[2024-01-24 14:19:17,216] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:17,219] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:17,220] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0713403-6c71-46f2-9bf8-3f0b75ff1fb3/dqc_reference
[2024-01-24 14:19:21,127] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:21,129] [INFO] Task started: Prodigal
[2024-01-24 14:19:21,130] [INFO] Running command: gunzip -c /var/lib/cwl/stg64a31dae-ae8a-4019-b4f9-ecc515f9547d/GCF_008365385.1_ASM836538v1_genomic.fna.gz | prodigal -d GCF_008365385.1_ASM836538v1_genomic.fna/cds.fna -a GCF_008365385.1_ASM836538v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:34,297] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:34,297] [INFO] Task started: HMMsearch
[2024-01-24 14:19:34,297] [INFO] Running command: hmmsearch --tblout GCF_008365385.1_ASM836538v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0713403-6c71-46f2-9bf8-3f0b75ff1fb3/dqc_reference/reference_markers.hmm GCF_008365385.1_ASM836538v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:34,618] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:34,620] [INFO] Found 6/6 markers.
[2024-01-24 14:19:34,663] [INFO] Query marker FASTA was written to GCF_008365385.1_ASM836538v1_genomic.fna/markers.fasta
[2024-01-24 14:19:34,664] [INFO] Task started: Blastn
[2024-01-24 14:19:34,664] [INFO] Running command: blastn -query GCF_008365385.1_ASM836538v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0713403-6c71-46f2-9bf8-3f0b75ff1fb3/dqc_reference/reference_markers.fasta -out GCF_008365385.1_ASM836538v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:36,070] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:36,073] [INFO] Selected 22 target genomes.
[2024-01-24 14:19:36,074] [INFO] Target genome list was writen to GCF_008365385.1_ASM836538v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:36,085] [INFO] Task started: fastANI
[2024-01-24 14:19:36,086] [INFO] Running command: fastANI --query /var/lib/cwl/stg64a31dae-ae8a-4019-b4f9-ecc515f9547d/GCF_008365385.1_ASM836538v1_genomic.fna.gz --refList GCF_008365385.1_ASM836538v1_genomic.fna/target_genomes.txt --output GCF_008365385.1_ASM836538v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:54,745] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:54,746] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0713403-6c71-46f2-9bf8-3f0b75ff1fb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:54,747] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0713403-6c71-46f2-9bf8-3f0b75ff1fb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:54,850] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:19:54,850] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:19:54,850] [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	79.611	519	1360	95	below_threshold
Halopseudomonas salina	strain=CGMCC 1.12482	GCA_014637955.1	1323744	1323744	type	True	79.5961	522	1360	95	below_threshold
Halopseudomonas litoralis	strain=2SM5	GCA_900105005.1	797277	797277	type	True	79.2365	397	1360	95	below_threshold
Halopseudomonas bauzanensis	strain=DSM 22558	GCA_900111225.1	653930	653930	type	True	79.0581	408	1360	95	below_threshold
Halopseudomonas bauzanensis	strain=CGMCC 1.9095	GCA_900114735.1	653930	653930	type	True	79.0391	410	1360	95	below_threshold
Pseudomonas profundi	strain=M5	GCA_008638305.1	1981513	1981513	type	True	78.9826	424	1360	95	below_threshold
Pseudomonas saliphila	strain=16W4-4-3	GCA_008638345.1	2586906	2586906	type	True	78.9202	470	1360	95	below_threshold
Halopseudomonas pachastrellae	strain=CCUG 46540	GCA_001989375.1	254161	254161	type	True	78.8706	438	1360	95	below_threshold
Halopseudomonas pachastrellae	strain=JCM 12285	GCA_900114765.1	254161	254161	type	True	78.8466	459	1360	95	below_threshold
Halopseudomonas aestusnigri	strain=VGXO14	GCA_002197985.1	857252	857252	type	True	78.8103	440	1360	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	77.8399	296	1360	95	below_threshold
Pseudomonas chlororaphis subsp. chlororaphis	strain=ATCC 9446	GCA_002095925.1	333	587753	type	True	77.4898	243	1360	95	below_threshold
Pseudomonas chlororaphis subsp. chlororaphis	strain=DSM 50083	GCA_007858335.1	333	587753	type	True	77.4844	245	1360	95	below_threshold
Pseudomonas chlororaphis subsp. chlororaphis		GCA_900625015.1	333	587753	type	True	77.4794	245	1360	95	below_threshold
Pseudomonas chlororaphis subsp. chlororaphis	strain=LMG 5004	GCA_001269625.1	333	587753	type	True	77.4572	248	1360	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	77.4517	263	1360	95	below_threshold
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	77.3929	258	1360	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=CFBP 1702	GCA_000935765.1	251701	251701	pathovar	True	77.3885	214	1360	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_900114065.1	1211807	1211807	type	True	77.2962	268	1360	95	below_threshold
Pseudomonas syringae	strain=ICMP 9617	GCA_000658965.1	317	317	pathovar	True	77.2578	223	1360	95	below_threshold
Pseudomonas syringae	strain=NCPPB 3739	GCA_000233835.2	317	317	pathovar	True	77.2371	201	1360	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	77.2177	259	1360	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:54,853] [INFO] DFAST Taxonomy check result was written to GCF_008365385.1_ASM836538v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:54,853] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:54,854] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:54,854] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0713403-6c71-46f2-9bf8-3f0b75ff1fb3/dqc_reference/checkm_data
[2024-01-24 14:19:54,863] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:54,910] [INFO] Task started: CheckM
[2024-01-24 14:19:54,910] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008365385.1_ASM836538v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008365385.1_ASM836538v1_genomic.fna/checkm_input GCF_008365385.1_ASM836538v1_genomic.fna/checkm_result
[2024-01-24 14:20:39,521] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:39,549] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:39,571] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:39,572] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:39,572] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008365385.1_ASM836538v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:39,572] [INFO] Task started: Blastn
[2024-01-24 14:20:39,573] [INFO] Running command: blastn -query GCF_008365385.1_ASM836538v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0713403-6c71-46f2-9bf8-3f0b75ff1fb3/dqc_reference/reference_markers_gtdb.fasta -out GCF_008365385.1_ASM836538v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:41,223] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:41,227] [INFO] Selected 10 target genomes.
[2024-01-24 14:20:41,228] [INFO] Target genome list was writen to GCF_008365385.1_ASM836538v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:41,237] [INFO] Task started: fastANI
[2024-01-24 14:20:41,237] [INFO] Running command: fastANI --query /var/lib/cwl/stg64a31dae-ae8a-4019-b4f9-ecc515f9547d/GCF_008365385.1_ASM836538v1_genomic.fna.gz --refList GCF_008365385.1_ASM836538v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008365385.1_ASM836538v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:50,886] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:50,937] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:50,937] [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_008365385.1	s__Pseudomonas_D laoshanensis	100.0	1358	1360	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	96.00	95.95	0.96	0.95	3	conclusive
GCF_009497895.1	s__Pseudomonas_D pelagia_A	94.5153	1242	1360	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_000410875.1	s__Pseudomonas_D pelagia	83.3811	914	1360	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_002840055.1	s__Pseudomonas_D sp002840055	79.7448	398	1360	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	79.6288	516	1360	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_016763285.1	s__Pseudomonas_D sp016763285	79.1107	444	1360	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	79.0554	477	1360	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_000939975.1	s__Pseudomonas_D saudimassiliensis	79.0429	386	1360	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014219065.1	s__Pseudomonas_D xiamenensis	78.9753	445	1360	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_019116555.1	s__Pseudomonas_D excrementavium	78.9034	318	1360	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:50,939] [INFO] GTDB search result was written to GCF_008365385.1_ASM836538v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:50,940] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:50,947] [INFO] DFAST_QC result json was written to GCF_008365385.1_ASM836538v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:50,948] [INFO] DFAST_QC completed!
[2024-01-24 14:20:50,948] [INFO] Total running time: 0h1m34s