[2024-01-24 11:34:41,452] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:41,454] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:41,454] [INFO] DQC Reference Directory: /var/lib/cwl/stg92e4709e-3474-456b-b9e3-0d881077583c/dqc_reference
[2024-01-24 11:34:42,853] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:42,853] [INFO] Task started: Prodigal
[2024-01-24 11:34:42,854] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb06c7f2-1d54-494e-af43-8e020d444b05/GCF_030409295.1_ASM3040929v1_genomic.fna.gz | prodigal -d GCF_030409295.1_ASM3040929v1_genomic.fna/cds.fna -a GCF_030409295.1_ASM3040929v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:55,954] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:55,954] [INFO] Task started: HMMsearch
[2024-01-24 11:34:55,954] [INFO] Running command: hmmsearch --tblout GCF_030409295.1_ASM3040929v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg92e4709e-3474-456b-b9e3-0d881077583c/dqc_reference/reference_markers.hmm GCF_030409295.1_ASM3040929v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:56,273] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:56,274] [INFO] Found 6/6 markers.
[2024-01-24 11:34:56,323] [INFO] Query marker FASTA was written to GCF_030409295.1_ASM3040929v1_genomic.fna/markers.fasta
[2024-01-24 11:34:56,323] [INFO] Task started: Blastn
[2024-01-24 11:34:56,323] [INFO] Running command: blastn -query GCF_030409295.1_ASM3040929v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92e4709e-3474-456b-b9e3-0d881077583c/dqc_reference/reference_markers.fasta -out GCF_030409295.1_ASM3040929v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:57,116] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:57,120] [INFO] Selected 11 target genomes.
[2024-01-24 11:34:57,120] [INFO] Target genome list was writen to GCF_030409295.1_ASM3040929v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:57,125] [INFO] Task started: fastANI
[2024-01-24 11:34:57,125] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb06c7f2-1d54-494e-af43-8e020d444b05/GCF_030409295.1_ASM3040929v1_genomic.fna.gz --refList GCF_030409295.1_ASM3040929v1_genomic.fna/target_genomes.txt --output GCF_030409295.1_ASM3040929v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:07,554] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:07,554] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg92e4709e-3474-456b-b9e3-0d881077583c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:07,555] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg92e4709e-3474-456b-b9e3-0d881077583c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:07,564] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:35:07,565] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:35:07,565] [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
Halomonas titanicae	strain=BH1	GCA_000336575.1	664683	664683	type	True	91.9359	1288	1612	95	below_threshold
Halomonas sedimenti	strain=QX-2	GCA_013416325.1	2729618	2729618	type	True	91.1236	1206	1612	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_002265845.1	223527	223527	type	True	87.7527	1107	1612	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_000236035.1	223527	223527	type	True	87.729	1101	1612	95	below_threshold
Halomonas glaciei	strain=DD39	GCA_013415125.1	186761	186761	type	True	86.5439	1071	1612	95	below_threshold
Halomonas maris	strain=QX-1	GCA_013371085.1	2729617	2729617	type	True	84.6996	1026	1612	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019504685.1	2852117	2852117	type	True	81.3647	762	1612	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019722725.1	2852117	2852117	type	True	81.3523	774	1612	95	below_threshold
Halomonas populi	strain=MC	GCA_003989825.1	2498858	2498858	type	True	79.6821	516	1612	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	77.79	275	1612	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	77.6015	289	1612	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:07,567] [INFO] DFAST Taxonomy check result was written to GCF_030409295.1_ASM3040929v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:07,570] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:07,570] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:07,570] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg92e4709e-3474-456b-b9e3-0d881077583c/dqc_reference/checkm_data
[2024-01-24 11:35:07,572] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:07,626] [INFO] Task started: CheckM
[2024-01-24 11:35:07,626] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030409295.1_ASM3040929v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030409295.1_ASM3040929v1_genomic.fna/checkm_input GCF_030409295.1_ASM3040929v1_genomic.fna/checkm_result
[2024-01-24 11:35:48,816] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:48,818] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:48,833] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:48,833] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:48,834] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030409295.1_ASM3040929v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:48,834] [INFO] Task started: Blastn
[2024-01-24 11:35:48,834] [INFO] Running command: blastn -query GCF_030409295.1_ASM3040929v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92e4709e-3474-456b-b9e3-0d881077583c/dqc_reference/reference_markers_gtdb.fasta -out GCF_030409295.1_ASM3040929v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:50,121] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:50,125] [INFO] Selected 9 target genomes.
[2024-01-24 11:35:50,125] [INFO] Target genome list was writen to GCF_030409295.1_ASM3040929v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:50,159] [INFO] Task started: fastANI
[2024-01-24 11:35:50,160] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb06c7f2-1d54-494e-af43-8e020d444b05/GCF_030409295.1_ASM3040929v1_genomic.fna.gz --refList GCF_030409295.1_ASM3040929v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030409295.1_ASM3040929v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:00,689] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:00,697] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:00,697] [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_004364445.1	s__Halomonas alkaliantarctica	99.1229	1467	1612	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.52	96.69	0.85	0.81	3	conclusive
GCF_000336575.1	s__Halomonas titanicae	91.9468	1288	1612	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.70	97.17	0.86	0.84	22	-
GCF_013416325.1	s__Halomonas sedimenti	91.1273	1205	1612	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.54	99.54	0.90	0.90	2	-
GCF_002211105.1	s__Halomonas campaniensis_A	90.5003	1224	1612	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.13	98.13	0.90	0.90	2	-
GCF_001882345.1	s__Halomonas sp001882345	89.5373	1081	1612	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004295565.1	s__Halomonas olivaria	88.8854	1269	1612	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002257525.1	s__Halomonas ventosae_B	88.3894	1220	1612	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.23	97.92	0.94	0.87	4	-
GCF_000236035.1	s__Halomonas boliviensis	87.7412	1100	1612	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.96	99.96	0.99	0.99	2	-
GCF_013415125.1	s__Halomonas glaciei	86.551	1070	1612	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.36	97.36	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:00,706] [INFO] GTDB search result was written to GCF_030409295.1_ASM3040929v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:00,707] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:00,710] [INFO] DFAST_QC result json was written to GCF_030409295.1_ASM3040929v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:00,710] [INFO] DFAST_QC completed!
[2024-01-24 11:36:00,710] [INFO] Total running time: 0h1m19s