[2024-01-24 13:28:12,587] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:12,589] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:12,589] [INFO] DQC Reference Directory: /var/lib/cwl/stg4437d173-aba9-4357-8acb-9f1c2e9c3b01/dqc_reference
[2024-01-24 13:28:13,877] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:13,878] [INFO] Task started: Prodigal
[2024-01-24 13:28:13,878] [INFO] Running command: gunzip -c /var/lib/cwl/stg399224f1-99e5-45bb-8260-fb3b72939e92/GCF_020387775.1_ASM2038777v1_genomic.fna.gz | prodigal -d GCF_020387775.1_ASM2038777v1_genomic.fna/cds.fna -a GCF_020387775.1_ASM2038777v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:28,416] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:28,416] [INFO] Task started: HMMsearch
[2024-01-24 13:28:28,417] [INFO] Running command: hmmsearch --tblout GCF_020387775.1_ASM2038777v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4437d173-aba9-4357-8acb-9f1c2e9c3b01/dqc_reference/reference_markers.hmm GCF_020387775.1_ASM2038777v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:28,800] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:28,801] [INFO] Found 6/6 markers.
[2024-01-24 13:28:28,841] [INFO] Query marker FASTA was written to GCF_020387775.1_ASM2038777v1_genomic.fna/markers.fasta
[2024-01-24 13:28:28,842] [INFO] Task started: Blastn
[2024-01-24 13:28:28,842] [INFO] Running command: blastn -query GCF_020387775.1_ASM2038777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4437d173-aba9-4357-8acb-9f1c2e9c3b01/dqc_reference/reference_markers.fasta -out GCF_020387775.1_ASM2038777v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:29,582] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:29,586] [INFO] Selected 18 target genomes.
[2024-01-24 13:28:29,586] [INFO] Target genome list was writen to GCF_020387775.1_ASM2038777v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:29,593] [INFO] Task started: fastANI
[2024-01-24 13:28:29,593] [INFO] Running command: fastANI --query /var/lib/cwl/stg399224f1-99e5-45bb-8260-fb3b72939e92/GCF_020387775.1_ASM2038777v1_genomic.fna.gz --refList GCF_020387775.1_ASM2038777v1_genomic.fna/target_genomes.txt --output GCF_020387775.1_ASM2038777v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:56,592] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:56,593] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4437d173-aba9-4357-8acb-9f1c2e9c3b01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:56,593] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4437d173-aba9-4357-8acb-9f1c2e9c3b01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:56,607] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:28:56,607] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:28:56,607] [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 kleinii	strain=DSM 23513	GCA_025384885.1	768034	768034	type	True	93.0836	1331	1629	95	below_threshold
Photorhabdus kayaii	strain=DSM 15194	GCA_025384895.1	230088	230088	type	True	92.6351	1304	1629	95	below_threshold
Photorhabdus bodei	strain=LJ24-63	GCA_003287735.1	2029681	2029681	type	True	92.623	1334	1629	95	below_threshold
Photorhabdus laumondii subsp. clarkei	strain=BOJ-47	GCA_003287575.1	2029685	2218628	type	True	92.3863	1298	1629	95	below_threshold
Photorhabdus laumondii subsp. laumondii	strain=TT01	GCA_003343245.1	141679	2218628	type	True	92.3047	1394	1629	95	below_threshold
Photorhabdus luminescens subsp. mexicana	strain=MEX47-22	GCA_004348775.1	2100167	29488	type	True	91.9926	1365	1629	95	below_threshold
Photorhabdus noenieputensis	strain=DSM 25462	GCA_023108895.1	1208607	1208607	type	True	91.3295	1359	1629	95	below_threshold
Photorhabdus aegyptia	strain=BA1	GCA_000612035.1	2805098	2805098	type	True	91.2026	1229	1629	95	below_threshold
Photorhabdus akhurstii	strain=DSM 15138	GCA_018448925.1	171438	171438	type	True	91.1361	1334	1629	95	below_threshold
Photorhabdus caribbeanensis	strain=HG29	GCA_018448885.1	1004165	1004165	type	True	91.1235	1296	1629	95	below_threshold
Photorhabdus hindustanensis	strain=H1	GCA_002968995.1	2918802	2918802	type	True	90.9638	1351	1629	95	below_threshold
Photorhabdus hainanensis	strain=DSM 22397	GCA_018448965.1	1004166	1004166	type	True	90.939	1355	1629	95	below_threshold
Photorhabdus khanii subsp. guanajuatensis	strain=MEX20-17	GCA_004348755.1	2100166	1004150	type	True	87.8039	1227	1629	95	below_threshold
Photorhabdus khanii	strain=NC19	GCA_000517265.1	1004150	1004150	type	True	87.6865	1217	1629	95	below_threshold
Photorhabdus stackebrandtii	strain=DSM 23271	GCA_011189495.1	1123042	1123042	type	True	87.333	1173	1629	95	below_threshold
Photorhabdus thracensis	strain=DSM 15199	GCA_001010285.1	230089	230089	type	True	87.0394	1209	1629	95	below_threshold
Photorhabdus temperata	strain=DSM 14550	GCA_025384845.1	574560	574560	type	True	86.9296	1177	1629	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:56,609] [INFO] DFAST Taxonomy check result was written to GCF_020387775.1_ASM2038777v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:56,609] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:56,609] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:56,610] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4437d173-aba9-4357-8acb-9f1c2e9c3b01/dqc_reference/checkm_data
[2024-01-24 13:28:56,611] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:56,662] [INFO] Task started: CheckM
[2024-01-24 13:28:56,662] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020387775.1_ASM2038777v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020387775.1_ASM2038777v1_genomic.fna/checkm_input GCF_020387775.1_ASM2038777v1_genomic.fna/checkm_result
[2024-01-24 13:29:45,576] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:45,578] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:45,598] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:45,598] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:45,599] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020387775.1_ASM2038777v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:45,599] [INFO] Task started: Blastn
[2024-01-24 13:29:45,599] [INFO] Running command: blastn -query GCF_020387775.1_ASM2038777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4437d173-aba9-4357-8acb-9f1c2e9c3b01/dqc_reference/reference_markers_gtdb.fasta -out GCF_020387775.1_ASM2038777v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:46,534] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:46,538] [INFO] Selected 12 target genomes.
[2024-01-24 13:29:46,539] [INFO] Target genome list was writen to GCF_020387775.1_ASM2038777v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:46,543] [INFO] Task started: fastANI
[2024-01-24 13:29:46,543] [INFO] Running command: fastANI --query /var/lib/cwl/stg399224f1-99e5-45bb-8260-fb3b72939e92/GCF_020387775.1_ASM2038777v1_genomic.fna.gz --refList GCF_020387775.1_ASM2038777v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020387775.1_ASM2038777v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:06,133] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:06,155] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:06,155] [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_003545805.1	s__Photorhabdus sp003545805	96.2865	1418	1629	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003287735.1	s__Photorhabdus bodei	92.6118	1335	1629	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	92.3111	1393	1629	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	92.2394	1371	1629	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	97.45	96.24	0.90	0.85	5	-
GCF_018448935.1	s__Photorhabdus noenieputensis	91.3999	1330	1629	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	91.1294	1335	1629	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.2863	97.65	96.64	0.91	0.87	12	-
GCF_018448885.1	s__Photorhabdus caribbeanensis	91.1116	1297	1629	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	90.7498	1362	1629	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.2863	N/A	N/A	N/A	N/A	1	-
GCF_000517265.1	s__Photorhabdus khanii	87.6754	1218	1629	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	97.69	95.89	0.90	0.86	5	-
GCF_001010285.1	s__Photorhabdus thracensis	86.9999	1213	1629	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	95.80	95.75	0.79	0.78	4	-
GCF_011189505.1	s__Photorhabdus tasmaniensis	86.8474	1190	1629	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	86.0584	1182	1629	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 13:30:06,158] [INFO] GTDB search result was written to GCF_020387775.1_ASM2038777v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:06,159] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:06,163] [INFO] DFAST_QC result json was written to GCF_020387775.1_ASM2038777v1_genomic.fna/dqc_result.json
[2024-01-24 13:30:06,163] [INFO] DFAST_QC completed!
[2024-01-24 13:30:06,163] [INFO] Total running time: 0h1m54s