[2024-01-24 13:01:38,116] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:38,118] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:38,118] [INFO] DQC Reference Directory: /var/lib/cwl/stg8398728b-39a7-4459-b0bf-63dd6409bd3c/dqc_reference
[2024-01-24 13:01:40,901] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:40,903] [INFO] Task started: Prodigal
[2024-01-24 13:01:40,904] [INFO] Running command: gunzip -c /var/lib/cwl/stg56104b40-f5de-48d9-b365-965819e4be54/GCF_004348775.1_ASM434877v1_genomic.fna.gz | prodigal -d GCF_004348775.1_ASM434877v1_genomic.fna/cds.fna -a GCF_004348775.1_ASM434877v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:57,879] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:57,879] [INFO] Task started: HMMsearch
[2024-01-24 13:01:57,879] [INFO] Running command: hmmsearch --tblout GCF_004348775.1_ASM434877v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8398728b-39a7-4459-b0bf-63dd6409bd3c/dqc_reference/reference_markers.hmm GCF_004348775.1_ASM434877v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:58,348] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:58,349] [INFO] Found 6/6 markers.
[2024-01-24 13:01:58,395] [INFO] Query marker FASTA was written to GCF_004348775.1_ASM434877v1_genomic.fna/markers.fasta
[2024-01-24 13:01:58,395] [INFO] Task started: Blastn
[2024-01-24 13:01:58,395] [INFO] Running command: blastn -query GCF_004348775.1_ASM434877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8398728b-39a7-4459-b0bf-63dd6409bd3c/dqc_reference/reference_markers.fasta -out GCF_004348775.1_ASM434877v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:59,127] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:59,131] [INFO] Selected 13 target genomes.
[2024-01-24 13:01:59,131] [INFO] Target genome list was writen to GCF_004348775.1_ASM434877v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:59,136] [INFO] Task started: fastANI
[2024-01-24 13:01:59,136] [INFO] Running command: fastANI --query /var/lib/cwl/stg56104b40-f5de-48d9-b365-965819e4be54/GCF_004348775.1_ASM434877v1_genomic.fna.gz --refList GCF_004348775.1_ASM434877v1_genomic.fna/target_genomes.txt --output GCF_004348775.1_ASM434877v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:22,690] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:22,691] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8398728b-39a7-4459-b0bf-63dd6409bd3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:22,691] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8398728b-39a7-4459-b0bf-63dd6409bd3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:22,702] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:02:22,702] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:22,702] [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	100.0	1873	1876	95	conclusive
Photorhabdus luminescens	strain=ATCC 29999	GCA_900102985.1	29488	29488	suspected-type	True	96.8509	1521	1876	95	conclusive
Photorhabdus luminescens subsp. luminescens	strain=DSM 3368	GCA_001083805.1	171439	29488	type	True	96.7959	1550	1876	95	conclusive
Photorhabdus noenieputensis	strain=DSM 25462	GCA_018448935.1	1208607	1208607	type	True	92.1572	1402	1876	95	below_threshold
Photorhabdus kleinii	strain=DSM 23513	GCA_025384885.1	768034	768034	type	True	92.1117	1369	1876	95	below_threshold
Photorhabdus noenieputensis	strain=DSM 25462	GCA_023108895.1	1208607	1208607	type	True	92.0907	1431	1876	95	below_threshold
Photorhabdus caribbeanensis	strain=HG29	GCA_018448885.1	1004165	1004165	type	True	92.0275	1418	1876	95	below_threshold
Photorhabdus aegyptia	strain=BA1	GCA_000612035.1	2805098	2805098	type	True	91.9504	1391	1876	95	below_threshold
Photorhabdus hindustanensis	strain=H1	GCA_002968995.1	2918802	2918802	type	True	91.628	1497	1876	95	below_threshold
Photorhabdus hainanensis	strain=DSM 22397	GCA_018448965.1	1004166	1004166	type	True	91.6079	1473	1876	95	below_threshold
Photorhabdus kayaii	strain=DSM 15194	GCA_025384895.1	230088	230088	type	True	91.4477	1308	1876	95	below_threshold
Photorhabdus namnaonensis	strain=PB45.5	GCA_001684335.1	1851568	1851568	type	True	91.437	1460	1876	95	below_threshold
Photorhabdus temperata	strain=DSM 14550	GCA_025384845.1	574560	574560	type	True	85.8097	1249	1876	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:22,704] [INFO] DFAST Taxonomy check result was written to GCF_004348775.1_ASM434877v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:22,704] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:22,705] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:22,705] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8398728b-39a7-4459-b0bf-63dd6409bd3c/dqc_reference/checkm_data
[2024-01-24 13:02:22,706] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:22,763] [INFO] Task started: CheckM
[2024-01-24 13:02:22,763] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004348775.1_ASM434877v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004348775.1_ASM434877v1_genomic.fna/checkm_input GCF_004348775.1_ASM434877v1_genomic.fna/checkm_result
[2024-01-24 13:03:16,018] [INFO] Task succeeded: CheckM
[2024-01-24 13:03:16,020] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:03:16,046] [INFO] ===== Completeness check finished =====
[2024-01-24 13:03:16,046] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:03:16,047] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004348775.1_ASM434877v1_genomic.fna/markers.fasta)
[2024-01-24 13:03:16,047] [INFO] Task started: Blastn
[2024-01-24 13:03:16,047] [INFO] Running command: blastn -query GCF_004348775.1_ASM434877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8398728b-39a7-4459-b0bf-63dd6409bd3c/dqc_reference/reference_markers_gtdb.fasta -out GCF_004348775.1_ASM434877v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:17,005] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:17,009] [INFO] Selected 11 target genomes.
[2024-01-24 13:03:17,009] [INFO] Target genome list was writen to GCF_004348775.1_ASM434877v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:03:17,017] [INFO] Task started: fastANI
[2024-01-24 13:03:17,017] [INFO] Running command: fastANI --query /var/lib/cwl/stg56104b40-f5de-48d9-b365-965819e4be54/GCF_004348775.1_ASM434877v1_genomic.fna.gz --refList GCF_004348775.1_ASM434877v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004348775.1_ASM434877v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:32,841] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:32,854] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:32,855] [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	96.7931	1550	1876	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	92.1675	1401	1876	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	92.0265	1417	1876	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	91.7346	1466	1876	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.2863	97.65	96.64	0.91	0.87	12	-
GCF_003545805.1	s__Photorhabdus sp003545805	91.6452	1360	1876	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001684335.1	s__Photorhabdus namnaonensis	91.427	1461	1876	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.2863	N/A	N/A	N/A	N/A	1	-
GCF_003287735.1	s__Photorhabdus bodei	91.3889	1349	1876	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	91.2753	1443	1876	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	99.39	97.32	0.96	0.88	22	-
GCF_003610465.1	s__Xenorhabdus ehlersii	78.783	376	1876	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.74	99.51	0.89	0.84	3	-
GCF_002632825.1	s__Xenorhabdus stockiae	78.691	346	1876	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	96.93	95.64	0.86	0.83	3	-
GCA_003533305.1	s__Providencia sp003533305	77.9085	171	1876	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	99.80	99.80	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:32,856] [INFO] GTDB search result was written to GCF_004348775.1_ASM434877v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:32,857] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:32,860] [INFO] DFAST_QC result json was written to GCF_004348775.1_ASM434877v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:32,861] [INFO] DFAST_QC completed!
[2024-01-24 13:03:32,861] [INFO] Total running time: 0h1m55s