[2024-01-24 15:10:48,137] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:48,139] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:48,139] [INFO] DQC Reference Directory: /var/lib/cwl/stg77da1fb9-4f26-4575-82bd-7a53730750ee/dqc_reference
[2024-01-24 15:10:51,748] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:51,749] [INFO] Task started: Prodigal
[2024-01-24 15:10:51,750] [INFO] Running command: gunzip -c /var/lib/cwl/stgcf5fdb5e-4178-4ad6-b4b6-3c135f1c2c5d/GCF_003386665.1_ASM338666v1_genomic.fna.gz | prodigal -d GCF_003386665.1_ASM338666v1_genomic.fna/cds.fna -a GCF_003386665.1_ASM338666v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:04,694] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:04,694] [INFO] Task started: HMMsearch
[2024-01-24 15:11:04,694] [INFO] Running command: hmmsearch --tblout GCF_003386665.1_ASM338666v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77da1fb9-4f26-4575-82bd-7a53730750ee/dqc_reference/reference_markers.hmm GCF_003386665.1_ASM338666v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:05,022] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:05,024] [INFO] Found 6/6 markers.
[2024-01-24 15:11:05,073] [INFO] Query marker FASTA was written to GCF_003386665.1_ASM338666v1_genomic.fna/markers.fasta
[2024-01-24 15:11:05,074] [INFO] Task started: Blastn
[2024-01-24 15:11:05,074] [INFO] Running command: blastn -query GCF_003386665.1_ASM338666v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77da1fb9-4f26-4575-82bd-7a53730750ee/dqc_reference/reference_markers.fasta -out GCF_003386665.1_ASM338666v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:05,860] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:05,864] [INFO] Selected 14 target genomes.
[2024-01-24 15:11:05,865] [INFO] Target genome list was writen to GCF_003386665.1_ASM338666v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:05,876] [INFO] Task started: fastANI
[2024-01-24 15:11:05,876] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf5fdb5e-4178-4ad6-b4b6-3c135f1c2c5d/GCF_003386665.1_ASM338666v1_genomic.fna.gz --refList GCF_003386665.1_ASM338666v1_genomic.fna/target_genomes.txt --output GCF_003386665.1_ASM338666v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:19,487] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:19,487] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77da1fb9-4f26-4575-82bd-7a53730750ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:19,488] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77da1fb9-4f26-4575-82bd-7a53730750ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:19,498] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:19,498] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:19,498] [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
Xenorhabdus cabanillasii	strain=DSM 17905	GCA_003386665.1	351673	351673	type	True	100.0	1444	1445	95	conclusive
Xenorhabdus budapestensis	strain=DSM 16342	GCA_002632465.1	290110	290110	type	True	93.3839	1129	1445	95	below_threshold
Xenorhabdus indica	strain=DSM 17382	GCA_014467235.1	333964	333964	type	True	92.6265	1134	1445	95	below_threshold
Xenorhabdus innexi	strain=DSM 16336	GCA_002632485.1	290109	290109	type	True	84.0068	949	1445	95	below_threshold
Xenorhabdus stockiae	strain=DSM 17904	GCA_002632825.1	351614	351614	type	True	83.5591	973	1445	95	below_threshold
Xenorhabdus bovienii	strain=T228	GCA_024721015.1	40576	40576	type	True	81.9515	772	1445	95	below_threshold
Xenorhabdus lircayensis	strain=VLS	GCA_016306625.1	2763499	2763499	type	True	81.9414	815	1445	95	below_threshold
Xenorhabdus eapokensis	strain=DL20	GCA_001908105.1	1873482	1873482	type	True	81.4751	752	1445	95	below_threshold
Xenorhabdus hominickii	strain=DSM 17903	GCA_002632725.1	351679	351679	type	True	81.45	828	1445	95	below_threshold
Pectobacterium quasiaquaticum	strain=A477-S1-J17	GCA_014946775.2	2774015	2774015	type	True	79.5265	124	1445	95	below_threshold
Hafnia paralvei	strain=ATCC 29927	GCA_023698525.1	546367	546367	type	True	79.0917	123	1445	95	below_threshold
Photorhabdus temperata	strain=DSM 14550	GCA_025384845.1	574560	574560	type	True	78.8721	399	1445	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:19,500] [INFO] DFAST Taxonomy check result was written to GCF_003386665.1_ASM338666v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:19,501] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:19,501] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:19,501] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77da1fb9-4f26-4575-82bd-7a53730750ee/dqc_reference/checkm_data
[2024-01-24 15:11:19,502] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:19,562] [INFO] Task started: CheckM
[2024-01-24 15:11:19,562] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003386665.1_ASM338666v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003386665.1_ASM338666v1_genomic.fna/checkm_input GCF_003386665.1_ASM338666v1_genomic.fna/checkm_result
[2024-01-24 15:12:05,140] [INFO] Task succeeded: CheckM
[2024-01-24 15:12:05,141] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:12:05,171] [INFO] ===== Completeness check finished =====
[2024-01-24 15:12:05,172] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:12:05,172] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003386665.1_ASM338666v1_genomic.fna/markers.fasta)
[2024-01-24 15:12:05,173] [INFO] Task started: Blastn
[2024-01-24 15:12:05,173] [INFO] Running command: blastn -query GCF_003386665.1_ASM338666v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77da1fb9-4f26-4575-82bd-7a53730750ee/dqc_reference/reference_markers_gtdb.fasta -out GCF_003386665.1_ASM338666v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:12:06,236] [INFO] Task succeeded: Blastn
[2024-01-24 15:12:06,242] [INFO] Selected 10 target genomes.
[2024-01-24 15:12:06,242] [INFO] Target genome list was writen to GCF_003386665.1_ASM338666v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:12:06,252] [INFO] Task started: fastANI
[2024-01-24 15:12:06,252] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf5fdb5e-4178-4ad6-b4b6-3c135f1c2c5d/GCF_003386665.1_ASM338666v1_genomic.fna.gz --refList GCF_003386665.1_ASM338666v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003386665.1_ASM338666v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:17,916] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:17,931] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:17,931] [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_003386665.1	s__Xenorhabdus cabanillasii	100.0	1444	1445	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	98.80	98.76	0.86	0.85	3	conclusive
GCF_002632465.1	s__Xenorhabdus budapestensis	93.3652	1130	1445	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	98.99	98.99	0.92	0.92	2	-
GCF_014467235.1	s__Xenorhabdus indica	92.658	1133	1445	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.18	99.18	0.92	0.92	2	-
GCF_002632485.1	s__Xenorhabdus innexi	84.0268	949	1445	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.93	99.93	0.99	0.99	2	-
GCF_002632825.1	s__Xenorhabdus stockiae	83.5769	971	1445	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	96.93	95.64	0.86	0.83	3	-
GCF_000027225.1	s__Xenorhabdus bovienii_C	82.3581	802	1445	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	97.07	95.57	0.88	0.81	4	-
GCF_000252955.1	s__Xenorhabdus nematophila	82.3109	782	1445	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.26	98.94	0.93	0.90	7	-
GCF_900113945.1	s__Xenorhabdus mauleonii	81.6301	752	1445	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001908105.1	s__Xenorhabdus eapokensis	81.4497	754	1445	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002632725.1	s__Xenorhabdus hominickii	81.4462	827	1445	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.90	99.90	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:17,933] [INFO] GTDB search result was written to GCF_003386665.1_ASM338666v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:17,934] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:17,939] [INFO] DFAST_QC result json was written to GCF_003386665.1_ASM338666v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:17,939] [INFO] DFAST_QC completed!
[2024-01-24 15:12:17,939] [INFO] Total running time: 0h1m30s