[2024-01-24 14:54:49,660] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:54:49,662] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:54:49,662] [INFO] DQC Reference Directory: /var/lib/cwl/stg8fb7bb66-7415-4a6d-af8d-24401d4276e2/dqc_reference
[2024-01-24 14:54:50,885] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:54:50,886] [INFO] Task started: Prodigal
[2024-01-24 14:54:50,886] [INFO] Running command: gunzip -c /var/lib/cwl/stgd0724869-d285-46de-a392-bfbf6b1c4e3f/GCF_003258515.1_ASM325851v1_genomic.fna.gz | prodigal -d GCF_003258515.1_ASM325851v1_genomic.fna/cds.fna -a GCF_003258515.1_ASM325851v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:04,954] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:04,955] [INFO] Task started: HMMsearch
[2024-01-24 14:55:04,955] [INFO] Running command: hmmsearch --tblout GCF_003258515.1_ASM325851v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8fb7bb66-7415-4a6d-af8d-24401d4276e2/dqc_reference/reference_markers.hmm GCF_003258515.1_ASM325851v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:05,249] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:05,250] [INFO] Found 6/6 markers.
[2024-01-24 14:55:05,292] [INFO] Query marker FASTA was written to GCF_003258515.1_ASM325851v1_genomic.fna/markers.fasta
[2024-01-24 14:55:05,292] [INFO] Task started: Blastn
[2024-01-24 14:55:05,292] [INFO] Running command: blastn -query GCF_003258515.1_ASM325851v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fb7bb66-7415-4a6d-af8d-24401d4276e2/dqc_reference/reference_markers.fasta -out GCF_003258515.1_ASM325851v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:06,245] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:06,248] [INFO] Selected 14 target genomes.
[2024-01-24 14:55:06,249] [INFO] Target genome list was writen to GCF_003258515.1_ASM325851v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:06,262] [INFO] Task started: fastANI
[2024-01-24 14:55:06,262] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0724869-d285-46de-a392-bfbf6b1c4e3f/GCF_003258515.1_ASM325851v1_genomic.fna.gz --refList GCF_003258515.1_ASM325851v1_genomic.fna/target_genomes.txt --output GCF_003258515.1_ASM325851v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:18,135] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:18,136] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8fb7bb66-7415-4a6d-af8d-24401d4276e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:18,136] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8fb7bb66-7415-4a6d-af8d-24401d4276e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:18,158] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:18,158] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:18,159] [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 bohaiensis	strain=T17	GCA_003258515.1	2201898	2201898	type	True	100.0	1579	1580	95	conclusive
Marinobacter halodurans	strain=YJ-S3-2	GCA_004327985.1	2528979	2528979	type	True	82.2336	984	1580	95	below_threshold
Marinobacter mangrovi	strain=CHFG3-1-5	GCA_016798325.1	2803918	2803918	type	True	82.2235	1048	1580	95	below_threshold
Marinobacter nanhaiticus	strain=D15-8W	GCA_000364845.1	1305740	1305740	type	True	80.1058	846	1580	95	below_threshold
Marinobacter fonticola	strain=CS412	GCA_008122265.1	2603215	2603215	type	True	79.7317	658	1580	95	below_threshold
Marinobacter gudaonensis	strain=CGMCC 1.6294	GCA_900115175.1	375760	375760	type	True	79.1869	472	1580	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	79.1671	479	1580	95	below_threshold
Marinobacter profundi	strain=PWS21	GCA_002744715.1	2666256	2666256	type	True	78.7781	452	1580	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	78.6499	420	1580	95	below_threshold
Tamilnaduibacter salinus	strain=Mi-7	GCA_002287355.1	1484056	1484056	type	True	78.2544	371	1580	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	77.5431	269	1580	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	77.2432	343	1580	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	77.1682	258	1580	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	76.9974	204	1580	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:18,161] [INFO] DFAST Taxonomy check result was written to GCF_003258515.1_ASM325851v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:18,161] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:18,162] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:18,162] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8fb7bb66-7415-4a6d-af8d-24401d4276e2/dqc_reference/checkm_data
[2024-01-24 14:55:18,164] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:18,210] [INFO] Task started: CheckM
[2024-01-24 14:55:18,211] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003258515.1_ASM325851v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003258515.1_ASM325851v1_genomic.fna/checkm_input GCF_003258515.1_ASM325851v1_genomic.fna/checkm_result
[2024-01-24 14:56:01,011] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:01,012] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:01,029] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:01,029] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:01,029] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003258515.1_ASM325851v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:01,030] [INFO] Task started: Blastn
[2024-01-24 14:56:01,030] [INFO] Running command: blastn -query GCF_003258515.1_ASM325851v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fb7bb66-7415-4a6d-af8d-24401d4276e2/dqc_reference/reference_markers_gtdb.fasta -out GCF_003258515.1_ASM325851v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:02,732] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:02,737] [INFO] Selected 10 target genomes.
[2024-01-24 14:56:02,738] [INFO] Target genome list was writen to GCF_003258515.1_ASM325851v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:02,747] [INFO] Task started: fastANI
[2024-01-24 14:56:02,747] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0724869-d285-46de-a392-bfbf6b1c4e3f/GCF_003258515.1_ASM325851v1_genomic.fna.gz --refList GCF_003258515.1_ASM325851v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003258515.1_ASM325851v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:12,003] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:12,012] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:12,012] [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_003258515.1	s__Marinobacter_A bohaiensis	100.0	1579	1580	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	98.52	98.52	0.96	0.96	2	conclusive
GCF_004327985.1	s__Marinobacter_A halodurans	82.2346	985	1580	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003789045.1	s__Marinobacter_A sp003789045	82.2024	1007	1580	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	97.70	97.70	0.91	0.91	2	-
GCF_000364845.1	s__Marinobacter_A nanhaiticus	80.0991	847	1580	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008122265.1	s__Marinobacter_A fonticola	79.7415	656	1580	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115175.1	s__Marinobacter gudaonensis	79.1831	473	1580	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623515.1	s__Marinobacter sp018623515	78.9709	398	1580	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001981305.1	s__Marinobacter lutaoensis	78.9606	549	1580	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.21	99.12	0.92	0.92	6	-
GCF_002744715.1	s__Marinobacter profundi	78.7876	451	1580	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.28	99.28	0.94	0.94	2	-
GCA_014762755.1	s__Marinobacter sp014762755	78.489	364	1580	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 14:56:12,013] [INFO] GTDB search result was written to GCF_003258515.1_ASM325851v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:12,014] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:12,017] [INFO] DFAST_QC result json was written to GCF_003258515.1_ASM325851v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:12,017] [INFO] DFAST_QC completed!
[2024-01-24 14:56:12,017] [INFO] Total running time: 0h1m22s