[2024-01-24 13:27:57,905] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:57,907] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:57,907] [INFO] DQC Reference Directory: /var/lib/cwl/stgef3bdb6d-0f6e-4f82-905e-7985ba1f4154/dqc_reference
[2024-01-24 13:27:59,127] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:59,128] [INFO] Task started: Prodigal
[2024-01-24 13:27:59,128] [INFO] Running command: gunzip -c /var/lib/cwl/stge1293cdd-6f7c-4abb-9ded-73ea80e26f7f/GCF_013277735.1_ASM1327773v1_genomic.fna.gz | prodigal -d GCF_013277735.1_ASM1327773v1_genomic.fna/cds.fna -a GCF_013277735.1_ASM1327773v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:11,613] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:11,613] [INFO] Task started: HMMsearch
[2024-01-24 13:28:11,613] [INFO] Running command: hmmsearch --tblout GCF_013277735.1_ASM1327773v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef3bdb6d-0f6e-4f82-905e-7985ba1f4154/dqc_reference/reference_markers.hmm GCF_013277735.1_ASM1327773v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:11,935] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:11,936] [INFO] Found 6/6 markers.
[2024-01-24 13:28:11,986] [INFO] Query marker FASTA was written to GCF_013277735.1_ASM1327773v1_genomic.fna/markers.fasta
[2024-01-24 13:28:11,986] [INFO] Task started: Blastn
[2024-01-24 13:28:11,986] [INFO] Running command: blastn -query GCF_013277735.1_ASM1327773v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef3bdb6d-0f6e-4f82-905e-7985ba1f4154/dqc_reference/reference_markers.fasta -out GCF_013277735.1_ASM1327773v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:12,747] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:12,752] [INFO] Selected 11 target genomes.
[2024-01-24 13:28:12,752] [INFO] Target genome list was writen to GCF_013277735.1_ASM1327773v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:12,761] [INFO] Task started: fastANI
[2024-01-24 13:28:12,762] [INFO] Running command: fastANI --query /var/lib/cwl/stge1293cdd-6f7c-4abb-9ded-73ea80e26f7f/GCF_013277735.1_ASM1327773v1_genomic.fna.gz --refList GCF_013277735.1_ASM1327773v1_genomic.fna/target_genomes.txt --output GCF_013277735.1_ASM1327773v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:30,941] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:30,942] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef3bdb6d-0f6e-4f82-905e-7985ba1f4154/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:30,942] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef3bdb6d-0f6e-4f82-905e-7985ba1f4154/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:30,951] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:28:30,952] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:30,952] [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 heterorhabditis subsp. aluminescens	strain=Q614	GCA_013277735.1	2805094	880156	type	True	100.0	1555	1563	95	conclusive
Photorhabdus heterorhabditis	strain=SF41	GCA_018448905.1	880156	880156	type	True	97.2702	1343	1563	95	conclusive
Photorhabdus cinerea	strain=DSM 19724	GCA_011189575.1	471575	471575	type	True	94.7975	1263	1563	95	below_threshold
Photorhabdus australis	strain=DSM 17609	GCA_000711895.1	286156	286156	type	True	91.4947	1258	1563	95	below_threshold
Photorhabdus australis subsp. thailandensis	strain=PB68.1	GCA_001696805.1	2805096	286156	type	True	91.3772	1234	1563	95	below_threshold
Photorhabdus asymbiotica	strain=DSM 15149	GCA_003634575.1	291112	291112	type	True	90.6234	1248	1563	95	below_threshold
Photorhabdus temperata	strain=DSM 14550	GCA_025384845.1	574560	574560	type	True	86.2454	1135	1563	95	below_threshold
Photorhabdus kayaii	strain=DSM 15194	GCA_025384895.1	230088	230088	type	True	86.0005	1110	1563	95	below_threshold
Photorhabdus noenieputensis	strain=DSM 25462	GCA_023108895.1	1208607	1208607	type	True	85.9449	1183	1563	95	below_threshold
Photorhabdus kleinii	strain=DSM 23513	GCA_025384885.1	768034	768034	type	True	85.5969	1123	1563	95	below_threshold
Photorhabdus hindustanensis	strain=H1	GCA_002968995.1	2918802	2918802	type	True	85.4894	1125	1563	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:30,953] [INFO] DFAST Taxonomy check result was written to GCF_013277735.1_ASM1327773v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:30,954] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:30,954] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:30,954] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef3bdb6d-0f6e-4f82-905e-7985ba1f4154/dqc_reference/checkm_data
[2024-01-24 13:28:30,955] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:31,004] [INFO] Task started: CheckM
[2024-01-24 13:28:31,004] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013277735.1_ASM1327773v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013277735.1_ASM1327773v1_genomic.fna/checkm_input GCF_013277735.1_ASM1327773v1_genomic.fna/checkm_result
[2024-01-24 13:29:15,174] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:15,175] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:15,194] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:15,194] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:15,194] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013277735.1_ASM1327773v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:15,195] [INFO] Task started: Blastn
[2024-01-24 13:29:15,195] [INFO] Running command: blastn -query GCF_013277735.1_ASM1327773v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef3bdb6d-0f6e-4f82-905e-7985ba1f4154/dqc_reference/reference_markers_gtdb.fasta -out GCF_013277735.1_ASM1327773v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:16,127] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:16,130] [INFO] Selected 11 target genomes.
[2024-01-24 13:29:16,130] [INFO] Target genome list was writen to GCF_013277735.1_ASM1327773v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:16,144] [INFO] Task started: fastANI
[2024-01-24 13:29:16,145] [INFO] Running command: fastANI --query /var/lib/cwl/stge1293cdd-6f7c-4abb-9ded-73ea80e26f7f/GCF_013277735.1_ASM1327773v1_genomic.fna.gz --refList GCF_013277735.1_ASM1327773v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013277735.1_ASM1327773v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:33,192] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:33,204] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:33,205] [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_018448905.1	s__Photorhabdus heterorhabditis	97.2581	1344	1563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	98.62	97.27	0.91	0.86	4	conclusive
GCF_011189575.1	s__Photorhabdus cinerea	94.7609	1266	1563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711895.1	s__Photorhabdus australis	91.5015	1257	1563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	97.53	97.53	0.89	0.89	2	-
GCF_003634575.1	s__Photorhabdus asymbiotica	90.6027	1250	1563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_011189505.1	s__Photorhabdus tasmaniensis	86.441	1135	1563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001010285.1	s__Photorhabdus thracensis	86.4297	1148	1563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	95.80	95.75	0.79	0.78	4	-
GCF_003343245.1	s__Photorhabdus laumondii	86.2176	1169	1563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	99.39	97.32	0.96	0.88	22	-
GCF_003287735.1	s__Photorhabdus bodei	86.1487	1146	1563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	97.51	96.35	0.89	0.86	10	-
GCF_000517265.1	s__Photorhabdus khanii	86.085	1172	1563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	97.69	95.89	0.90	0.86	5	-
GCF_003545805.1	s__Photorhabdus sp003545805	85.9389	1120	1563	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	85.5297	1156	1563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.2863	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:33,206] [INFO] GTDB search result was written to GCF_013277735.1_ASM1327773v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:33,207] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:33,210] [INFO] DFAST_QC result json was written to GCF_013277735.1_ASM1327773v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:33,210] [INFO] DFAST_QC completed!
[2024-01-24 13:29:33,211] [INFO] Total running time: 0h1m35s