[2024-01-24 13:37:10,241] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:10,244] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:10,245] [INFO] DQC Reference Directory: /var/lib/cwl/stg341a10b1-223f-40ee-91e2-8f580eab483d/dqc_reference
[2024-01-24 13:37:11,506] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:11,507] [INFO] Task started: Prodigal
[2024-01-24 13:37:11,507] [INFO] Running command: gunzip -c /var/lib/cwl/stgdd3062a2-aa3f-4d90-a420-73fef871c65d/GCF_019504685.1_ASM1950468v1_genomic.fna.gz | prodigal -d GCF_019504685.1_ASM1950468v1_genomic.fna/cds.fna -a GCF_019504685.1_ASM1950468v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:21,380] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:21,381] [INFO] Task started: HMMsearch
[2024-01-24 13:37:21,381] [INFO] Running command: hmmsearch --tblout GCF_019504685.1_ASM1950468v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg341a10b1-223f-40ee-91e2-8f580eab483d/dqc_reference/reference_markers.hmm GCF_019504685.1_ASM1950468v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:21,682] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:21,684] [INFO] Found 6/6 markers.
[2024-01-24 13:37:21,716] [INFO] Query marker FASTA was written to GCF_019504685.1_ASM1950468v1_genomic.fna/markers.fasta
[2024-01-24 13:37:21,716] [INFO] Task started: Blastn
[2024-01-24 13:37:21,717] [INFO] Running command: blastn -query GCF_019504685.1_ASM1950468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg341a10b1-223f-40ee-91e2-8f580eab483d/dqc_reference/reference_markers.fasta -out GCF_019504685.1_ASM1950468v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:22,454] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:22,458] [INFO] Selected 12 target genomes.
[2024-01-24 13:37:22,458] [INFO] Target genome list was writen to GCF_019504685.1_ASM1950468v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:22,462] [INFO] Task started: fastANI
[2024-01-24 13:37:22,462] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd3062a2-aa3f-4d90-a420-73fef871c65d/GCF_019504685.1_ASM1950468v1_genomic.fna.gz --refList GCF_019504685.1_ASM1950468v1_genomic.fna/target_genomes.txt --output GCF_019504685.1_ASM1950468v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:32,730] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:32,730] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg341a10b1-223f-40ee-91e2-8f580eab483d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:32,731] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg341a10b1-223f-40ee-91e2-8f580eab483d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:32,741] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:37:32,742] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:32,742] [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 profundi	strain=MT13	GCA_019504685.1	2852117	2852117	type	True	100.0	1188	1190	95	conclusive
Halomonas profundi	strain=MT13	GCA_019722725.1	2852117	2852117	type	True	99.9991	1189	1190	95	conclusive
Halomonas maris	strain=QX-1	GCA_013371085.1	2729617	2729617	type	True	81.3718	726	1190	95	below_threshold
Halomonas glaciei	strain=DD39	GCA_013415125.1	186761	186761	type	True	81.2186	751	1190	95	below_threshold
Halomonas sedimenti	strain=QX-2	GCA_013416325.1	2729618	2729618	type	True	81.2147	772	1190	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_000236035.1	223527	223527	type	True	81.0338	738	1190	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_002265845.1	223527	223527	type	True	81.0303	734	1190	95	below_threshold
Halomonas titanicae	strain=BH1	GCA_000336575.1	664683	664683	type	True	81.0033	786	1190	95	below_threshold
Halomonas johnsoniae	strain=KCTC 22157	GCA_014651795.1	502832	502832	type	True	79.0823	421	1190	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	77.1976	155	1190	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	77.1148	132	1190	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	76.9032	160	1190	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:32,744] [INFO] DFAST Taxonomy check result was written to GCF_019504685.1_ASM1950468v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:32,744] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:32,745] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:32,745] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg341a10b1-223f-40ee-91e2-8f580eab483d/dqc_reference/checkm_data
[2024-01-24 13:37:32,746] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:32,788] [INFO] Task started: CheckM
[2024-01-24 13:37:32,788] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019504685.1_ASM1950468v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019504685.1_ASM1950468v1_genomic.fna/checkm_input GCF_019504685.1_ASM1950468v1_genomic.fna/checkm_result
[2024-01-24 13:38:07,731] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:07,732] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:07,761] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:07,761] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:07,762] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019504685.1_ASM1950468v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:07,762] [INFO] Task started: Blastn
[2024-01-24 13:38:07,762] [INFO] Running command: blastn -query GCF_019504685.1_ASM1950468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg341a10b1-223f-40ee-91e2-8f580eab483d/dqc_reference/reference_markers_gtdb.fasta -out GCF_019504685.1_ASM1950468v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:09,004] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:09,008] [INFO] Selected 15 target genomes.
[2024-01-24 13:38:09,008] [INFO] Target genome list was writen to GCF_019504685.1_ASM1950468v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:09,026] [INFO] Task started: fastANI
[2024-01-24 13:38:09,026] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd3062a2-aa3f-4d90-a420-73fef871c65d/GCF_019504685.1_ASM1950468v1_genomic.fna.gz --refList GCF_019504685.1_ASM1950468v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019504685.1_ASM1950468v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:22,026] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:22,046] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:38:22,046] [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_002332255.1	s__Halomonas sp002332255	92.5931	1035	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.35	99.20	0.94	0.94	3	-
GCA_001507855.1	s__Halomonas sp001507855	81.4296	621	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	0.98	0.98	2	-
GCF_013371085.1	s__Halomonas maris	81.3685	727	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000235725.1	s__Halomonas sp000235725	81.3681	737	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.32	95.32	0.80	0.80	2	-
GCF_002257525.1	s__Halomonas ventosae_B	81.2801	815	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.23	97.92	0.94	0.87	4	-
GCF_004364445.1	s__Halomonas alkaliantarctica	81.2621	767	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.52	96.69	0.85	0.81	3	-
GCF_001882345.1	s__Halomonas sp001882345	81.2526	772	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013416325.1	s__Halomonas sedimenti	81.2191	772	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.54	99.54	0.90	0.90	2	-
GCF_000236035.1	s__Halomonas boliviensis	81.0397	738	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.96	99.96	0.99	0.99	2	-
GCF_000336575.1	s__Halomonas titanicae	81.0231	782	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.70	97.17	0.86	0.84	22	-
GCA_002366715.1	s__Halomonas sp002366715	81.0071	674	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002211105.1	s__Halomonas campaniensis_A	80.9229	751	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.13	98.13	0.90	0.90	2	-
GCF_001651035.1	s__Halomonas sp001651035	80.9105	743	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.79	97.57	0.91	0.81	5	-
GCA_011050415.1	s__Halomonas sp011050415	80.8492	729	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_007991175.1	s__Halomonas variabilis	80.6993	655	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:22,048] [INFO] GTDB search result was written to GCF_019504685.1_ASM1950468v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:22,048] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:22,052] [INFO] DFAST_QC result json was written to GCF_019504685.1_ASM1950468v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:22,052] [INFO] DFAST_QC completed!
[2024-01-24 13:38:22,052] [INFO] Total running time: 0h1m12s