[2024-01-24 13:19:00,046] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:00,047] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:00,048] [INFO] DQC Reference Directory: /var/lib/cwl/stg03836016-4918-4630-8fe2-0fe851b4668e/dqc_reference
[2024-01-24 13:19:01,369] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:01,370] [INFO] Task started: Prodigal
[2024-01-24 13:19:01,371] [INFO] Running command: gunzip -c /var/lib/cwl/stgcfd9ca80-6f15-49e1-8ca7-c7dcae4bd330/GCF_008124675.1_ASM812467v1_genomic.fna.gz | prodigal -d GCF_008124675.1_ASM812467v1_genomic.fna/cds.fna -a GCF_008124675.1_ASM812467v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:11,923] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:11,923] [INFO] Task started: HMMsearch
[2024-01-24 13:19:11,923] [INFO] Running command: hmmsearch --tblout GCF_008124675.1_ASM812467v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03836016-4918-4630-8fe2-0fe851b4668e/dqc_reference/reference_markers.hmm GCF_008124675.1_ASM812467v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:12,236] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:12,239] [INFO] Found 6/6 markers.
[2024-01-24 13:19:12,273] [INFO] Query marker FASTA was written to GCF_008124675.1_ASM812467v1_genomic.fna/markers.fasta
[2024-01-24 13:19:12,273] [INFO] Task started: Blastn
[2024-01-24 13:19:12,274] [INFO] Running command: blastn -query GCF_008124675.1_ASM812467v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03836016-4918-4630-8fe2-0fe851b4668e/dqc_reference/reference_markers.fasta -out GCF_008124675.1_ASM812467v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:13,213] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:13,216] [INFO] Selected 20 target genomes.
[2024-01-24 13:19:13,216] [INFO] Target genome list was writen to GCF_008124675.1_ASM812467v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:13,237] [INFO] Task started: fastANI
[2024-01-24 13:19:13,238] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfd9ca80-6f15-49e1-8ca7-c7dcae4bd330/GCF_008124675.1_ASM812467v1_genomic.fna.gz --refList GCF_008124675.1_ASM812467v1_genomic.fna/target_genomes.txt --output GCF_008124675.1_ASM812467v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:36,080] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:36,081] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03836016-4918-4630-8fe2-0fe851b4668e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:36,081] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03836016-4918-4630-8fe2-0fe851b4668e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:36,093] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:19:36,093] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:36,093] [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=DSM 17909	GCA_008124675.1	351671	351671	type	True	100.0	1257	1268	95	conclusive
Xenorhabdus doucetiae	strain=FRM16	GCA_000968195.1	351671	351671	type	True	99.9799	1264	1268	95	conclusive
Xenorhabdus ehlersii	strain=DSM 16337	GCA_003610465.1	290111	290111	type	True	86.7532	945	1268	95	below_threshold
Xenorhabdus ehlersii	strain=DSM 16337	GCA_002632445.1	290111	290111	type	True	86.7279	952	1268	95	below_threshold
Xenorhabdus eapokensis	strain=DL20	GCA_001908105.1	1873482	1873482	type	True	86.3312	903	1268	95	below_threshold
Xenorhabdus thuongxuanensis	strain=30TX1	GCA_001908095.1	1873484	1873484	type	True	86.2534	917	1268	95	below_threshold
Xenorhabdus ishibashii	strain=DSM 22670	GCA_002632755.1	1034471	1034471	type	True	86.1283	905	1268	95	below_threshold
Xenorhabdus kozodoii	strain=DSM 17907	GCA_002632875.1	351676	351676	type	True	85.9803	951	1268	95	below_threshold
Xenorhabdus vietnamensis	strain=DSM 22392	GCA_002127535.1	351656	351656	type	True	85.1428	944	1268	95	below_threshold
Xenorhabdus lircayensis	strain=VLS	GCA_016306625.1	2763499	2763499	type	True	84.4866	905	1268	95	below_threshold
Xenorhabdus bovienii	strain=T228	GCA_024721015.1	40576	40576	type	True	82.067	755	1268	95	below_threshold
Photorhabdus hindustanensis	strain=H1	GCA_002968995.1	2918802	2918802	type	True	78.5499	375	1268	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.0086	136	1268	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	77.8438	137	1268	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:36,095] [INFO] DFAST Taxonomy check result was written to GCF_008124675.1_ASM812467v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:36,095] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:36,096] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:36,096] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03836016-4918-4630-8fe2-0fe851b4668e/dqc_reference/checkm_data
[2024-01-24 13:19:36,097] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:36,139] [INFO] Task started: CheckM
[2024-01-24 13:19:36,139] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008124675.1_ASM812467v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008124675.1_ASM812467v1_genomic.fna/checkm_input GCF_008124675.1_ASM812467v1_genomic.fna/checkm_result
[2024-01-24 13:20:12,407] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:12,409] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:12,428] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:12,428] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:12,429] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008124675.1_ASM812467v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:12,429] [INFO] Task started: Blastn
[2024-01-24 13:20:12,429] [INFO] Running command: blastn -query GCF_008124675.1_ASM812467v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03836016-4918-4630-8fe2-0fe851b4668e/dqc_reference/reference_markers_gtdb.fasta -out GCF_008124675.1_ASM812467v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:13,571] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:13,576] [INFO] Selected 15 target genomes.
[2024-01-24 13:20:13,576] [INFO] Target genome list was writen to GCF_008124675.1_ASM812467v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:13,596] [INFO] Task started: fastANI
[2024-01-24 13:20:13,596] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfd9ca80-6f15-49e1-8ca7-c7dcae4bd330/GCF_008124675.1_ASM812467v1_genomic.fna.gz --refList GCF_008124675.1_ASM812467v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008124675.1_ASM812467v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:28,620] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:28,642] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:28,643] [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	99.9799	1264	1268	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	86.703	950	1268	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	86.4614	928	1268	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	86.3729	895	1268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.95	99.95	0.97	0.97	2	-
GCF_001908105.1	s__Xenorhabdus eapokensis	86.3659	902	1268	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	86.2629	916	1268	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	86.1929	896	1268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.94	99.94	0.96	0.96	2	-
GCF_002632755.1	s__Xenorhabdus ishibashii	86.133	905	1268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002632875.1	s__Xenorhabdus kozodoii	85.9913	949	1268	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	85.1477	944	1268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016306625.1	s__Xenorhabdus sp016306625	84.4697	906	1268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001037465.1	s__Xenorhabdus khoisanae	83.7439	862	1268	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	83.4526	912	1268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	95.51	95.51	0.84	0.84	2	-
GCF_002632465.1	s__Xenorhabdus budapestensis	81.2345	684	1268	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	80.9554	720	1268	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 13:20:28,644] [INFO] GTDB search result was written to GCF_008124675.1_ASM812467v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:28,645] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:28,648] [INFO] DFAST_QC result json was written to GCF_008124675.1_ASM812467v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:28,649] [INFO] DFAST_QC completed!
[2024-01-24 13:20:28,649] [INFO] Total running time: 0h1m29s