[2024-01-24 13:18:44,059] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:44,061] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:44,061] [INFO] DQC Reference Directory: /var/lib/cwl/stg85fa198f-91b1-48c3-a2e8-637b1b2c0952/dqc_reference
[2024-01-24 13:18:45,316] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:45,317] [INFO] Task started: Prodigal
[2024-01-24 13:18:45,317] [INFO] Running command: gunzip -c /var/lib/cwl/stg51504d81-a3fe-4124-a77d-77a430e9eba4/GCF_003344045.1_ASM334404v1_genomic.fna.gz | prodigal -d GCF_003344045.1_ASM334404v1_genomic.fna/cds.fna -a GCF_003344045.1_ASM334404v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:57,144] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:57,144] [INFO] Task started: HMMsearch
[2024-01-24 13:18:57,144] [INFO] Running command: hmmsearch --tblout GCF_003344045.1_ASM334404v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85fa198f-91b1-48c3-a2e8-637b1b2c0952/dqc_reference/reference_markers.hmm GCF_003344045.1_ASM334404v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:57,434] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:57,436] [INFO] Found 6/6 markers.
[2024-01-24 13:18:57,467] [INFO] Query marker FASTA was written to GCF_003344045.1_ASM334404v1_genomic.fna/markers.fasta
[2024-01-24 13:18:57,468] [INFO] Task started: Blastn
[2024-01-24 13:18:57,468] [INFO] Running command: blastn -query GCF_003344045.1_ASM334404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85fa198f-91b1-48c3-a2e8-637b1b2c0952/dqc_reference/reference_markers.fasta -out GCF_003344045.1_ASM334404v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:58,311] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:58,314] [INFO] Selected 10 target genomes.
[2024-01-24 13:18:58,314] [INFO] Target genome list was writen to GCF_003344045.1_ASM334404v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:58,319] [INFO] Task started: fastANI
[2024-01-24 13:18:58,320] [INFO] Running command: fastANI --query /var/lib/cwl/stg51504d81-a3fe-4124-a77d-77a430e9eba4/GCF_003344045.1_ASM334404v1_genomic.fna.gz --refList GCF_003344045.1_ASM334404v1_genomic.fna/target_genomes.txt --output GCF_003344045.1_ASM334404v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:07,053] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:07,053] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85fa198f-91b1-48c3-a2e8-637b1b2c0952/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:07,054] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85fa198f-91b1-48c3-a2e8-637b1b2c0952/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:07,063] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:19:07,064] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:07,064] [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
Marinobacter vulgaris	strain=F01	GCA_003344045.1	1928331	1928331	type	True	100.0	1251	1252	95	conclusive
Marinobacter vulgaris	strain=F01	GCA_007559285.1	1928331	1928331	type	True	99.9989	1250	1252	95	conclusive
Marinobacter orientalis	strain=W62	GCA_004792665.1	1928859	1928859	type	True	86.4333	1004	1252	95	below_threshold
Marinobacter orientalis	strain=W62	GCA_012956055.1	1928859	1928859	type	True	86.4204	1032	1252	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	83.2864	919	1252	95	below_threshold
Marinobacter algicola	strain=DG893	GCA_000170835.1	236100	236100	type	True	81.455	700	1252	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	79.6537	542	1252	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	79.2955	534	1252	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	79.0206	468	1252	95	below_threshold
Marinobacter koreensis	strain=DSM 17924	GCA_023156285.1	335974	335974	type	True	78.9153	433	1252	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:07,065] [INFO] DFAST Taxonomy check result was written to GCF_003344045.1_ASM334404v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:07,066] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:07,066] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:07,067] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85fa198f-91b1-48c3-a2e8-637b1b2c0952/dqc_reference/checkm_data
[2024-01-24 13:19:07,068] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:07,107] [INFO] Task started: CheckM
[2024-01-24 13:19:07,107] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003344045.1_ASM334404v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003344045.1_ASM334404v1_genomic.fna/checkm_input GCF_003344045.1_ASM334404v1_genomic.fna/checkm_result
[2024-01-24 13:19:44,047] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:44,048] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:44,082] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:44,082] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:44,082] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003344045.1_ASM334404v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:44,083] [INFO] Task started: Blastn
[2024-01-24 13:19:44,083] [INFO] Running command: blastn -query GCF_003344045.1_ASM334404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85fa198f-91b1-48c3-a2e8-637b1b2c0952/dqc_reference/reference_markers_gtdb.fasta -out GCF_003344045.1_ASM334404v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:45,452] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:45,457] [INFO] Selected 7 target genomes.
[2024-01-24 13:19:45,457] [INFO] Target genome list was writen to GCF_003344045.1_ASM334404v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:45,466] [INFO] Task started: fastANI
[2024-01-24 13:19:45,467] [INFO] Running command: fastANI --query /var/lib/cwl/stg51504d81-a3fe-4124-a77d-77a430e9eba4/GCF_003344045.1_ASM334404v1_genomic.fna.gz --refList GCF_003344045.1_ASM334404v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003344045.1_ASM334404v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:52,394] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:52,401] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:52,401] [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_003344045.1	s__Marinobacter vulgaris	100.0	1251	1252	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_004792665.1	s__Marinobacter orientalis	86.4333	1004	1252	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005298175.1	s__Marinobacter sp005298175	84.5274	998	1252	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008795955.1	s__Marinobacter sp008795955	83.2864	919	1252	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000686085.1	s__Marinobacter sp000686085	83.0261	923	1252	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000831005.1	s__Marinobacter salarius	81.5783	743	1252	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.84	96.73	0.88	0.79	21	-
GCF_000170835.1	s__Marinobacter algicola	81.4585	700	1252	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:52,403] [INFO] GTDB search result was written to GCF_003344045.1_ASM334404v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:52,404] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:52,407] [INFO] DFAST_QC result json was written to GCF_003344045.1_ASM334404v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:52,407] [INFO] DFAST_QC completed!
[2024-01-24 13:19:52,407] [INFO] Total running time: 0h1m8s