[2024-01-25 19:53:20,554] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:53:20,556] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:53:20,556] [INFO] DQC Reference Directory: /var/lib/cwl/stgcbb70e86-391e-435d-92ab-54c094f0be17/dqc_reference
[2024-01-25 19:53:21,792] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:53:21,793] [INFO] Task started: Prodigal
[2024-01-25 19:53:21,793] [INFO] Running command: gunzip -c /var/lib/cwl/stg85d01383-24d2-435e-8929-bc33cdd12ef6/GCF_024267675.1_ASM2426767v1_genomic.fna.gz | prodigal -d GCF_024267675.1_ASM2426767v1_genomic.fna/cds.fna -a GCF_024267675.1_ASM2426767v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:53:35,168] [INFO] Task succeeded: Prodigal
[2024-01-25 19:53:35,168] [INFO] Task started: HMMsearch
[2024-01-25 19:53:35,168] [INFO] Running command: hmmsearch --tblout GCF_024267675.1_ASM2426767v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcbb70e86-391e-435d-92ab-54c094f0be17/dqc_reference/reference_markers.hmm GCF_024267675.1_ASM2426767v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:53:35,425] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:53:35,426] [INFO] Found 6/6 markers.
[2024-01-25 19:53:35,468] [INFO] Query marker FASTA was written to GCF_024267675.1_ASM2426767v1_genomic.fna/markers.fasta
[2024-01-25 19:53:35,468] [INFO] Task started: Blastn
[2024-01-25 19:53:35,468] [INFO] Running command: blastn -query GCF_024267675.1_ASM2426767v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcbb70e86-391e-435d-92ab-54c094f0be17/dqc_reference/reference_markers.fasta -out GCF_024267675.1_ASM2426767v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:53:36,119] [INFO] Task succeeded: Blastn
[2024-01-25 19:53:36,121] [INFO] Selected 20 target genomes.
[2024-01-25 19:53:36,121] [INFO] Target genome list was writen to GCF_024267675.1_ASM2426767v1_genomic.fna/target_genomes.txt
[2024-01-25 19:53:36,129] [INFO] Task started: fastANI
[2024-01-25 19:53:36,129] [INFO] Running command: fastANI --query /var/lib/cwl/stg85d01383-24d2-435e-8929-bc33cdd12ef6/GCF_024267675.1_ASM2426767v1_genomic.fna.gz --refList GCF_024267675.1_ASM2426767v1_genomic.fna/target_genomes.txt --output GCF_024267675.1_ASM2426767v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:53:54,044] [INFO] Task succeeded: fastANI
[2024-01-25 19:53:54,044] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcbb70e86-391e-435d-92ab-54c094f0be17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:53:54,045] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcbb70e86-391e-435d-92ab-54c094f0be17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:53:54,057] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:53:54,057] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:53:54,057] [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
Marinobacterium aestuarii	strain=ST58-10	GCA_001651805.1	1821621	1821621	type	True	90.0269	1316	1725	95	below_threshold
Marinobacterium profundum	strain=PAMC 27536	GCA_001528745.1	1714300	1714300	type	True	88.1198	1211	1725	95	below_threshold
Marinobacterium rhizophilum	strain=DSM 18822	GCA_000378045.1	420402	420402	type	True	84.7716	1165	1725	95	below_threshold
Marinobacterium nitratireducens	strain=CGMCC 1.7286	GCA_014645375.1	518897	518897	type	True	79.4124	725	1725	95	below_threshold
Marinobacterium ramblicola	strain=D7	GCA_019084545.1	2849041	2849041	type	True	77.9095	348	1725	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	77.8431	356	1725	95	below_threshold
Marinobacterium lutimaris	strain=DSM 22012	GCA_900108065.1	568106	568106	type	True	77.7373	284	1725	95	below_threshold
Marinobacterium zhoushanense	strain=CGMCC 1.15341	GCA_014641945.1	1679163	1679163	type	True	77.6976	341	1725	95	below_threshold
Marinobacterium georgiense	strain=DSM 11526	GCA_900107855.1	48076	48076	type	True	77.4432	221	1725	95	below_threshold
Marinobacterium litorale	strain=DSM 23545	GCA_000428985.1	404770	404770	type	True	77.4356	206	1725	95	below_threshold
Microbulbifer flavimaris	strain=WRN-8	GCA_001641755.2	1781068	1781068	type	True	76.9395	92	1725	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	76.9305	179	1725	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.7527	184	1725	95	below_threshold
Motiliproteus coralliicola	strain=C34	GCA_003345655.1	2283196	2283196	type	True	76.7305	159	1725	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.7203	173	1725	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	76.602	172	1725	95	below_threshold
Stutzerimonas balearica	strain=DSM 6083	GCA_900103375.1	74829	74829	type	True	76.5523	139	1725	95	below_threshold
Stutzerimonas balearica	strain=DSM6083 (=SP1402)	GCA_000818015.1	74829	74829	type	True	76.5265	141	1725	95	below_threshold
Marinobacter halodurans	strain=YJ-S3-2	GCA_004327985.1	2528979	2528979	type	True	76.4308	151	1725	95	below_threshold
Saccharospirillum salsuginis	strain=KCTC 22169	GCA_014651855.1	418750	418750	type	True	76.3637	128	1725	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:53:54,059] [INFO] DFAST Taxonomy check result was written to GCF_024267675.1_ASM2426767v1_genomic.fna/tc_result.tsv
[2024-01-25 19:53:54,059] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:53:54,059] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:53:54,060] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcbb70e86-391e-435d-92ab-54c094f0be17/dqc_reference/checkm_data
[2024-01-25 19:53:54,060] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:53:54,115] [INFO] Task started: CheckM
[2024-01-25 19:53:54,115] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024267675.1_ASM2426767v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024267675.1_ASM2426767v1_genomic.fna/checkm_input GCF_024267675.1_ASM2426767v1_genomic.fna/checkm_result
[2024-01-25 19:54:34,006] [INFO] Task succeeded: CheckM
[2024-01-25 19:54:34,007] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:54:34,023] [INFO] ===== Completeness check finished =====
[2024-01-25 19:54:34,023] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:54:34,024] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024267675.1_ASM2426767v1_genomic.fna/markers.fasta)
[2024-01-25 19:54:34,024] [INFO] Task started: Blastn
[2024-01-25 19:54:34,024] [INFO] Running command: blastn -query GCF_024267675.1_ASM2426767v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcbb70e86-391e-435d-92ab-54c094f0be17/dqc_reference/reference_markers_gtdb.fasta -out GCF_024267675.1_ASM2426767v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:54:35,062] [INFO] Task succeeded: Blastn
[2024-01-25 19:54:35,065] [INFO] Selected 8 target genomes.
[2024-01-25 19:54:35,065] [INFO] Target genome list was writen to GCF_024267675.1_ASM2426767v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:54:35,074] [INFO] Task started: fastANI
[2024-01-25 19:54:35,074] [INFO] Running command: fastANI --query /var/lib/cwl/stg85d01383-24d2-435e-8929-bc33cdd12ef6/GCF_024267675.1_ASM2426767v1_genomic.fna.gz --refList GCF_024267675.1_ASM2426767v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024267675.1_ASM2426767v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:54:44,022] [INFO] Task succeeded: fastANI
[2024-01-25 19:54:44,028] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:54:44,029] [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_001651805.1	s__Marinobacterium_A aestuarii	90.0225	1316	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001528745.1	s__Marinobacterium_A profundum	88.1328	1210	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378045.1	s__Marinobacterium_A rhizophilum	84.7449	1169	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645375.1	s__Marinobacterium_A nitratireducens	79.4397	721	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373085.1	s__Marinobacterium_A sp013373085	79.4044	688	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019061305.1	s__Marinobacterium sp019061305	77.9677	290	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641945.1	s__Marinobacterium zhoushanense	77.6998	340	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207935.1	s__Pseudomonas_E fluvialis_A	76.8921	144	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:54:44,031] [INFO] GTDB search result was written to GCF_024267675.1_ASM2426767v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:54:44,031] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:54:44,034] [INFO] DFAST_QC result json was written to GCF_024267675.1_ASM2426767v1_genomic.fna/dqc_result.json
[2024-01-25 19:54:44,035] [INFO] DFAST_QC completed!
[2024-01-25 19:54:44,035] [INFO] Total running time: 0h1m23s