[2024-01-24 12:36:22,290] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:22,298] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:22,299] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f2c1ed7-2f4b-463c-b7b2-1b005365fb95/dqc_reference
[2024-01-24 12:36:23,538] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:23,539] [INFO] Task started: Prodigal
[2024-01-24 12:36:23,539] [INFO] Running command: gunzip -c /var/lib/cwl/stga33a0872-b7d7-4a19-8a9c-23ee437a3fc8/GCF_001684335.1_ASM168433v1_genomic.fna.gz | prodigal -d GCF_001684335.1_ASM168433v1_genomic.fna/cds.fna -a GCF_001684335.1_ASM168433v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:35,682] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:35,683] [INFO] Task started: HMMsearch
[2024-01-24 12:36:35,683] [INFO] Running command: hmmsearch --tblout GCF_001684335.1_ASM168433v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f2c1ed7-2f4b-463c-b7b2-1b005365fb95/dqc_reference/reference_markers.hmm GCF_001684335.1_ASM168433v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:35,999] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:36,000] [INFO] Found 6/6 markers.
[2024-01-24 12:36:36,050] [INFO] Query marker FASTA was written to GCF_001684335.1_ASM168433v1_genomic.fna/markers.fasta
[2024-01-24 12:36:36,051] [INFO] Task started: Blastn
[2024-01-24 12:36:36,051] [INFO] Running command: blastn -query GCF_001684335.1_ASM168433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f2c1ed7-2f4b-463c-b7b2-1b005365fb95/dqc_reference/reference_markers.fasta -out GCF_001684335.1_ASM168433v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:36,763] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:36,766] [INFO] Selected 10 target genomes.
[2024-01-24 12:36:36,766] [INFO] Target genome list was writen to GCF_001684335.1_ASM168433v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:36,770] [INFO] Task started: fastANI
[2024-01-24 12:36:36,770] [INFO] Running command: fastANI --query /var/lib/cwl/stga33a0872-b7d7-4a19-8a9c-23ee437a3fc8/GCF_001684335.1_ASM168433v1_genomic.fna.gz --refList GCF_001684335.1_ASM168433v1_genomic.fna/target_genomes.txt --output GCF_001684335.1_ASM168433v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:36:53,298] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:53,299] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f2c1ed7-2f4b-463c-b7b2-1b005365fb95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:36:53,300] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f2c1ed7-2f4b-463c-b7b2-1b005365fb95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:36:53,310] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 12:36:53,311] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:36:53,311] [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
Photorhabdus namnaonensis	strain=PB45.5	GCA_001684335.1	1851568	1851568	type	True	100.0	1764	1768	95	inconclusive
Photorhabdus hindustanensis	strain=H1	GCA_002968995.1	2918802	2918802	type	True	95.816	1557	1768	95	inconclusive
Photorhabdus hainanensis	strain=DSM 22397	GCA_018448965.1	1004166	1004166	type	True	95.3743	1514	1768	95	inconclusive
Photorhabdus akhurstii	strain=DSM 15138	GCA_018448925.1	171438	171438	type	True	95.2863	1516	1768	95	inconclusive
Photorhabdus aegyptia	strain=BA1	GCA_000612035.1	2805098	2805098	type	True	94.4883	1354	1768	95	below_threshold
Photorhabdus noenieputensis	strain=DSM 25462	GCA_023108895.1	1208607	1208607	type	True	92.7266	1432	1768	95	below_threshold
Photorhabdus kayaii	strain=DSM 15194	GCA_025384895.1	230088	230088	type	True	91.6624	1337	1768	95	below_threshold
Photorhabdus kleinii	strain=DSM 23513	GCA_025384885.1	768034	768034	type	True	91.4778	1346	1768	95	below_threshold
Photorhabdus luminescens	strain=ATCC 29999	GCA_900102985.1	29488	29488	suspected-type	True	91.3676	1458	1768	95	below_threshold
Photorhabdus temperata	strain=DSM 14550	GCA_025384845.1	574560	574560	type	True	86.0	1221	1768	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:36:53,313] [INFO] DFAST Taxonomy check result was written to GCF_001684335.1_ASM168433v1_genomic.fna/tc_result.tsv
[2024-01-24 12:36:53,313] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:36:53,313] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:36:53,314] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f2c1ed7-2f4b-463c-b7b2-1b005365fb95/dqc_reference/checkm_data
[2024-01-24 12:36:53,315] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:36:53,367] [INFO] Task started: CheckM
[2024-01-24 12:36:53,367] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001684335.1_ASM168433v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001684335.1_ASM168433v1_genomic.fna/checkm_input GCF_001684335.1_ASM168433v1_genomic.fna/checkm_result
[2024-01-24 12:37:33,908] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:33,909] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:33,925] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:33,925] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:33,926] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001684335.1_ASM168433v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:33,926] [INFO] Task started: Blastn
[2024-01-24 12:37:33,926] [INFO] Running command: blastn -query GCF_001684335.1_ASM168433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f2c1ed7-2f4b-463c-b7b2-1b005365fb95/dqc_reference/reference_markers_gtdb.fasta -out GCF_001684335.1_ASM168433v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:34,812] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:34,817] [INFO] Selected 10 target genomes.
[2024-01-24 12:37:34,817] [INFO] Target genome list was writen to GCF_001684335.1_ASM168433v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:34,827] [INFO] Task started: fastANI
[2024-01-24 12:37:34,827] [INFO] Running command: fastANI --query /var/lib/cwl/stga33a0872-b7d7-4a19-8a9c-23ee437a3fc8/GCF_001684335.1_ASM168433v1_genomic.fna.gz --refList GCF_001684335.1_ASM168433v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001684335.1_ASM168433v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:37:51,201] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:51,214] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:37:51,214] [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_001684335.1	s__Photorhabdus namnaonensis	100.0	1764	1768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.2863	N/A	N/A	N/A	N/A	1	conclusive
GCF_018448925.1	s__Photorhabdus akhurstii	95.2863	1516	1768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.2863	97.65	96.64	0.91	0.87	12	conclusive
GCF_018448885.1	s__Photorhabdus caribbeanensis	92.8021	1430	1768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018448935.1	s__Photorhabdus noenieputensis	92.6391	1402	1768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003287735.1	s__Photorhabdus bodei	92.0278	1361	1768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	97.51	96.35	0.89	0.86	10	-
GCF_003343245.1	s__Photorhabdus laumondii	91.397	1470	1768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	99.39	97.32	0.96	0.88	22	-
GCF_001083805.1	s__Photorhabdus luminescens	91.3778	1482	1768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	97.45	96.24	0.90	0.85	5	-
GCF_003545805.1	s__Photorhabdus sp003545805	90.4865	1344	1768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018448905.1	s__Photorhabdus heterorhabditis	85.5098	1157	1768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	98.62	97.27	0.91	0.86	4	-
GCF_000711895.1	s__Photorhabdus australis	85.3185	1132	1768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	97.53	97.53	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:37:51,218] [INFO] GTDB search result was written to GCF_001684335.1_ASM168433v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:37:51,219] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:37:51,223] [INFO] DFAST_QC result json was written to GCF_001684335.1_ASM168433v1_genomic.fna/dqc_result.json
[2024-01-24 12:37:51,223] [INFO] DFAST_QC completed!
[2024-01-24 12:37:51,223] [INFO] Total running time: 0h1m29s