[2024-01-24 13:31:57,447] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:57,449] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:57,449] [INFO] DQC Reference Directory: /var/lib/cwl/stgc968fc93-df2a-4919-b90d-8d7343e0d897/dqc_reference
[2024-01-24 13:31:58,899] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:58,900] [INFO] Task started: Prodigal
[2024-01-24 13:31:58,900] [INFO] Running command: gunzip -c /var/lib/cwl/stg2b4ee50c-562b-4ad4-a6b6-dd92a6146ad1/GCF_001083805.1_ASM108380v1_genomic.fna.gz | prodigal -d GCF_001083805.1_ASM108380v1_genomic.fna/cds.fna -a GCF_001083805.1_ASM108380v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:16,917] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:16,918] [INFO] Task started: HMMsearch
[2024-01-24 13:32:16,918] [INFO] Running command: hmmsearch --tblout GCF_001083805.1_ASM108380v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc968fc93-df2a-4919-b90d-8d7343e0d897/dqc_reference/reference_markers.hmm GCF_001083805.1_ASM108380v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:17,235] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:17,238] [INFO] Found 6/6 markers.
[2024-01-24 13:32:17,298] [INFO] Query marker FASTA was written to GCF_001083805.1_ASM108380v1_genomic.fna/markers.fasta
[2024-01-24 13:32:17,299] [INFO] Task started: Blastn
[2024-01-24 13:32:17,299] [INFO] Running command: blastn -query GCF_001083805.1_ASM108380v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc968fc93-df2a-4919-b90d-8d7343e0d897/dqc_reference/reference_markers.fasta -out GCF_001083805.1_ASM108380v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:18,066] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:18,071] [INFO] Selected 13 target genomes.
[2024-01-24 13:32:18,071] [INFO] Target genome list was writen to GCF_001083805.1_ASM108380v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:18,077] [INFO] Task started: fastANI
[2024-01-24 13:32:18,078] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b4ee50c-562b-4ad4-a6b6-dd92a6146ad1/GCF_001083805.1_ASM108380v1_genomic.fna.gz --refList GCF_001083805.1_ASM108380v1_genomic.fna/target_genomes.txt --output GCF_001083805.1_ASM108380v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:38,805] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:38,806] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc968fc93-df2a-4919-b90d-8d7343e0d897/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:38,806] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc968fc93-df2a-4919-b90d-8d7343e0d897/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:38,816] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:32:38,817] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:38,817] [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. luminescens	strain=DSM 3368	GCA_001083805.1	171439	29488	type	True	100.0	1813	1813	95	conclusive
Photorhabdus luminescens	strain=ATCC 29999	GCA_900102985.1	29488	29488	suspected-type	True	99.9417	1717	1813	95	conclusive
Photorhabdus luminescens subsp. mexicana	strain=MEX47-22	GCA_004348775.1	2100167	29488	type	True	96.76	1544	1813	95	conclusive
Photorhabdus kleinii	strain=DSM 23513	GCA_025384885.1	768034	768034	type	True	92.2233	1378	1813	95	below_threshold
Photorhabdus noenieputensis	strain=DSM 25462	GCA_023108895.1	1208607	1208607	type	True	92.1542	1481	1813	95	below_threshold
Photorhabdus caribbeanensis	strain=HG29	GCA_018448885.1	1004165	1004165	type	True	91.9741	1433	1813	95	below_threshold
Photorhabdus aegyptia	strain=BA1	GCA_000612035.1	2805098	2805098	type	True	91.967	1328	1813	95	below_threshold
Photorhabdus hindustanensis	strain=H1	GCA_002968995.1	2918802	2918802	type	True	91.6255	1476	1813	95	below_threshold
Photorhabdus hainanensis	strain=DSM 22397	GCA_018448965.1	1004166	1004166	type	True	91.6198	1466	1813	95	below_threshold
Photorhabdus kayaii	strain=DSM 15194	GCA_025384895.1	230088	230088	type	True	91.5028	1315	1813	95	below_threshold
Photorhabdus namnaonensis	strain=PB45.5	GCA_001684335.1	1851568	1851568	type	True	91.3821	1461	1813	95	below_threshold
Photorhabdus temperata	strain=DSM 14550	GCA_025384845.1	574560	574560	type	True	85.9389	1224	1813	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:38,818] [INFO] DFAST Taxonomy check result was written to GCF_001083805.1_ASM108380v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:38,819] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:38,819] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:38,819] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc968fc93-df2a-4919-b90d-8d7343e0d897/dqc_reference/checkm_data
[2024-01-24 13:32:38,821] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:38,880] [INFO] Task started: CheckM
[2024-01-24 13:32:38,881] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001083805.1_ASM108380v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001083805.1_ASM108380v1_genomic.fna/checkm_input GCF_001083805.1_ASM108380v1_genomic.fna/checkm_result
[2024-01-24 13:33:35,843] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:35,845] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:35,869] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:35,869] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:35,870] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001083805.1_ASM108380v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:35,870] [INFO] Task started: Blastn
[2024-01-24 13:33:35,870] [INFO] Running command: blastn -query GCF_001083805.1_ASM108380v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc968fc93-df2a-4919-b90d-8d7343e0d897/dqc_reference/reference_markers_gtdb.fasta -out GCF_001083805.1_ASM108380v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:36,847] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:36,850] [INFO] Selected 11 target genomes.
[2024-01-24 13:33:36,850] [INFO] Target genome list was writen to GCF_001083805.1_ASM108380v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:36,863] [INFO] Task started: fastANI
[2024-01-24 13:33:36,863] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b4ee50c-562b-4ad4-a6b6-dd92a6146ad1/GCF_001083805.1_ASM108380v1_genomic.fna.gz --refList GCF_001083805.1_ASM108380v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001083805.1_ASM108380v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:55,519] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:55,534] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:55,534] [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	100.0	1813	1813	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	92.179	1429	1813	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	91.9763	1433	1813	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	91.7259	1367	1813	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	91.6947	1505	1813	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	91.5461	1356	1813	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	91.3683	1463	1813	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	91.3573	1472	1813	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	85.8297	1212	1813	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	85.5043	1211	1813	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	98.62	97.27	0.91	0.86	4	-
GCF_000711895.1	s__Photorhabdus australis	85.1957	1174	1813	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	97.53	97.53	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:55,537] [INFO] GTDB search result was written to GCF_001083805.1_ASM108380v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:55,537] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:55,541] [INFO] DFAST_QC result json was written to GCF_001083805.1_ASM108380v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:55,541] [INFO] DFAST_QC completed!
[2024-01-24 13:33:55,541] [INFO] Total running time: 0h1m58s