[2024-01-24 13:57:43,799] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:43,800] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:43,801] [INFO] DQC Reference Directory: /var/lib/cwl/stg6eff62b5-dfbe-43d1-8ef2-ca4cb1473946/dqc_reference
[2024-01-24 13:57:45,060] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:45,061] [INFO] Task started: Prodigal
[2024-01-24 13:57:45,061] [INFO] Running command: gunzip -c /var/lib/cwl/stg38763caa-41d6-4bee-b0cb-e9cab68343d5/GCF_026154485.1_ASM2615448v1_genomic.fna.gz | prodigal -d GCF_026154485.1_ASM2615448v1_genomic.fna/cds.fna -a GCF_026154485.1_ASM2615448v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:03,695] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:03,695] [INFO] Task started: HMMsearch
[2024-01-24 13:58:03,696] [INFO] Running command: hmmsearch --tblout GCF_026154485.1_ASM2615448v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6eff62b5-dfbe-43d1-8ef2-ca4cb1473946/dqc_reference/reference_markers.hmm GCF_026154485.1_ASM2615448v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:04,025] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:04,027] [INFO] Found 6/6 markers.
[2024-01-24 13:58:04,069] [INFO] Query marker FASTA was written to GCF_026154485.1_ASM2615448v1_genomic.fna/markers.fasta
[2024-01-24 13:58:04,069] [INFO] Task started: Blastn
[2024-01-24 13:58:04,069] [INFO] Running command: blastn -query GCF_026154485.1_ASM2615448v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6eff62b5-dfbe-43d1-8ef2-ca4cb1473946/dqc_reference/reference_markers.fasta -out GCF_026154485.1_ASM2615448v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:04,805] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:04,809] [INFO] Selected 13 target genomes.
[2024-01-24 13:58:04,810] [INFO] Target genome list was writen to GCF_026154485.1_ASM2615448v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:04,831] [INFO] Task started: fastANI
[2024-01-24 13:58:04,832] [INFO] Running command: fastANI --query /var/lib/cwl/stg38763caa-41d6-4bee-b0cb-e9cab68343d5/GCF_026154485.1_ASM2615448v1_genomic.fna.gz --refList GCF_026154485.1_ASM2615448v1_genomic.fna/target_genomes.txt --output GCF_026154485.1_ASM2615448v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:28,161] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:28,162] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6eff62b5-dfbe-43d1-8ef2-ca4cb1473946/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:28,162] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6eff62b5-dfbe-43d1-8ef2-ca4cb1473946/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:28,174] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:58:28,174] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:28,174] [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 luminescens subsp. mexicana	strain=MEX47-22	GCA_004348775.1	2100167	29488	type	True	97.3376	1522	1767	95	conclusive
Photorhabdus luminescens	strain=ATCC 29999	GCA_900102985.1	29488	29488	suspected-type	True	97.0701	1517	1767	95	conclusive
Photorhabdus luminescens subsp. luminescens	strain=DSM 3368	GCA_001083805.1	171439	29488	type	True	97.0337	1542	1767	95	conclusive
Photorhabdus kleinii	strain=DSM 23513	GCA_025384885.1	768034	768034	type	True	92.201	1354	1767	95	below_threshold
Photorhabdus noenieputensis	strain=DSM 25462	GCA_023108895.1	1208607	1208607	type	True	92.1248	1416	1767	95	below_threshold
Photorhabdus caribbeanensis	strain=HG29	GCA_018448885.1	1004165	1004165	type	True	91.9569	1409	1767	95	below_threshold
Photorhabdus aegyptia	strain=BA1	GCA_000612035.1	2805098	2805098	type	True	91.9372	1300	1767	95	below_threshold
Photorhabdus hindustanensis	strain=H1	GCA_002968995.1	2918802	2918802	type	True	91.6214	1456	1767	95	below_threshold
Photorhabdus hainanensis	strain=DSM 22397	GCA_018448965.1	1004166	1004166	type	True	91.5769	1448	1767	95	below_threshold
Photorhabdus kayaii	strain=DSM 15194	GCA_025384895.1	230088	230088	type	True	91.5109	1308	1767	95	below_threshold
Photorhabdus namnaonensis	strain=PB45.5	GCA_001684335.1	1851568	1851568	type	True	91.4394	1459	1767	95	below_threshold
Photorhabdus temperata	strain=DSM 14550	GCA_025384845.1	574560	574560	type	True	85.8143	1215	1767	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:28,176] [INFO] DFAST Taxonomy check result was written to GCF_026154485.1_ASM2615448v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:28,176] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:28,177] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:28,177] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6eff62b5-dfbe-43d1-8ef2-ca4cb1473946/dqc_reference/checkm_data
[2024-01-24 13:58:28,178] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:28,233] [INFO] Task started: CheckM
[2024-01-24 13:58:28,233] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026154485.1_ASM2615448v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026154485.1_ASM2615448v1_genomic.fna/checkm_input GCF_026154485.1_ASM2615448v1_genomic.fna/checkm_result
[2024-01-24 13:59:29,194] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:29,196] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:29,219] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:29,220] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:29,220] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026154485.1_ASM2615448v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:29,220] [INFO] Task started: Blastn
[2024-01-24 13:59:29,221] [INFO] Running command: blastn -query GCF_026154485.1_ASM2615448v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6eff62b5-dfbe-43d1-8ef2-ca4cb1473946/dqc_reference/reference_markers_gtdb.fasta -out GCF_026154485.1_ASM2615448v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:30,109] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:30,112] [INFO] Selected 10 target genomes.
[2024-01-24 13:59:30,113] [INFO] Target genome list was writen to GCF_026154485.1_ASM2615448v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:30,168] [INFO] Task started: fastANI
[2024-01-24 13:59:30,169] [INFO] Running command: fastANI --query /var/lib/cwl/stg38763caa-41d6-4bee-b0cb-e9cab68343d5/GCF_026154485.1_ASM2615448v1_genomic.fna.gz --refList GCF_026154485.1_ASM2615448v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026154485.1_ASM2615448v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:47,067] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:47,077] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:47,078] [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_001083805.1	s__Photorhabdus luminescens	97.0443	1540	1767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	97.45	96.24	0.90	0.85	5	conclusive
GCF_018448935.1	s__Photorhabdus noenieputensis	92.1658	1399	1767	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	91.9332	1411	1767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003545805.1	s__Photorhabdus sp003545805	91.8594	1372	1767	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	91.6847	1464	1767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.2863	97.65	96.64	0.91	0.87	12	-
GCF_003287735.1	s__Photorhabdus bodei	91.499	1335	1767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	97.51	96.35	0.89	0.86	10	-
GCF_001684335.1	s__Photorhabdus namnaonensis	91.4244	1461	1767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.2863	N/A	N/A	N/A	N/A	1	-
GCF_003343245.1	s__Photorhabdus laumondii	91.3673	1438	1767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	99.39	97.32	0.96	0.88	22	-
GCF_011189505.1	s__Photorhabdus tasmaniensis	85.659	1173	1767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018448905.1	s__Photorhabdus heterorhabditis	85.5239	1159	1767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	98.62	97.27	0.91	0.86	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:47,080] [INFO] GTDB search result was written to GCF_026154485.1_ASM2615448v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:47,081] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:47,085] [INFO] DFAST_QC result json was written to GCF_026154485.1_ASM2615448v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:47,085] [INFO] DFAST_QC completed!
[2024-01-24 13:59:47,085] [INFO] Total running time: 0h2m3s