[2024-01-24 12:14:10,196] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:10,199] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:10,199] [INFO] DQC Reference Directory: /var/lib/cwl/stga6f9be78-dcb1-4662-a05b-077175edfa24/dqc_reference
[2024-01-24 12:14:11,594] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:11,595] [INFO] Task started: Prodigal
[2024-01-24 12:14:11,596] [INFO] Running command: gunzip -c /var/lib/cwl/stg9457049c-8a75-4553-8d16-68f4daed67b4/GCF_000968195.1_ASM96819v1_genomic.fna.gz | prodigal -d GCF_000968195.1_ASM96819v1_genomic.fna/cds.fna -a GCF_000968195.1_ASM96819v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:23,058] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:23,058] [INFO] Task started: HMMsearch
[2024-01-24 12:14:23,058] [INFO] Running command: hmmsearch --tblout GCF_000968195.1_ASM96819v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6f9be78-dcb1-4662-a05b-077175edfa24/dqc_reference/reference_markers.hmm GCF_000968195.1_ASM96819v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:23,388] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:23,390] [INFO] Found 6/6 markers.
[2024-01-24 12:14:23,443] [INFO] Query marker FASTA was written to GCF_000968195.1_ASM96819v1_genomic.fna/markers.fasta
[2024-01-24 12:14:23,444] [INFO] Task started: Blastn
[2024-01-24 12:14:23,444] [INFO] Running command: blastn -query GCF_000968195.1_ASM96819v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6f9be78-dcb1-4662-a05b-077175edfa24/dqc_reference/reference_markers.fasta -out GCF_000968195.1_ASM96819v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:24,220] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:24,225] [INFO] Selected 18 target genomes.
[2024-01-24 12:14:24,226] [INFO] Target genome list was writen to GCF_000968195.1_ASM96819v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:24,244] [INFO] Task started: fastANI
[2024-01-24 12:14:24,244] [INFO] Running command: fastANI --query /var/lib/cwl/stg9457049c-8a75-4553-8d16-68f4daed67b4/GCF_000968195.1_ASM96819v1_genomic.fna.gz --refList GCF_000968195.1_ASM96819v1_genomic.fna/target_genomes.txt --output GCF_000968195.1_ASM96819v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:44,580] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:44,580] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6f9be78-dcb1-4662-a05b-077175edfa24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:44,580] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6f9be78-dcb1-4662-a05b-077175edfa24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:44,593] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:14:44,593] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:44,593] [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
Xenorhabdus doucetiae	strain=FRM16	GCA_000968195.1	351671	351671	type	True	100.0	1399	1400	95	conclusive
Xenorhabdus doucetiae	strain=DSM 17909	GCA_008124675.1	351671	351671	type	True	99.897	1254	1400	95	conclusive
Xenorhabdus ehlersii	strain=DSM 16337	GCA_003610465.1	290111	290111	type	True	86.7862	981	1400	95	below_threshold
Xenorhabdus ehlersii	strain=DSM 16337	GCA_002632445.1	290111	290111	type	True	86.6832	973	1400	95	below_threshold
Xenorhabdus ishibashii	strain=DSM 22670	GCA_002632755.1	1034471	1034471	type	True	86.3271	917	1400	95	below_threshold
Xenorhabdus eapokensis	strain=DL20	GCA_001908105.1	1873482	1873482	type	True	86.2296	949	1400	95	below_threshold
Xenorhabdus thuongxuanensis	strain=30TX1	GCA_001908095.1	1873484	1873484	type	True	86.2081	934	1400	95	below_threshold
Xenorhabdus kozodoii	strain=DSM 17907	GCA_002632875.1	351676	351676	type	True	86.0028	981	1400	95	below_threshold
Xenorhabdus vietnamensis	strain=DSM 22392	GCA_002127535.1	351656	351656	type	True	85.2238	965	1400	95	below_threshold
Xenorhabdus lircayensis	strain=VLS	GCA_016306625.1	2763499	2763499	type	True	84.4707	933	1400	95	below_threshold
Xenorhabdus bovienii	strain=T228	GCA_024721015.1	40576	40576	type	True	82.1017	772	1400	95	below_threshold
Vibrio cidicii	strain=2756-81	GCA_009763805.1	1763883	1763883	type	True	79.8505	54	1400	95	below_threshold
Photorhabdus hindustanensis	strain=H1	GCA_002968995.1	2918802	2918802	type	True	78.8194	355	1400	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.2519	137	1400	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	77.8029	142	1400	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:44,596] [INFO] DFAST Taxonomy check result was written to GCF_000968195.1_ASM96819v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:44,597] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:44,597] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:44,597] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6f9be78-dcb1-4662-a05b-077175edfa24/dqc_reference/checkm_data
[2024-01-24 12:14:44,599] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:44,655] [INFO] Task started: CheckM
[2024-01-24 12:14:44,655] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000968195.1_ASM96819v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000968195.1_ASM96819v1_genomic.fna/checkm_input GCF_000968195.1_ASM96819v1_genomic.fna/checkm_result
[2024-01-24 12:15:24,703] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:24,704] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:24,727] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:24,728] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:24,728] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000968195.1_ASM96819v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:24,729] [INFO] Task started: Blastn
[2024-01-24 12:15:24,729] [INFO] Running command: blastn -query GCF_000968195.1_ASM96819v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6f9be78-dcb1-4662-a05b-077175edfa24/dqc_reference/reference_markers_gtdb.fasta -out GCF_000968195.1_ASM96819v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:25,734] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:25,738] [INFO] Selected 14 target genomes.
[2024-01-24 12:15:25,738] [INFO] Target genome list was writen to GCF_000968195.1_ASM96819v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:25,752] [INFO] Task started: fastANI
[2024-01-24 12:15:25,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg9457049c-8a75-4553-8d16-68f4daed67b4/GCF_000968195.1_ASM96819v1_genomic.fna.gz --refList GCF_000968195.1_ASM96819v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000968195.1_ASM96819v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:41,017] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:41,034] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:41,035] [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_000968195.1	s__Xenorhabdus doucetiae	100.0	1398	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCF_003610465.1	s__Xenorhabdus ehlersii	86.7735	987	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.74	99.51	0.89	0.84	3	-
GCF_015163665.1	s__Xenorhabdus sp015163665	86.4151	966	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001028135.1	s__Xenorhabdus griffiniae_A	86.4035	901	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.95	99.95	0.97	0.97	2	-
GCF_002632755.1	s__Xenorhabdus ishibashii	86.3041	916	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001908095.1	s__Xenorhabdus thuongxuanensis	86.2553	929	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001908105.1	s__Xenorhabdus eapokensis	86.2078	951	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015163655.1	s__Xenorhabdus griffiniae	86.1294	935	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.94	99.94	0.96	0.96	2	-
GCF_002632875.1	s__Xenorhabdus kozodoii	86.0321	977	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002127535.1	s__Xenorhabdus vietnamensis	85.1967	965	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002632615.1	s__Xenorhabdus miraniensis	83.6043	956	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	95.51	95.51	0.84	0.84	2	-
GCF_001037465.1	s__Xenorhabdus khoisanae	83.588	888	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002632465.1	s__Xenorhabdus budapestensis	81.3549	713	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	98.99	98.99	0.92	0.92	2	-
GCF_014467235.1	s__Xenorhabdus indica	81.1646	736	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.18	99.18	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:41,036] [INFO] GTDB search result was written to GCF_000968195.1_ASM96819v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:41,037] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:41,040] [INFO] DFAST_QC result json was written to GCF_000968195.1_ASM96819v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:41,040] [INFO] DFAST_QC completed!
[2024-01-24 12:15:41,040] [INFO] Total running time: 0h1m31s