[2024-01-24 12:29:37,427] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:37,430] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:37,430] [INFO] DQC Reference Directory: /var/lib/cwl/stg01eafbd9-dd69-4553-badd-41dc3a990019/dqc_reference
[2024-01-24 12:29:38,734] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:38,735] [INFO] Task started: Prodigal
[2024-01-24 12:29:38,736] [INFO] Running command: gunzip -c /var/lib/cwl/stg0574a52a-35a1-4621-a573-c0f5447b9900/GCF_025384885.1_ASM2538488v1_genomic.fna.gz | prodigal -d GCF_025384885.1_ASM2538488v1_genomic.fna/cds.fna -a GCF_025384885.1_ASM2538488v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:51,736] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:51,737] [INFO] Task started: HMMsearch
[2024-01-24 12:29:51,737] [INFO] Running command: hmmsearch --tblout GCF_025384885.1_ASM2538488v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01eafbd9-dd69-4553-badd-41dc3a990019/dqc_reference/reference_markers.hmm GCF_025384885.1_ASM2538488v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:52,043] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:52,045] [INFO] Found 6/6 markers.
[2024-01-24 12:29:52,087] [INFO] Query marker FASTA was written to GCF_025384885.1_ASM2538488v1_genomic.fna/markers.fasta
[2024-01-24 12:29:52,088] [INFO] Task started: Blastn
[2024-01-24 12:29:52,088] [INFO] Running command: blastn -query GCF_025384885.1_ASM2538488v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01eafbd9-dd69-4553-badd-41dc3a990019/dqc_reference/reference_markers.fasta -out GCF_025384885.1_ASM2538488v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:52,814] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:52,819] [INFO] Selected 9 target genomes.
[2024-01-24 12:29:52,820] [INFO] Target genome list was writen to GCF_025384885.1_ASM2538488v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:52,825] [INFO] Task started: fastANI
[2024-01-24 12:29:52,825] [INFO] Running command: fastANI --query /var/lib/cwl/stg0574a52a-35a1-4621-a573-c0f5447b9900/GCF_025384885.1_ASM2538488v1_genomic.fna.gz --refList GCF_025384885.1_ASM2538488v1_genomic.fna/target_genomes.txt --output GCF_025384885.1_ASM2538488v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:09,033] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:09,034] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01eafbd9-dd69-4553-badd-41dc3a990019/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:09,034] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01eafbd9-dd69-4553-badd-41dc3a990019/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:09,044] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:30:09,044] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:30:09,045] [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	100.0	1636	1640	95	inconclusive
Photorhabdus bodei	strain=LJ24-63	GCA_003287735.1	2029681	2029681	type	True	96.4793	1382	1640	95	inconclusive
Photorhabdus kayaii	strain=DSM 15194	GCA_025384895.1	230088	230088	type	True	95.5329	1334	1640	95	inconclusive
Photorhabdus laumondii subsp. clarkei	strain=BOJ-47	GCA_003287575.1	2029685	2218628	type	True	93.9384	1342	1640	95	below_threshold
Photorhabdus laumondii subsp. laumondii	strain=TT01	GCA_003343245.1	141679	2218628	type	True	93.7172	1414	1640	95	below_threshold
Photorhabdus noenieputensis	strain=DSM 25462	GCA_023108895.1	1208607	1208607	type	True	92.1236	1371	1640	95	below_threshold
Photorhabdus aegyptia	strain=BA1	GCA_000612035.1	2805098	2805098	type	True	92.0544	1243	1640	95	below_threshold
Photorhabdus hindustanensis	strain=H1	GCA_002968995.1	2918802	2918802	type	True	91.7714	1363	1640	95	below_threshold
Photorhabdus temperata	strain=DSM 14550	GCA_025384845.1	574560	574560	type	True	86.429	1180	1640	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:09,047] [INFO] DFAST Taxonomy check result was written to GCF_025384885.1_ASM2538488v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:09,047] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:09,047] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:09,048] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01eafbd9-dd69-4553-badd-41dc3a990019/dqc_reference/checkm_data
[2024-01-24 12:30:09,049] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:09,099] [INFO] Task started: CheckM
[2024-01-24 12:30:09,100] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025384885.1_ASM2538488v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025384885.1_ASM2538488v1_genomic.fna/checkm_input GCF_025384885.1_ASM2538488v1_genomic.fna/checkm_result
[2024-01-24 12:30:54,670] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:54,671] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:54,692] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:54,693] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:54,693] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025384885.1_ASM2538488v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:54,693] [INFO] Task started: Blastn
[2024-01-24 12:30:54,693] [INFO] Running command: blastn -query GCF_025384885.1_ASM2538488v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01eafbd9-dd69-4553-badd-41dc3a990019/dqc_reference/reference_markers_gtdb.fasta -out GCF_025384885.1_ASM2538488v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:55,636] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:55,640] [INFO] Selected 12 target genomes.
[2024-01-24 12:30:55,640] [INFO] Target genome list was writen to GCF_025384885.1_ASM2538488v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:55,664] [INFO] Task started: fastANI
[2024-01-24 12:30:55,665] [INFO] Running command: fastANI --query /var/lib/cwl/stg0574a52a-35a1-4621-a573-c0f5447b9900/GCF_025384885.1_ASM2538488v1_genomic.fna.gz --refList GCF_025384885.1_ASM2538488v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025384885.1_ASM2538488v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:13,780] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:13,791] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:13,791] [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_003287735.1	s__Photorhabdus bodei	96.4969	1381	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	97.51	96.35	0.89	0.86	10	conclusive
GCF_003343245.1	s__Photorhabdus laumondii	93.6931	1417	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	99.39	97.32	0.96	0.88	22	-
GCF_003545805.1	s__Photorhabdus sp003545805	93.0108	1313	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001083805.1	s__Photorhabdus luminescens	92.3462	1370	1640	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	92.1445	1342	1640	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	91.9817	1301	1640	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	91.9321	1350	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.2863	97.65	96.64	0.91	0.87	12	-
GCF_001684335.1	s__Photorhabdus namnaonensis	91.512	1351	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.2863	N/A	N/A	N/A	N/A	1	-
GCF_011189505.1	s__Photorhabdus tasmaniensis	86.2055	1179	1640	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	85.7497	1166	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	98.62	97.27	0.91	0.86	4	-
GCF_014467235.1	s__Xenorhabdus indica	78.6915	388	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.18	99.18	0.92	0.92	2	-
GCF_002095315.1	s__Pantoea conspicua	77.8257	83	1640	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:13,793] [INFO] GTDB search result was written to GCF_025384885.1_ASM2538488v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:13,794] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:13,797] [INFO] DFAST_QC result json was written to GCF_025384885.1_ASM2538488v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:13,797] [INFO] DFAST_QC completed!
[2024-01-24 12:31:13,797] [INFO] Total running time: 0h1m36s