[2024-01-24 10:47:06,547] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,552] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,552] [INFO] DQC Reference Directory: /var/lib/cwl/stg94750899-733b-493c-ac49-648abeb7ca46/dqc_reference
[2024-01-24 10:47:12,103] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,104] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,104] [INFO] Running command: gunzip -c /var/lib/cwl/stg634e5657-d7a8-4309-bbc0-ca209a81ccda/GCF_018448925.1_ASM1844892v1_genomic.fna.gz | prodigal -d GCF_018448925.1_ASM1844892v1_genomic.fna/cds.fna -a GCF_018448925.1_ASM1844892v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:24,703] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:24,704] [INFO] Task started: HMMsearch
[2024-01-24 10:47:24,704] [INFO] Running command: hmmsearch --tblout GCF_018448925.1_ASM1844892v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg94750899-733b-493c-ac49-648abeb7ca46/dqc_reference/reference_markers.hmm GCF_018448925.1_ASM1844892v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:25,060] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:25,063] [INFO] Found 6/6 markers.
[2024-01-24 10:47:25,107] [INFO] Query marker FASTA was written to GCF_018448925.1_ASM1844892v1_genomic.fna/markers.fasta
[2024-01-24 10:47:25,108] [INFO] Task started: Blastn
[2024-01-24 10:47:25,108] [INFO] Running command: blastn -query GCF_018448925.1_ASM1844892v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg94750899-733b-493c-ac49-648abeb7ca46/dqc_reference/reference_markers.fasta -out GCF_018448925.1_ASM1844892v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:25,914] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:25,921] [INFO] Selected 10 target genomes.
[2024-01-24 10:47:25,922] [INFO] Target genome list was writen to GCF_018448925.1_ASM1844892v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:25,938] [INFO] Task started: fastANI
[2024-01-24 10:47:25,939] [INFO] Running command: fastANI --query /var/lib/cwl/stg634e5657-d7a8-4309-bbc0-ca209a81ccda/GCF_018448925.1_ASM1844892v1_genomic.fna.gz --refList GCF_018448925.1_ASM1844892v1_genomic.fna/target_genomes.txt --output GCF_018448925.1_ASM1844892v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:42,828] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:42,829] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg94750899-733b-493c-ac49-648abeb7ca46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:42,829] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg94750899-733b-493c-ac49-648abeb7ca46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:42,838] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 10:47:42,838] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 10:47:42,838] [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 akhurstii	strain=DSM 15138	GCA_018448925.1	171438	171438	type	True	100.0	1784	1789	95	inconclusive
Photorhabdus hindustanensis	strain=H1	GCA_002968995.1	2918802	2918802	type	True	96.9214	1564	1789	95	inconclusive
Photorhabdus aegyptia	strain=BA1	GCA_000612035.1	2805098	2805098	type	True	96.6575	1414	1789	95	inconclusive
Photorhabdus hainanensis	strain=DSM 22397	GCA_018448965.1	1004166	1004166	type	True	96.5337	1579	1789	95	inconclusive
Photorhabdus namnaonensis	strain=PB45.5	GCA_001684335.1	1851568	1851568	type	True	95.2868	1527	1789	95	inconclusive
Photorhabdus caribbeanensis	strain=HG29	GCA_018448885.1	1004165	1004165	type	True	93.6251	1494	1789	95	below_threshold
Photorhabdus noenieputensis	strain=DSM 25462	GCA_023108895.1	1208607	1208607	type	True	93.3293	1502	1789	95	below_threshold
Photorhabdus kayaii	strain=DSM 15194	GCA_025384895.1	230088	230088	type	True	92.0122	1319	1789	95	below_threshold
Photorhabdus kleinii	strain=DSM 23513	GCA_025384885.1	768034	768034	type	True	91.8396	1352	1789	95	below_threshold
Photorhabdus temperata	strain=DSM 14550	GCA_025384845.1	574560	574560	type	True	85.9639	1240	1789	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:42,840] [INFO] DFAST Taxonomy check result was written to GCF_018448925.1_ASM1844892v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:42,841] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:42,841] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:42,841] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg94750899-733b-493c-ac49-648abeb7ca46/dqc_reference/checkm_data
[2024-01-24 10:47:42,842] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:42,895] [INFO] Task started: CheckM
[2024-01-24 10:47:42,895] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018448925.1_ASM1844892v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018448925.1_ASM1844892v1_genomic.fna/checkm_input GCF_018448925.1_ASM1844892v1_genomic.fna/checkm_result
[2024-01-24 10:48:23,069] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:23,070] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:23,086] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:23,087] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:23,087] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018448925.1_ASM1844892v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:23,087] [INFO] Task started: Blastn
[2024-01-24 10:48:23,087] [INFO] Running command: blastn -query GCF_018448925.1_ASM1844892v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg94750899-733b-493c-ac49-648abeb7ca46/dqc_reference/reference_markers_gtdb.fasta -out GCF_018448925.1_ASM1844892v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:24,247] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:24,250] [INFO] Selected 7 target genomes.
[2024-01-24 10:48:24,250] [INFO] Target genome list was writen to GCF_018448925.1_ASM1844892v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:24,276] [INFO] Task started: fastANI
[2024-01-24 10:48:24,276] [INFO] Running command: fastANI --query /var/lib/cwl/stg634e5657-d7a8-4309-bbc0-ca209a81ccda/GCF_018448925.1_ASM1844892v1_genomic.fna.gz --refList GCF_018448925.1_ASM1844892v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018448925.1_ASM1844892v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:36,336] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:36,344] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:36,344] [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_018448925.1	s__Photorhabdus akhurstii	100.0	1784	1789	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_001684335.1	s__Photorhabdus namnaonensis	95.2672	1529	1789	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.2863	N/A	N/A	N/A	N/A	1	-
GCF_018448885.1	s__Photorhabdus caribbeanensis	93.6265	1494	1789	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	93.4407	1463	1789	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	92.4121	1362	1789	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	91.9312	1483	1789	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	91.6787	1503	1789	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	97.45	96.24	0.90	0.85	5	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:36,346] [INFO] GTDB search result was written to GCF_018448925.1_ASM1844892v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:36,346] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:36,350] [INFO] DFAST_QC result json was written to GCF_018448925.1_ASM1844892v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:36,351] [INFO] DFAST_QC completed!
[2024-01-24 10:48:36,351] [INFO] Total running time: 0h1m30s