[2024-01-24 15:26:52,559] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:52,563] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:52,563] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc2a893f-451c-4749-9de5-58fade8369d6/dqc_reference
[2024-01-24 15:26:53,766] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:53,767] [INFO] Task started: Prodigal
[2024-01-24 15:26:53,767] [INFO] Running command: gunzip -c /var/lib/cwl/stg79af0fc9-da4c-4c16-97bd-e04a1903c8d8/GCF_900457075.1_36672_B01_genomic.fna.gz | prodigal -d GCF_900457075.1_36672_B01_genomic.fna/cds.fna -a GCF_900457075.1_36672_B01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:11,756] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:11,757] [INFO] Task started: HMMsearch
[2024-01-24 15:27:11,757] [INFO] Running command: hmmsearch --tblout GCF_900457075.1_36672_B01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc2a893f-451c-4749-9de5-58fade8369d6/dqc_reference/reference_markers.hmm GCF_900457075.1_36672_B01_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:12,087] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:12,088] [INFO] Found 6/6 markers.
[2024-01-24 15:27:12,138] [INFO] Query marker FASTA was written to GCF_900457075.1_36672_B01_genomic.fna/markers.fasta
[2024-01-24 15:27:12,138] [INFO] Task started: Blastn
[2024-01-24 15:27:12,138] [INFO] Running command: blastn -query GCF_900457075.1_36672_B01_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc2a893f-451c-4749-9de5-58fade8369d6/dqc_reference/reference_markers.fasta -out GCF_900457075.1_36672_B01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:12,982] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:12,985] [INFO] Selected 16 target genomes.
[2024-01-24 15:27:12,986] [INFO] Target genome list was writen to GCF_900457075.1_36672_B01_genomic.fna/target_genomes.txt
[2024-01-24 15:27:12,992] [INFO] Task started: fastANI
[2024-01-24 15:27:12,992] [INFO] Running command: fastANI --query /var/lib/cwl/stg79af0fc9-da4c-4c16-97bd-e04a1903c8d8/GCF_900457075.1_36672_B01_genomic.fna.gz --refList GCF_900457075.1_36672_B01_genomic.fna/target_genomes.txt --output GCF_900457075.1_36672_B01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:32,900] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:32,901] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc2a893f-451c-4749-9de5-58fade8369d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:32,901] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc2a893f-451c-4749-9de5-58fade8369d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:32,912] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:32,912] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:32,912] [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 quinivorans	strain=NCTC11544	GCA_900457075.1	137545	137545	suspected-type	True	100.0	1955	1957	95	conclusive
Serratia proteamaculans	strain=CCUG 14510	GCA_008830365.1	28151	28151	type	True	91.9086	1515	1957	95	below_threshold
Serratia liquefaciens	strain=ATCC 27592	GCA_000422085.1	614	614	type	True	88.4614	1446	1957	95	below_threshold
Serratia grimesii	strain=NCTC11543	GCA_900456935.1	82995	82995	type	True	88.0573	1451	1957	95	below_threshold
Serratia grimesii	strain=NBRC 13537	GCA_001590905.1	82995	82995	type	True	88.0513	1400	1957	95	below_threshold
Serratia plymuthica	strain=FDAARGOS_895	GCA_016027675.1	82996	82996	type	True	87.3026	1382	1957	95	below_threshold
Serratia inhibens	strain=S40	GCA_003591175.1	2338073	2338073	type	True	87.1709	1374	1957	95	below_threshold
Serratia plymuthica	strain=NBRC 102599	GCA_001590925.1	82996	82996	type	True	87.1134	1369	1957	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	85.5172	1305	1957	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	84.4712	1267	1957	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	84.3589	1214	1957	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	79.3657	625	1957	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	79.141	618	1957	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:32,915] [INFO] DFAST Taxonomy check result was written to GCF_900457075.1_36672_B01_genomic.fna/tc_result.tsv
[2024-01-24 15:27:32,915] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:32,916] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:32,916] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc2a893f-451c-4749-9de5-58fade8369d6/dqc_reference/checkm_data
[2024-01-24 15:27:32,917] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:32,973] [INFO] Task started: CheckM
[2024-01-24 15:27:32,973] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900457075.1_36672_B01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900457075.1_36672_B01_genomic.fna/checkm_input GCF_900457075.1_36672_B01_genomic.fna/checkm_result
[2024-01-24 15:28:22,123] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:22,124] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:22,143] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:22,143] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:22,143] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900457075.1_36672_B01_genomic.fna/markers.fasta)
[2024-01-24 15:28:22,144] [INFO] Task started: Blastn
[2024-01-24 15:28:22,144] [INFO] Running command: blastn -query GCF_900457075.1_36672_B01_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc2a893f-451c-4749-9de5-58fade8369d6/dqc_reference/reference_markers_gtdb.fasta -out GCF_900457075.1_36672_B01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:23,238] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:23,242] [INFO] Selected 13 target genomes.
[2024-01-24 15:28:23,242] [INFO] Target genome list was writen to GCF_900457075.1_36672_B01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:23,250] [INFO] Task started: fastANI
[2024-01-24 15:28:23,250] [INFO] Running command: fastANI --query /var/lib/cwl/stg79af0fc9-da4c-4c16-97bd-e04a1903c8d8/GCF_900457075.1_36672_B01_genomic.fna.gz --refList GCF_900457075.1_36672_B01_genomic.fna/target_genomes_gtdb.txt --output GCF_900457075.1_36672_B01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:39,732] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:39,744] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:39,744] [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_900457075.1	s__Serratia quinivorans	100.0	1955	1957	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	98.38	95.64	0.93	0.85	9	conclusive
GCF_013337185.1	s__Serratia proteamaculans_D	94.6967	1566	1957	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	97.78	95.57	0.96	0.91	3	-
GCF_008830365.1	s__Serratia proteamaculans	91.9086	1515	1957	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	97.96	95.51	0.92	0.86	11	-
GCF_000422085.1	s__Serratia liquefaciens	88.4553	1444	1957	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	88.3517	1449	1957	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	97.92	97.90	0.90	0.89	3	-
GCF_001590905.1	s__Serratia grimesii	88.0513	1400	1957	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	99.09	98.89	0.96	0.93	7	-
GCF_018336935.1	s__Serratia plymuthica_B	87.3534	1392	1957	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017832355.1	s__Serratia sp017832355	87.3123	1440	1957	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003591175.1	s__Serratia inhibens	87.1839	1372	1957	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	96.90	95.73	0.88	0.85	4	-
GCF_001590925.1	s__Serratia plymuthica	87.1134	1369	1957	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	85.6109	1370	1957	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	84.4918	1295	1957	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.1913	98.92	98.92	0.95	0.95	2	-
GCF_003996855.1	s__Morganella morganii_C	78.4741	268	1957	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Morganella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:39,745] [INFO] GTDB search result was written to GCF_900457075.1_36672_B01_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:39,746] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:39,749] [INFO] DFAST_QC result json was written to GCF_900457075.1_36672_B01_genomic.fna/dqc_result.json
[2024-01-24 15:28:39,749] [INFO] DFAST_QC completed!
[2024-01-24 15:28:39,750] [INFO] Total running time: 0h1m47s