[2024-01-25 18:45:05,504] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:45:05,505] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:45:05,505] [INFO] DQC Reference Directory: /var/lib/cwl/stg6bea9bb8-f56e-4fdc-aea2-73b11a07aaa6/dqc_reference
[2024-01-25 18:45:06,667] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:45:06,669] [INFO] Task started: Prodigal
[2024-01-25 18:45:06,669] [INFO] Running command: gunzip -c /var/lib/cwl/stg939be72f-9902-4877-853a-cb03bec241fd/GCF_000410875.1_KCCM90073_genomic.fna.gz | prodigal -d GCF_000410875.1_KCCM90073_genomic.fna/cds.fna -a GCF_000410875.1_KCCM90073_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:45:19,016] [INFO] Task succeeded: Prodigal
[2024-01-25 18:45:19,016] [INFO] Task started: HMMsearch
[2024-01-25 18:45:19,017] [INFO] Running command: hmmsearch --tblout GCF_000410875.1_KCCM90073_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6bea9bb8-f56e-4fdc-aea2-73b11a07aaa6/dqc_reference/reference_markers.hmm GCF_000410875.1_KCCM90073_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:45:19,285] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:45:19,286] [INFO] Found 6/6 markers.
[2024-01-25 18:45:19,333] [INFO] Query marker FASTA was written to GCF_000410875.1_KCCM90073_genomic.fna/markers.fasta
[2024-01-25 18:45:19,333] [INFO] Task started: Blastn
[2024-01-25 18:45:19,333] [INFO] Running command: blastn -query GCF_000410875.1_KCCM90073_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bea9bb8-f56e-4fdc-aea2-73b11a07aaa6/dqc_reference/reference_markers.fasta -out GCF_000410875.1_KCCM90073_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:20,174] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:20,179] [INFO] Selected 21 target genomes.
[2024-01-25 18:45:20,180] [INFO] Target genome list was writen to GCF_000410875.1_KCCM90073_genomic.fna/target_genomes.txt
[2024-01-25 18:45:20,205] [INFO] Task started: fastANI
[2024-01-25 18:45:20,205] [INFO] Running command: fastANI --query /var/lib/cwl/stg939be72f-9902-4877-853a-cb03bec241fd/GCF_000410875.1_KCCM90073_genomic.fna.gz --refList GCF_000410875.1_KCCM90073_genomic.fna/target_genomes.txt --output GCF_000410875.1_KCCM90073_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:45:36,709] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:36,709] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6bea9bb8-f56e-4fdc-aea2-73b11a07aaa6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:45:36,709] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6bea9bb8-f56e-4fdc-aea2-73b11a07aaa6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:45:36,722] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:45:36,722] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:45:36,722] [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
Halopseudomonas salina	strain=XCD-X85	GCA_008641105.1	1323744	1323744	type	True	79.6314	510	1508	95	below_threshold
Halopseudomonas salina	strain=CGMCC 1.12482	GCA_014637955.1	1323744	1323744	type	True	79.5426	517	1508	95	below_threshold
Halopseudomonas litoralis	strain=2SM5	GCA_900105005.1	797277	797277	type	True	79.3878	401	1508	95	below_threshold
Pseudomonas profundi	strain=M5	GCA_008638305.1	1981513	1981513	type	True	78.7489	391	1508	95	below_threshold
Halopseudomonas bauzanensis	strain=DSM 22558	GCA_900111225.1	653930	653930	type	True	78.6429	390	1508	95	below_threshold
Pseudomonas saliphila	strain=16W4-4-3	GCA_008638345.1	2586906	2586906	type	True	78.6097	415	1508	95	below_threshold
Halopseudomonas bauzanensis	strain=CGMCC 1.9095	GCA_900114735.1	653930	653930	type	True	78.5782	393	1508	95	below_threshold
Halopseudomonas oceani	strain=DSM 100277	GCA_002903165.1	1708783	1708783	type	True	78.5698	389	1508	95	below_threshold
Halopseudomonas pachastrellae	strain=CCUG 46540	GCA_001989375.1	254161	254161	type	True	78.5027	438	1508	95	below_threshold
Halopseudomonas pachastrellae	strain=JCM 12285	GCA_900114765.1	254161	254161	type	True	78.4748	440	1508	95	below_threshold
Halopseudomonas aestusnigri	strain=VGXO14	GCA_002197985.1	857252	857252	type	True	78.4521	414	1508	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	77.8719	225	1508	95	below_threshold
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	77.6784	243	1508	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_900114065.1	1211807	1211807	type	True	77.656	246	1508	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	77.6404	242	1508	95	below_threshold
Pseudomonas cavernicola	strain=K1S02-6	GCA_003596405.1	2320866	2320866	type	True	77.5023	223	1508	95	below_threshold
Pseudomonas massiliensis	strain=CB1	GCA_000826105.1	522492	522492	type	True	77.0908	155	1508	95	below_threshold
Marinobacter flavimaris	strain=LMG 23834	GCA_002933295.1	262076	262076	type	True	76.8922	79	1508	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	76.5472	95	1508	95	below_threshold
Marinobacter subterrani	strain=JG233	GCA_001045555.1	1658765	1658765	type	True	76.306	86	1508	95	below_threshold
Marinobacter caseinilyticus	strain=M3-13	GCA_011074955.1	2692195	2692195	type	True	76.1042	54	1508	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:45:36,726] [INFO] DFAST Taxonomy check result was written to GCF_000410875.1_KCCM90073_genomic.fna/tc_result.tsv
[2024-01-25 18:45:36,730] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:45:36,730] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:45:36,730] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6bea9bb8-f56e-4fdc-aea2-73b11a07aaa6/dqc_reference/checkm_data
[2024-01-25 18:45:36,731] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:45:36,777] [INFO] Task started: CheckM
[2024-01-25 18:45:36,778] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000410875.1_KCCM90073_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000410875.1_KCCM90073_genomic.fna/checkm_input GCF_000410875.1_KCCM90073_genomic.fna/checkm_result
[2024-01-25 18:46:14,607] [INFO] Task succeeded: CheckM
[2024-01-25 18:46:14,609] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:46:14,626] [INFO] ===== Completeness check finished =====
[2024-01-25 18:46:14,626] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:46:14,629] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000410875.1_KCCM90073_genomic.fna/markers.fasta)
[2024-01-25 18:46:14,629] [INFO] Task started: Blastn
[2024-01-25 18:46:14,629] [INFO] Running command: blastn -query GCF_000410875.1_KCCM90073_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bea9bb8-f56e-4fdc-aea2-73b11a07aaa6/dqc_reference/reference_markers_gtdb.fasta -out GCF_000410875.1_KCCM90073_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:16,168] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:16,172] [INFO] Selected 11 target genomes.
[2024-01-25 18:46:16,172] [INFO] Target genome list was writen to GCF_000410875.1_KCCM90073_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:46:16,184] [INFO] Task started: fastANI
[2024-01-25 18:46:16,185] [INFO] Running command: fastANI --query /var/lib/cwl/stg939be72f-9902-4877-853a-cb03bec241fd/GCF_000410875.1_KCCM90073_genomic.fna.gz --refList GCF_000410875.1_KCCM90073_genomic.fna/target_genomes_gtdb.txt --output GCF_000410875.1_KCCM90073_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:46:24,973] [INFO] Task succeeded: fastANI
[2024-01-25 18:46:24,980] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:46:24,980] [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_000410875.1	s__Pseudomonas_D pelagia	100.0	1506	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008365385.1	s__Pseudomonas_D laoshanensis	83.488	906	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	96.00	95.95	0.96	0.95	3	-
GCF_009497895.1	s__Pseudomonas_D pelagia_A	83.2098	965	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008641105.1	s__Pseudomonas_D salina	79.6337	508	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	100.00	100.00	0.99	0.99	2	-
GCA_002840055.1	s__Pseudomonas_D sp002840055	79.5112	407	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016763285.1	s__Pseudomonas_D sp016763285	79.0317	407	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105255.1	s__Pseudomonas_D sabulinigri	78.9024	454	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003797905.1	s__Pseudomonas_D sp002683975	78.8558	383	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	98.94	98.05	0.94	0.90	5	-
GCF_003444685.1	s__Pseudomonas_D gallaeciensis	78.4861	444	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.87	97.82	0.88	0.85	8	-
GCA_019116555.1	s__Pseudomonas_D excrementavium	78.4445	306	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826105.1	s__Pseudomonas_E massiliensis	77.062	155	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:46:24,982] [INFO] GTDB search result was written to GCF_000410875.1_KCCM90073_genomic.fna/result_gtdb.tsv
[2024-01-25 18:46:24,983] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:46:24,987] [INFO] DFAST_QC result json was written to GCF_000410875.1_KCCM90073_genomic.fna/dqc_result.json
[2024-01-25 18:46:24,987] [INFO] DFAST_QC completed!
[2024-01-25 18:46:24,987] [INFO] Total running time: 0h1m19s