[2024-01-24 14:28:08,531] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:08,536] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:08,536] [INFO] DQC Reference Directory: /var/lib/cwl/stg15925690-7480-47f1-ab51-ad2f796470b0/dqc_reference
[2024-01-24 14:28:10,417] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:10,419] [INFO] Task started: Prodigal
[2024-01-24 14:28:10,419] [INFO] Running command: gunzip -c /var/lib/cwl/stgca1461f2-1472-48fd-b281-f02ef638cf44/GCF_900451015.1_28193_C01_genomic.fna.gz | prodigal -d GCF_900451015.1_28193_C01_genomic.fna/cds.fna -a GCF_900451015.1_28193_C01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:25,455] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:25,455] [INFO] Task started: HMMsearch
[2024-01-24 14:28:25,455] [INFO] Running command: hmmsearch --tblout GCF_900451015.1_28193_C01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15925690-7480-47f1-ab51-ad2f796470b0/dqc_reference/reference_markers.hmm GCF_900451015.1_28193_C01_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:25,791] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:25,793] [INFO] Found 6/6 markers.
[2024-01-24 14:28:25,847] [INFO] Query marker FASTA was written to GCF_900451015.1_28193_C01_genomic.fna/markers.fasta
[2024-01-24 14:28:25,847] [INFO] Task started: Blastn
[2024-01-24 14:28:25,847] [INFO] Running command: blastn -query GCF_900451015.1_28193_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stg15925690-7480-47f1-ab51-ad2f796470b0/dqc_reference/reference_markers.fasta -out GCF_900451015.1_28193_C01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:26,855] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:26,858] [INFO] Selected 15 target genomes.
[2024-01-24 14:28:26,859] [INFO] Target genome list was writen to GCF_900451015.1_28193_C01_genomic.fna/target_genomes.txt
[2024-01-24 14:28:26,865] [INFO] Task started: fastANI
[2024-01-24 14:28:26,865] [INFO] Running command: fastANI --query /var/lib/cwl/stgca1461f2-1472-48fd-b281-f02ef638cf44/GCF_900451015.1_28193_C01_genomic.fna.gz --refList GCF_900451015.1_28193_C01_genomic.fna/target_genomes.txt --output GCF_900451015.1_28193_C01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:44,696] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:44,696] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15925690-7480-47f1-ab51-ad2f796470b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:44,697] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15925690-7480-47f1-ab51-ad2f796470b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:44,710] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:28:44,710] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:44,710] [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
Ewingella americana	strain=NCTC12157	GCA_900451015.1	41202	41202	type	True	100.0	1646	1646	95	conclusive
Ewingella americana	strain=CCUG 14506T	GCA_008693045.1	41202	41202	type	True	99.9337	1628	1646	95	conclusive
Ewingella americana	strain=ATCC 33852	GCA_000735345.1	41202	41202	type	True	99.9156	1582	1646	95	conclusive
Rahnella victoriana	strain=DSM 27397	GCA_004330295.1	1510570	1510570	type	True	81.8397	913	1646	95	below_threshold
Rahnella inusitata	strain=DSM 30078	GCA_003602055.1	58169	58169	type	True	81.7752	921	1646	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	81.7634	922	1646	95	below_threshold
Rahnella inusitata	strain=DSM 30078	GCA_003263515.1	58169	58169	type	True	81.7412	900	1646	95	below_threshold
Rahnella laticis	strain=SAP-17	GCA_015644585.1	2787622	2787622	type	True	81.7012	927	1646	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	81.5839	891	1646	95	below_threshold
Rahnella bonaserana	strain=H11b	GCA_019049675.1	2816248	2816248	type	True	81.51	911	1646	95	below_threshold
Rahnella contaminans	strain=Lac-M11	GCA_011065485.1	2703882	2703882	type	True	81.4961	921	1646	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	79.771	664	1646	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	79.6892	647	1646	95	below_threshold
Serratia rhizosphaerae	strain=KUDC3025	GCA_009817885.1	2597702	2597702	type	True	79.4779	585	1646	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	79.4069	635	1646	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:44,712] [INFO] DFAST Taxonomy check result was written to GCF_900451015.1_28193_C01_genomic.fna/tc_result.tsv
[2024-01-24 14:28:44,712] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:44,712] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:44,713] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15925690-7480-47f1-ab51-ad2f796470b0/dqc_reference/checkm_data
[2024-01-24 14:28:44,714] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:44,769] [INFO] Task started: CheckM
[2024-01-24 14:28:44,769] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900451015.1_28193_C01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900451015.1_28193_C01_genomic.fna/checkm_input GCF_900451015.1_28193_C01_genomic.fna/checkm_result
[2024-01-24 14:29:30,647] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:30,649] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:30,671] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:30,671] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:30,671] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900451015.1_28193_C01_genomic.fna/markers.fasta)
[2024-01-24 14:29:30,672] [INFO] Task started: Blastn
[2024-01-24 14:29:30,672] [INFO] Running command: blastn -query GCF_900451015.1_28193_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stg15925690-7480-47f1-ab51-ad2f796470b0/dqc_reference/reference_markers_gtdb.fasta -out GCF_900451015.1_28193_C01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:32,056] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:32,060] [INFO] Selected 16 target genomes.
[2024-01-24 14:29:32,060] [INFO] Target genome list was writen to GCF_900451015.1_28193_C01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:32,081] [INFO] Task started: fastANI
[2024-01-24 14:29:32,081] [INFO] Running command: fastANI --query /var/lib/cwl/stgca1461f2-1472-48fd-b281-f02ef638cf44/GCF_900451015.1_28193_C01_genomic.fna.gz --refList GCF_900451015.1_28193_C01_genomic.fna/target_genomes_gtdb.txt --output GCF_900451015.1_28193_C01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:50,006] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:50,020] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:50,021] [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_000735345.1	s__Ewingella americana	99.9156	1582	1646	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Ewingella	95.0	98.48	96.44	0.97	0.94	5	conclusive
GCA_003864575.1	s__Ewingella sp003864575	83.2806	836	1646	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Ewingella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006438725.1	s__Ewingella americana_A	82.9057	1049	1646	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Ewingella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014639435.1	s__Ewingella psychrotolerans	81.8955	848	1646	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Ewingella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004330295.1	s__Rahnella victoriana	81.826	915	1646	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	98.74	98.62	0.94	0.93	5	-
GCF_002951615.1	s__Rahnella sp002951615	81.7974	912	1646	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003263515.1	s__Rahnella inusitata	81.7536	899	1646	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	99.32	98.94	0.97	0.94	4	-
GCF_015644585.1	s__Rahnella laticis	81.7355	924	1646	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	96.65	95.20	0.90	0.83	8	-
GCF_003610915.1	s__Rahnella variigena	81.6847	929	1646	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	97.86	97.35	0.92	0.89	8	-
GCF_019049675.1	s__Rahnella sp019049675	81.5387	906	1646	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002834385.1	s__Rahnella sp002834385	81.3969	873	1646	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011684115.1	s__Rahnella aceris	81.3225	896	1646	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	99.19	98.40	0.95	0.89	21	-
GCF_009208105.1	s__Rouxiella sp009208105	80.4127	678	1646	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rouxiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017299535.1	s__Serratia marcescens	79.72	657	1646	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.8494	99.42	98.47	0.97	0.85	72	-
GCF_013375155.1	s__Serratia ureilytica	79.516	647	1646	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.3985	98.73	97.62	0.94	0.88	142	-
GCF_009817885.1	s__Serratia_B rhizosphaerae	79.4963	582	1646	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_B	95.0	97.16	97.09	0.90	0.89	7	-
--------------------------------------------------------------------------------
[2024-01-24 14:29:50,022] [INFO] GTDB search result was written to GCF_900451015.1_28193_C01_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:50,023] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:50,030] [INFO] DFAST_QC result json was written to GCF_900451015.1_28193_C01_genomic.fna/dqc_result.json
[2024-01-24 14:29:50,030] [INFO] DFAST_QC completed!
[2024-01-24 14:29:50,031] [INFO] Total running time: 0h1m41s