --output GCF_003591175.1_ASM359117v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:19:23,551] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:23,552] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb8895c7f-ef4c-4104-80a8-280c7b0c4adb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:19:23,552] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb8895c7f-ef4c-4104-80a8-280c7b0c4adb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:19:23,561] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:19:23,561] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:19:23,561] [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 inhibens	strain=S40	GCA_003591175.1	2338073	2338073	type	True	100.0	1780	1781	95	conclusive
Serratia plymuthica	strain=NBRC 102599	GCA_001590925.1	82996	82996	type	True	94.0671	1509	1781	95	below_threshold
Serratia plymuthica	strain=FDAARGOS_895	GCA_016027675.1	82996	82996	type	True	94.065	1542	1781	95	below_threshold
Serratia proteamaculans	strain=CCUG 14510	GCA_008830365.1	28151	28151	type	True	87.2707	1372	1781	95	below_threshold
Serratia quinivorans	strain=NCTC11544	GCA_900457075.1	137545	137545	suspected-type	True	87.2077	1372	1781	95	below_threshold
Serratia liquefaciens	strain=ATCC 27592	GCA_000422085.1	614	614	type	True	86.9376	1342	1781	95	below_threshold
Serratia ficaria	strain=NBRC 102596	GCA_001590885.1	61651	61651	type	True	86.5595	1297	1781	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	86.3416	1262	1781	95	below_threshold
Serratia grimesii	strain=NCTC11543	GCA_900456935.1	82995	82995	type	True	85.555	1308	1781	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	85.254	1199	1781	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	85.0807	1178	1781	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	79.3249	645	1781	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	79.046	600	1781	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:19:23,562] [INFO] DFAST Taxonomy check result was written to GCF_003591175.1_ASM359117v1_genomic.fna/tc_result.tsv
[2024-01-25 20:19:23,563] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:19:23,563] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:19:23,563] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb8895c7f-ef4c-4104-80a8-280c7b0c4adb/dqc_reference/checkm_data
[2024-01-25 20:19:23,564] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:19:23,617] [INFO] Task started: CheckM
[2024-01-25 20:19:23,617] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003591175.1_ASM359117v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003591175.1_ASM359117v1_genomic.fna/checkm_input GCF_003591175.1_ASM359117v1_genomic.fna/checkm_result
[2024-01-25 20:20:09,020] [INFO] Task succeeded: CheckM
[2024-01-25 20:20:09,021] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:20:09,037] [INFO] ===== Completeness check finished =====
[2024-01-25 20:20:09,038] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:20:09,038] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003591175.1_ASM359117v1_genomic.fna/markers.fasta)
[2024-01-25 20:20:09,039] [INFO] Task started: Blastn
[2024-01-25 20:20:09,039] [INFO] Running command: blastn -query GCF_003591175.1_ASM359117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8895c7f-ef4c-4104-80a8-280c7b0c4adb/dqc_reference/reference_markers_gtdb.fasta -out GCF_003591175.1_ASM359117v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:10,419] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:10,422] [INFO] Selected 10 target genomes.
[2024-01-25 20:20:10,422] [INFO] Target genome list was writen to GCF_003591175.1_ASM359117v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:20:10,434] [INFO] Task started: fastANI
[2024-01-25 20:20:10,434] [INFO] Running command: fastANI --query /var/lib/cwl/stg3898a93c-f188-4bf6-8e96-5bcbb7eae3ee/GCF_003591175.1_ASM359117v1_genomic.fna.gz --refList GCF_003591175.1_ASM359117v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003591175.1_ASM359117v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:20:23,669] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:23,676] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:20:23,676] [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_003591175.1	s__Serratia inhibens	100.0	1780	1781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	96.90	95.73	0.88	0.85	4	conclusive
GCF_018336935.1	s__Serratia plymuthica_B	94.8339	1521	1781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001590925.1	s__Serratia plymuthica	94.0671	1509	1781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	97.90	96.52	0.93	0.88	29	-
GCF_008830365.1	s__Serratia proteamaculans	87.2762	1371	1781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	97.96	95.51	0.92	0.86	11	-
GCF_900457075.1	s__Serratia quinivorans	87.1985	1373	1781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	98.38	95.64	0.93	0.85	9	-
GCF_013337185.1	s__Serratia proteamaculans_D	87.0509	1372	1781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	97.78	95.57	0.96	0.91	3	-
GCF_000422085.1	s__Serratia liquefaciens	86.9378	1342	1781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	98.63	98.20	0.94	0.91	25	-
GCA_012719855.1	s__Serratia liquefaciens_A	86.9208	1321	1781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	97.92	97.90	0.90	0.89	3	-
GCF_900187015.1	s__Serratia ficaria	86.552	1332	1781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	99.70	99.56	0.95	0.92	5	-
GCF_001590905.1	s__Serratia grimesii	85.5152	1289	1781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	99.09	98.89	0.96	0.93	7	-
--------------------------------------------------------------------------------
[2024-01-25 20:20:23,678] [INFO] GTDB search result was written to GCF_003591175.1_ASM359117v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:20:23,678] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:20:23,687] [INFO] DFAST_QC result json was written to GCF_003591175.1_ASM359117v1_genomic.fna/dqc_result.json
[2024-01-25 20:20:23,687] [INFO] DFAST_QC completed!
[2024-01-25 20:20:23,687] [INFO] Total running time: 0h1m33s