[2024-01-25 18:42:05,886] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:42:05,890] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:42:05,890] [INFO] DQC Reference Directory: /var/lib/cwl/stg49f1c628-c9fa-46bf-bcd2-990660a87719/dqc_reference
[2024-01-25 18:42:07,073] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:42:07,074] [INFO] Task started: Prodigal
[2024-01-25 18:42:07,074] [INFO] Running command: gunzip -c /var/lib/cwl/stg26b68870-c120-449b-ba13-c9dbbe1f9809/GCF_025384895.1_ASM2538489v1_genomic.fna.gz | prodigal -d GCF_025384895.1_ASM2538489v1_genomic.fna/cds.fna -a GCF_025384895.1_ASM2538489v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:42:18,702] [INFO] Task succeeded: Prodigal
[2024-01-25 18:42:18,702] [INFO] Task started: HMMsearch
[2024-01-25 18:42:18,702] [INFO] Running command: hmmsearch --tblout GCF_025384895.1_ASM2538489v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg49f1c628-c9fa-46bf-bcd2-990660a87719/dqc_reference/reference_markers.hmm GCF_025384895.1_ASM2538489v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:42:19,012] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:42:19,013] [INFO] Found 6/6 markers.
[2024-01-25 18:42:19,051] [INFO] Query marker FASTA was written to GCF_025384895.1_ASM2538489v1_genomic.fna/markers.fasta
[2024-01-25 18:42:19,051] [INFO] Task started: Blastn
[2024-01-25 18:42:19,051] [INFO] Running command: blastn -query GCF_025384895.1_ASM2538489v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49f1c628-c9fa-46bf-bcd2-990660a87719/dqc_reference/reference_markers.fasta -out GCF_025384895.1_ASM2538489v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:19,746] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:19,749] [INFO] Selected 11 target genomes.
[2024-01-25 18:42:19,749] [INFO] Target genome list was writen to GCF_025384895.1_ASM2538489v1_genomic.fna/target_genomes.txt
[2024-01-25 18:42:19,752] [INFO] Task started: fastANI
[2024-01-25 18:42:19,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg26b68870-c120-449b-ba13-c9dbbe1f9809/GCF_025384895.1_ASM2538489v1_genomic.fna.gz --refList GCF_025384895.1_ASM2538489v1_genomic.fna/target_genomes.txt --output GCF_025384895.1_ASM2538489v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:42:37,023] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:37,024] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg49f1c628-c9fa-46bf-bcd2-990660a87719/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:42:37,024] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg49f1c628-c9fa-46bf-bcd2-990660a87719/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:42:37,032] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 18:42:37,032] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 18:42:37,032] [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 kayaii	strain=DSM 15194	GCA_025384895.1	230088	230088	type	True	100.0	1585	1593	95	inconclusive
Photorhabdus bodei	strain=LJ24-63	GCA_003287735.1	2029681	2029681	type	True	96.3287	1359	1593	95	inconclusive
Photorhabdus kleinii	strain=DSM 23513	GCA_025384885.1	768034	768034	type	True	95.6167	1330	1593	95	inconclusive
Photorhabdus laumondii subsp. clarkei	strain=BOJ-47	GCA_003287575.1	2029685	2218628	type	True	94.8235	1323	1593	95	below_threshold
Photorhabdus laumondii subsp. laumondii	strain=TT01	GCA_003343245.1	141679	2218628	type	True	94.6704	1372	1593	95	below_threshold
Photorhabdus noenieputensis	strain=DSM 25462	GCA_023108895.1	1208607	1208607	type	True	92.3613	1326	1593	95	below_threshold
Photorhabdus aegyptia	strain=BA1	GCA_000612035.1	2805098	2805098	type	True	92.1936	1203	1593	95	below_threshold
Photorhabdus akhurstii	strain=DSM 15138	GCA_018448925.1	171438	171438	type	True	92.1402	1315	1593	95	below_threshold
Photorhabdus hainanensis	strain=DSM 22397	GCA_018448965.1	1004166	1004166	type	True	91.9848	1336	1593	95	below_threshold
Photorhabdus hindustanensis	strain=H1	GCA_002968995.1	2918802	2918802	type	True	91.8922	1324	1593	95	below_threshold
Photorhabdus temperata	strain=DSM 14550	GCA_025384845.1	574560	574560	type	True	86.532	1158	1593	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:42:37,034] [INFO] DFAST Taxonomy check result was written to GCF_025384895.1_ASM2538489v1_genomic.fna/tc_result.tsv
[2024-01-25 18:42:37,035] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:42:37,035] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:42:37,035] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg49f1c628-c9fa-46bf-bcd2-990660a87719/dqc_reference/checkm_data
[2024-01-25 18:42:37,036] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:42:37,087] [INFO] Task started: CheckM
[2024-01-25 18:42:37,087] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025384895.1_ASM2538489v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025384895.1_ASM2538489v1_genomic.fna/checkm_input GCF_025384895.1_ASM2538489v1_genomic.fna/checkm_result
[2024-01-25 18:43:17,359] [INFO] Task succeeded: CheckM
[2024-01-25 18:43:17,360] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:43:17,381] [INFO] ===== Completeness check finished =====
[2024-01-25 18:43:17,381] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:43:17,382] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025384895.1_ASM2538489v1_genomic.fna/markers.fasta)
[2024-01-25 18:43:17,382] [INFO] Task started: Blastn
[2024-01-25 18:43:17,382] [INFO] Running command: blastn -query GCF_025384895.1_ASM2538489v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49f1c628-c9fa-46bf-bcd2-990660a87719/dqc_reference/reference_markers_gtdb.fasta -out GCF_025384895.1_ASM2538489v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:18,319] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:18,322] [INFO] Selected 9 target genomes.
[2024-01-25 18:43:18,322] [INFO] Target genome list was writen to GCF_025384895.1_ASM2538489v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:43:18,329] [INFO] Task started: fastANI
[2024-01-25 18:43:18,329] [INFO] Running command: fastANI --query /var/lib/cwl/stg26b68870-c120-449b-ba13-c9dbbe1f9809/GCF_025384895.1_ASM2538489v1_genomic.fna.gz --refList GCF_025384895.1_ASM2538489v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025384895.1_ASM2538489v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:43:33,352] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:33,359] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:43:33,359] [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_003287735.1	s__Photorhabdus bodei	96.3043	1361	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	97.51	96.35	0.89	0.86	10	conclusive
GCF_003343245.1	s__Photorhabdus laumondii	94.6435	1375	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	99.39	97.32	0.96	0.88	22	-
GCF_003545805.1	s__Photorhabdus sp003545805	92.5095	1278	1593	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	92.3763	1304	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018448885.1	s__Photorhabdus caribbeanensis	92.1742	1279	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018448925.1	s__Photorhabdus akhurstii	92.1357	1316	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.2863	97.65	96.64	0.91	0.87	12	-
GCF_001684335.1	s__Photorhabdus namnaonensis	91.7378	1342	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.2863	N/A	N/A	N/A	N/A	1	-
GCF_001083805.1	s__Photorhabdus luminescens	91.5186	1325	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	97.45	96.24	0.90	0.85	5	-
GCF_011189505.1	s__Photorhabdus tasmaniensis	86.3731	1166	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:43:33,360] [INFO] GTDB search result was written to GCF_025384895.1_ASM2538489v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:43:33,361] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:43:33,364] [INFO] DFAST_QC result json was written to GCF_025384895.1_ASM2538489v1_genomic.fna/dqc_result.json
[2024-01-25 18:43:33,364] [INFO] DFAST_QC completed!
[2024-01-25 18:43:33,364] [INFO] Total running time: 0h1m27s