[2024-01-24 10:57:07,060] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:07,062] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:07,062] [INFO] DQC Reference Directory: /var/lib/cwl/stg5cc6a028-056c-46d6-8451-c7988a7678e3/dqc_reference
[2024-01-24 10:57:08,295] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:08,296] [INFO] Task started: Prodigal
[2024-01-24 10:57:08,296] [INFO] Running command: gunzip -c /var/lib/cwl/stge390ef23-3582-4e47-a3d4-047093bd5dfd/GCF_030160655.1_ASM3016065v1_genomic.fna.gz | prodigal -d GCF_030160655.1_ASM3016065v1_genomic.fna/cds.fna -a GCF_030160655.1_ASM3016065v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:19,010] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:19,010] [INFO] Task started: HMMsearch
[2024-01-24 10:57:19,011] [INFO] Running command: hmmsearch --tblout GCF_030160655.1_ASM3016065v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5cc6a028-056c-46d6-8451-c7988a7678e3/dqc_reference/reference_markers.hmm GCF_030160655.1_ASM3016065v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:19,310] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:19,312] [INFO] Found 6/6 markers.
[2024-01-24 10:57:19,366] [INFO] Query marker FASTA was written to GCF_030160655.1_ASM3016065v1_genomic.fna/markers.fasta
[2024-01-24 10:57:19,366] [INFO] Task started: Blastn
[2024-01-24 10:57:19,367] [INFO] Running command: blastn -query GCF_030160655.1_ASM3016065v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5cc6a028-056c-46d6-8451-c7988a7678e3/dqc_reference/reference_markers.fasta -out GCF_030160655.1_ASM3016065v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:20,070] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:20,074] [INFO] Selected 29 target genomes.
[2024-01-24 10:57:20,074] [INFO] Target genome list was writen to GCF_030160655.1_ASM3016065v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:20,648] [INFO] Task started: fastANI
[2024-01-24 10:57:20,649] [INFO] Running command: fastANI --query /var/lib/cwl/stge390ef23-3582-4e47-a3d4-047093bd5dfd/GCF_030160655.1_ASM3016065v1_genomic.fna.gz --refList GCF_030160655.1_ASM3016065v1_genomic.fna/target_genomes.txt --output GCF_030160655.1_ASM3016065v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:38,948] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:38,948] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5cc6a028-056c-46d6-8451-c7988a7678e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:38,949] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5cc6a028-056c-46d6-8451-c7988a7678e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:38,969] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:57:38,969] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:57:38,969] [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
Alteromonas naphthalenivorans	strain=SN2	GCA_000213655.1	715451	715451	type	True	78.2158	62	1546	95	below_threshold
Ningiella ruwaisensis	strain=B66	GCA_004798935.1	2364274	2364274	type	True	77.8062	108	1546	95	below_threshold
Alteromonas profundi	strain=345S023	GCA_010500865.1	2696062	2696062	type	True	77.7632	56	1546	95	below_threshold
Aliiglaciecola lipolytica	strain=E3	GCA_000314975.1	477689	477689	type	True	77.5462	58	1546	95	below_threshold
Glaciecola pallidula	strain=ACAM 615	GCA_000315035.1	56807	56807	type	True	77.4666	68	1546	95	below_threshold
Alteromonas lipolytica	strain=JW12	GCA_001758465.1	1856405	1856405	type	True	77.4589	52	1546	95	below_threshold
Glaciecola pallidula	strain=DSM 14239	GCA_000428905.1	56807	56807	type	True	77.4465	67	1546	95	below_threshold
Alteromonas lipolytica	strain=CGMCC 1.15735	GCA_014643555.1	1856405	1856405	type	True	77.415	53	1546	95	below_threshold
Glaciecola punicea	strain=ACAM 611	GCA_000252165.2	56804	56804	type	True	77.3385	60	1546	95	below_threshold
Alteromonas lipotrueae	strain=MD_652	GCA_019249215.1	2803814	2803814	type	True	77.1787	62	1546	95	below_threshold
Alteromonas hispanica	strain=LMG 22958	GCA_010500915.1	315421	315421	type	True	77.094	55	1546	95	below_threshold
Glaciecola nitratireducens	strain=FR1064	GCA_000226565.1	300231	300231	type	True	76.9826	100	1546	95	below_threshold
Paraglaciecola arctica	strain=BSs20135	GCA_000314995.1	1128911	1128911	type	True	76.9352	62	1546	95	below_threshold
Paraglaciecola mesophila	strain=KMM 241	GCA_000315015.1	197222	197222	type	True	76.3275	65	1546	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:38,971] [INFO] DFAST Taxonomy check result was written to GCF_030160655.1_ASM3016065v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:38,972] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:38,972] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:38,972] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5cc6a028-056c-46d6-8451-c7988a7678e3/dqc_reference/checkm_data
[2024-01-24 10:57:38,973] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:39,024] [INFO] Task started: CheckM
[2024-01-24 10:57:39,024] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030160655.1_ASM3016065v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030160655.1_ASM3016065v1_genomic.fna/checkm_input GCF_030160655.1_ASM3016065v1_genomic.fna/checkm_result
[2024-01-24 10:58:15,018] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:15,019] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:15,038] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:15,038] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:15,038] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030160655.1_ASM3016065v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:15,039] [INFO] Task started: Blastn
[2024-01-24 10:58:15,039] [INFO] Running command: blastn -query GCF_030160655.1_ASM3016065v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5cc6a028-056c-46d6-8451-c7988a7678e3/dqc_reference/reference_markers_gtdb.fasta -out GCF_030160655.1_ASM3016065v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:16,224] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:16,228] [INFO] Selected 33 target genomes.
[2024-01-24 10:58:16,228] [INFO] Target genome list was writen to GCF_030160655.1_ASM3016065v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:16,308] [INFO] Task started: fastANI
[2024-01-24 10:58:16,309] [INFO] Running command: fastANI --query /var/lib/cwl/stge390ef23-3582-4e47-a3d4-047093bd5dfd/GCF_030160655.1_ASM3016065v1_genomic.fna.gz --refList GCF_030160655.1_ASM3016065v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030160655.1_ASM3016065v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:38,495] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:38,518] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:58:38,518] [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_000213655.1	s__Alteromonas naphthalenivorans	78.2037	61	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.31	95.95	0.86	0.84	6	-
GCF_000155775.1	s__Glaciecola sp000155775	77.9838	63	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003203515.1	s__Glaciecola sp003203515	77.8146	86	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500865.1	s__Alteromonas profundi	77.7632	56	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538345.1	s__Alteromonas sp006538345	77.5098	59	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015595035.1	s__Glaciecola sp015595035	77.5084	80	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001758465.1	s__Alteromonas lipolytica	77.4589	52	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000428905.1	s__Glaciecola pallidula	77.4465	67	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000252165.1	s__Glaciecola punicea	77.3411	59	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	99.53	99.53	0.94	0.94	2	-
GCF_005117025.1	s__Alteromonas portus	77.2808	64	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018100795.1	s__Alteromonas sp018100795	77.2705	65	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836745.1	s__Glaciecola sp002836745	77.2619	75	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506055.1	s__Alteromonas lipotrueae	77.2593	62	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.66	99.49	0.97	0.95	4	-
GCA_019249245.1	s__Alteromonas lipotrueiana	77.131	62	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500915.1	s__Alteromonas hispanica	77.094	55	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.81	97.72	0.82	0.79	5	-
GCF_000226565.1	s__Glaciecola nitratireducens	76.9826	100	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009906955.1	s__Paraglaciecola mesophila_A	76.6239	58	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002340325.1	s__Glaciecola sp002340325	76.4805	64	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315015.1	s__Paraglaciecola mesophila	76.3275	65	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	98.29	98.05	0.87	0.80	4	-
GCA_002338515.1	s__Glaciecola sp002338515	76.3253	78	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:38,520] [INFO] GTDB search result was written to GCF_030160655.1_ASM3016065v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:38,520] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:38,524] [INFO] DFAST_QC result json was written to GCF_030160655.1_ASM3016065v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:38,524] [INFO] DFAST_QC completed!
[2024-01-24 10:58:38,524] [INFO] Total running time: 0h1m31s