[2024-01-24 11:59:10,894] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:10,898] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:10,898] [INFO] DQC Reference Directory: /var/lib/cwl/stga6ad79eb-f43f-4618-ac44-76ac8c81a944/dqc_reference
[2024-01-24 11:59:12,247] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:12,255] [INFO] Task started: Prodigal
[2024-01-24 11:59:12,255] [INFO] Running command: gunzip -c /var/lib/cwl/stgd1753930-82ad-4a23-9025-54c0cbe1f655/GCF_023282985.1_ASM2328298v1_genomic.fna.gz | prodigal -d GCF_023282985.1_ASM2328298v1_genomic.fna/cds.fna -a GCF_023282985.1_ASM2328298v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:27,122] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:27,122] [INFO] Task started: HMMsearch
[2024-01-24 11:59:27,122] [INFO] Running command: hmmsearch --tblout GCF_023282985.1_ASM2328298v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6ad79eb-f43f-4618-ac44-76ac8c81a944/dqc_reference/reference_markers.hmm GCF_023282985.1_ASM2328298v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:27,519] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:27,520] [INFO] Found 6/6 markers.
[2024-01-24 11:59:27,588] [INFO] Query marker FASTA was written to GCF_023282985.1_ASM2328298v1_genomic.fna/markers.fasta
[2024-01-24 11:59:27,588] [INFO] Task started: Blastn
[2024-01-24 11:59:27,588] [INFO] Running command: blastn -query GCF_023282985.1_ASM2328298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6ad79eb-f43f-4618-ac44-76ac8c81a944/dqc_reference/reference_markers.fasta -out GCF_023282985.1_ASM2328298v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:28,613] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:28,618] [INFO] Selected 21 target genomes.
[2024-01-24 11:59:28,618] [INFO] Target genome list was writen to GCF_023282985.1_ASM2328298v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:28,675] [INFO] Task started: fastANI
[2024-01-24 11:59:28,675] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1753930-82ad-4a23-9025-54c0cbe1f655/GCF_023282985.1_ASM2328298v1_genomic.fna.gz --refList GCF_023282985.1_ASM2328298v1_genomic.fna/target_genomes.txt --output GCF_023282985.1_ASM2328298v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:52,711] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:52,712] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6ad79eb-f43f-4618-ac44-76ac8c81a944/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:52,713] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6ad79eb-f43f-4618-ac44-76ac8c81a944/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:52,736] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:59:52,737] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:59:52,737] [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 fonticola	strain=DSM 4576	GCA_001006005.1	47917	47917	suspected-type	True	93.9678	1387	1612	95	below_threshold
Serratia fonticola	strain=LMG 7882	GCA_000469035.1	47917	47917	suspected-type	True	93.9036	1282	1612	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	82.7436	955	1612	95	below_threshold
Serratia inhibens	strain=S40	GCA_003591175.1	2338073	2338073	type	True	82.6341	955	1612	95	below_threshold
Serratia plymuthica	strain=FDAARGOS_895	GCA_016027675.1	82996	82996	type	True	82.5911	976	1612	95	below_threshold
Serratia plymuthica	strain=NBRC 102599	GCA_001590925.1	82996	82996	type	True	82.4978	942	1612	95	below_threshold
Serratia ficaria	strain=NCTC12148	GCA_900187015.1	61651	61651	type	True	82.4708	976	1612	95	below_threshold
Serratia ficaria	strain=NBRC 102596	GCA_001590885.1	61651	61651	type	True	82.4677	949	1612	95	below_threshold
Serratia liquefaciens	strain=ATCC 27592	GCA_000422085.1	614	614	type	True	82.4392	967	1612	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	82.4363	941	1612	95	below_threshold
Serratia marcescens	strain=ATCC 13880	GCA_017654245.1	615	615	suspected-type	True	82.2674	960	1612	95	below_threshold
Serratia marcescens	strain=ATCC 13880 substr. Sm_S65_jyu2015	GCA_017298975.1	615	615	suspected-type	True	82.2543	968	1612	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	82.1731	930	1612	95	below_threshold
Serratia grimesii	strain=NCTC11543	GCA_900456935.1	82995	82995	type	True	81.9224	886	1612	95	below_threshold
Serratia grimesii	strain=NBRC 13537	GCA_001590905.1	82995	82995	type	True	81.8962	882	1612	95	below_threshold
Chania multitudinisentens	strain=RB-25	GCA_000520015.2	1639108	1639108	type	True	81.7903	928	1612	95	below_threshold
Chania multitudinisentens	strain=RB-25	GCA_000568195.1	1639108	1639108	type	True	81.7547	927	1612	95	below_threshold
Serratia rubidaea	strain=CIP 103234	GCA_001304675.1	61652	61652	type	True	81.4751	823	1612	95	below_threshold
Gibbsiella quercinecans	strain=FRB97	GCA_003666185.1	929813	929813	type	True	80.9306	763	1612	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	79.3481	470	1612	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	78.8882	494	1612	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:52,740] [INFO] DFAST Taxonomy check result was written to GCF_023282985.1_ASM2328298v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:52,742] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:52,742] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:52,742] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6ad79eb-f43f-4618-ac44-76ac8c81a944/dqc_reference/checkm_data
[2024-01-24 11:59:52,745] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:52,793] [INFO] Task started: CheckM
[2024-01-24 11:59:52,794] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023282985.1_ASM2328298v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023282985.1_ASM2328298v1_genomic.fna/checkm_input GCF_023282985.1_ASM2328298v1_genomic.fna/checkm_result
[2024-01-24 12:00:37,459] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:37,460] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:37,480] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:37,480] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:37,480] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023282985.1_ASM2328298v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:37,481] [INFO] Task started: Blastn
[2024-01-24 12:00:37,481] [INFO] Running command: blastn -query GCF_023282985.1_ASM2328298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6ad79eb-f43f-4618-ac44-76ac8c81a944/dqc_reference/reference_markers_gtdb.fasta -out GCF_023282985.1_ASM2328298v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:38,924] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:38,928] [INFO] Selected 13 target genomes.
[2024-01-24 12:00:38,929] [INFO] Target genome list was writen to GCF_023282985.1_ASM2328298v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:38,940] [INFO] Task started: fastANI
[2024-01-24 12:00:38,940] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1753930-82ad-4a23-9025-54c0cbe1f655/GCF_023282985.1_ASM2328298v1_genomic.fna.gz --refList GCF_023282985.1_ASM2328298v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023282985.1_ASM2328298v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:53,592] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:53,615] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:00:53,615] [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_001006005.1	s__Serratia_A fonticola	93.9678	1387	1612	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_A	95.0	96.10	95.03	0.87	0.81	45	-
GCF_000633355.1	s__Serratia_A sp000633355	90.1926	1302	1612	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006715025.1	s__Serratia_A fonticola_A	84.8646	1194	1612	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_A	95.0	100.00	100.00	1.00	1.00	4	-
GCF_001976145.1	s__Chania oryzae	83.3675	951	1612	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Chania	95.0	98.90	98.79	0.94	0.94	3	-
GCF_003591175.1	s__Serratia inhibens	82.643	953	1612	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	96.90	95.73	0.88	0.85	4	-
GCF_000743355.1	s__Chania sp000743355	82.5943	936	1612	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Chania	95.0	99.97	99.97	0.98	0.98	2	-
GCF_013337185.1	s__Serratia proteamaculans_D	82.5728	951	1612	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	97.78	95.57	0.96	0.91	3	-
GCF_001590925.1	s__Serratia plymuthica	82.4967	942	1612	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	97.90	96.52	0.93	0.88	29	-
GCF_900187015.1	s__Serratia ficaria	82.4644	976	1612	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	99.70	99.56	0.95	0.92	5	-
GCF_000422085.1	s__Serratia liquefaciens	82.4473	966	1612	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	98.63	98.20	0.94	0.91	25	-
GCF_016742975.1	s__Serratia nevei	82.3951	837	1612	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.1913	97.82	96.26	0.83	0.75	139	-
GCA_012719855.1	s__Serratia liquefaciens_A	82.3076	931	1612	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	97.92	97.90	0.90	0.89	3	-
GCA_901472405.1	s__Serratia_B rubidaea	81.5214	872	1612	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_B	95.0	98.79	97.55	0.96	0.91	11	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:53,617] [INFO] GTDB search result was written to GCF_023282985.1_ASM2328298v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:53,618] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:53,623] [INFO] DFAST_QC result json was written to GCF_023282985.1_ASM2328298v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:53,623] [INFO] DFAST_QC completed!
[2024-01-24 12:00:53,623] [INFO] Total running time: 0h1m43s