[2024-01-24 13:58:11,174] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:11,176] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:11,176] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa3d3d77-2a99-4362-9836-6bb4bdb421d2/dqc_reference
[2024-01-24 13:58:12,592] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:12,594] [INFO] Task started: Prodigal
[2024-01-24 13:58:12,594] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b177420-1c48-4ab3-a45c-ad965dd2a79d/GCF_004348755.1_ASM434875v1_genomic.fna.gz | prodigal -d GCF_004348755.1_ASM434875v1_genomic.fna/cds.fna -a GCF_004348755.1_ASM434875v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:30,995] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:30,995] [INFO] Task started: HMMsearch
[2024-01-24 13:58:30,995] [INFO] Running command: hmmsearch --tblout GCF_004348755.1_ASM434875v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa3d3d77-2a99-4362-9836-6bb4bdb421d2/dqc_reference/reference_markers.hmm GCF_004348755.1_ASM434875v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:31,332] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:31,334] [INFO] Found 6/6 markers.
[2024-01-24 13:58:31,382] [INFO] Query marker FASTA was written to GCF_004348755.1_ASM434875v1_genomic.fna/markers.fasta
[2024-01-24 13:58:31,385] [INFO] Task started: Blastn
[2024-01-24 13:58:31,385] [INFO] Running command: blastn -query GCF_004348755.1_ASM434875v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa3d3d77-2a99-4362-9836-6bb4bdb421d2/dqc_reference/reference_markers.fasta -out GCF_004348755.1_ASM434875v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:32,222] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:32,226] [INFO] Selected 10 target genomes.
[2024-01-24 13:58:32,227] [INFO] Target genome list was writen to GCF_004348755.1_ASM434875v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:32,238] [INFO] Task started: fastANI
[2024-01-24 13:58:32,238] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b177420-1c48-4ab3-a45c-ad965dd2a79d/GCF_004348755.1_ASM434875v1_genomic.fna.gz --refList GCF_004348755.1_ASM434875v1_genomic.fna/target_genomes.txt --output GCF_004348755.1_ASM434875v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:49,216] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:49,217] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa3d3d77-2a99-4362-9836-6bb4bdb421d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:49,217] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa3d3d77-2a99-4362-9836-6bb4bdb421d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:49,228] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:58:49,228] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:49,229] [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 khanii subsp. guanajuatensis	strain=MEX20-17	GCA_004348755.1	2100166	1004150	type	True	100.0	1732	1739	95	conclusive
Photorhabdus khanii	strain=NC19	GCA_000517265.1	1004150	1004150	type	True	96.6732	1490	1739	95	conclusive
Photorhabdus stackebrandtii	strain=DSM 23271	GCA_011189495.1	1123042	1123042	type	True	94.3526	1283	1739	95	below_threshold
Photorhabdus temperata	strain=DSM 14550	GCA_025384845.1	574560	574560	type	True	93.1569	1363	1739	95	below_threshold
Photorhabdus thracensis	strain=DSM 15199	GCA_001010285.1	230089	230089	type	True	93.0571	1321	1739	95	below_threshold
Photorhabdus tasmaniensis	strain=T327	GCA_011189505.1	1004159	1004159	type	True	92.3156	1321	1739	95	below_threshold
Photorhabdus kleinii	strain=DSM 23513	GCA_025384885.1	768034	768034	type	True	86.8193	1233	1739	95	below_threshold
Photorhabdus kayaii	strain=DSM 15194	GCA_025384895.1	230088	230088	type	True	86.5265	1177	1739	95	below_threshold
Photorhabdus noenieputensis	strain=DSM 25462	GCA_023108895.1	1208607	1208607	type	True	86.2509	1282	1739	95	below_threshold
Photorhabdus hindustanensis	strain=H1	GCA_002968995.1	2918802	2918802	type	True	86.0352	1289	1739	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:49,230] [INFO] DFAST Taxonomy check result was written to GCF_004348755.1_ASM434875v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:49,231] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:49,231] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:49,232] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa3d3d77-2a99-4362-9836-6bb4bdb421d2/dqc_reference/checkm_data
[2024-01-24 13:58:49,233] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:49,290] [INFO] Task started: CheckM
[2024-01-24 13:58:49,290] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004348755.1_ASM434875v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004348755.1_ASM434875v1_genomic.fna/checkm_input GCF_004348755.1_ASM434875v1_genomic.fna/checkm_result
[2024-01-24 13:59:45,037] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:45,038] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:45,056] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:45,057] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:45,057] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004348755.1_ASM434875v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:45,057] [INFO] Task started: Blastn
[2024-01-24 13:59:45,057] [INFO] Running command: blastn -query GCF_004348755.1_ASM434875v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa3d3d77-2a99-4362-9836-6bb4bdb421d2/dqc_reference/reference_markers_gtdb.fasta -out GCF_004348755.1_ASM434875v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:46,247] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:46,259] [INFO] Selected 9 target genomes.
[2024-01-24 13:59:46,260] [INFO] Target genome list was writen to GCF_004348755.1_ASM434875v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:46,270] [INFO] Task started: fastANI
[2024-01-24 13:59:46,270] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b177420-1c48-4ab3-a45c-ad965dd2a79d/GCF_004348755.1_ASM434875v1_genomic.fna.gz --refList GCF_004348755.1_ASM434875v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004348755.1_ASM434875v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:01,051] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:01,060] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:01,060] [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_000517265.1	s__Photorhabdus khanii	96.6926	1489	1739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	97.69	95.89	0.90	0.86	5	conclusive
GCF_001010285.1	s__Photorhabdus thracensis	93.0433	1323	1739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	95.80	95.75	0.79	0.78	4	-
GCF_011189505.1	s__Photorhabdus tasmaniensis	92.3029	1323	1739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003545805.1	s__Photorhabdus sp003545805	88.1503	1236	1739	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	86.6198	1207	1739	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	86.3486	1267	1739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	99.39	97.32	0.96	0.88	22	-
GCF_011189575.1	s__Photorhabdus cinerea	86.2328	1179	1739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001083805.1	s__Photorhabdus luminescens	86.2306	1282	1739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	97.45	96.24	0.90	0.85	5	-
GCF_018448885.1	s__Photorhabdus caribbeanensis	85.8371	1269	1739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:01,062] [INFO] GTDB search result was written to GCF_004348755.1_ASM434875v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:01,062] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:01,065] [INFO] DFAST_QC result json was written to GCF_004348755.1_ASM434875v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:01,066] [INFO] DFAST_QC completed!
[2024-01-24 14:00:01,066] [INFO] Total running time: 0h1m50s