[2024-01-24 12:06:11,996] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:11,998] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:11,999] [INFO] DQC Reference Directory: /var/lib/cwl/stgb4b34b5d-d3d4-4e31-a46a-ee82a59cea24/dqc_reference
[2024-01-24 12:06:13,391] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:13,392] [INFO] Task started: Prodigal
[2024-01-24 12:06:13,393] [INFO] Running command: gunzip -c /var/lib/cwl/stgd4a916d2-67ba-4f52-8337-c0cfcaace597/GCF_019722725.1_ASM1972272v1_genomic.fna.gz | prodigal -d GCF_019722725.1_ASM1972272v1_genomic.fna/cds.fna -a GCF_019722725.1_ASM1972272v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:23,437] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:23,437] [INFO] Task started: HMMsearch
[2024-01-24 12:06:23,437] [INFO] Running command: hmmsearch --tblout GCF_019722725.1_ASM1972272v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb4b34b5d-d3d4-4e31-a46a-ee82a59cea24/dqc_reference/reference_markers.hmm GCF_019722725.1_ASM1972272v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:23,715] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:23,716] [INFO] Found 6/6 markers.
[2024-01-24 12:06:23,756] [INFO] Query marker FASTA was written to GCF_019722725.1_ASM1972272v1_genomic.fna/markers.fasta
[2024-01-24 12:06:23,757] [INFO] Task started: Blastn
[2024-01-24 12:06:23,757] [INFO] Running command: blastn -query GCF_019722725.1_ASM1972272v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4b34b5d-d3d4-4e31-a46a-ee82a59cea24/dqc_reference/reference_markers.fasta -out GCF_019722725.1_ASM1972272v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:24,524] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:24,527] [INFO] Selected 12 target genomes.
[2024-01-24 12:06:24,528] [INFO] Target genome list was writen to GCF_019722725.1_ASM1972272v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:24,535] [INFO] Task started: fastANI
[2024-01-24 12:06:24,535] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4a916d2-67ba-4f52-8337-c0cfcaace597/GCF_019722725.1_ASM1972272v1_genomic.fna.gz --refList GCF_019722725.1_ASM1972272v1_genomic.fna/target_genomes.txt --output GCF_019722725.1_ASM1972272v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:34,578] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:34,579] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb4b34b5d-d3d4-4e31-a46a-ee82a59cea24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:34,579] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb4b34b5d-d3d4-4e31-a46a-ee82a59cea24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:34,590] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:06:34,590] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:34,590] [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_019722725.1	2852117	2852117	type	True	100.0	1212	1214	95	conclusive
Halomonas profundi	strain=MT13	GCA_019504685.1	2852117	2852117	type	True	99.9936	1187	1214	95	conclusive
Halomonas maris	strain=QX-1	GCA_013371085.1	2729617	2729617	type	True	81.4297	725	1214	95	below_threshold
Halomonas glaciei	strain=DD39	GCA_013415125.1	186761	186761	type	True	81.3783	744	1214	95	below_threshold
Halomonas sedimenti	strain=QX-2	GCA_013416325.1	2729618	2729618	type	True	81.193	778	1214	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_000236035.1	223527	223527	type	True	81.1253	732	1214	95	below_threshold
Halomonas titanicae	strain=BH1	GCA_000336575.1	664683	664683	type	True	81.1224	800	1214	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_002265845.1	223527	223527	type	True	81.0946	730	1214	95	below_threshold
Halomonas johnsoniae	strain=KCTC 22157	GCA_014651795.1	502832	502832	type	True	79.1387	422	1214	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	78.1091	152	1214	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	77.318	130	1214	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	77.2864	154	1214	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:34,592] [INFO] DFAST Taxonomy check result was written to GCF_019722725.1_ASM1972272v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:34,592] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:34,592] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:34,593] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb4b34b5d-d3d4-4e31-a46a-ee82a59cea24/dqc_reference/checkm_data
[2024-01-24 12:06:34,594] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:34,634] [INFO] Task started: CheckM
[2024-01-24 12:06:34,634] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019722725.1_ASM1972272v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019722725.1_ASM1972272v1_genomic.fna/checkm_input GCF_019722725.1_ASM1972272v1_genomic.fna/checkm_result
[2024-01-24 12:07:08,861] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:08,863] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:08,888] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:08,889] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:08,890] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019722725.1_ASM1972272v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:08,890] [INFO] Task started: Blastn
[2024-01-24 12:07:08,890] [INFO] Running command: blastn -query GCF_019722725.1_ASM1972272v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4b34b5d-d3d4-4e31-a46a-ee82a59cea24/dqc_reference/reference_markers_gtdb.fasta -out GCF_019722725.1_ASM1972272v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:10,101] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:10,104] [INFO] Selected 15 target genomes.
[2024-01-24 12:07:10,105] [INFO] Target genome list was writen to GCF_019722725.1_ASM1972272v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:10,116] [INFO] Task started: fastANI
[2024-01-24 12:07:10,116] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4a916d2-67ba-4f52-8337-c0cfcaace597/GCF_019722725.1_ASM1972272v1_genomic.fna.gz --refList GCF_019722725.1_ASM1972272v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019722725.1_ASM1972272v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:22,954] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:22,973] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:07:22,974] [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	92.6861	1039	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.35	99.20	0.94	0.94	3	-
GCF_002257525.1	s__Halomonas ventosae_B	81.6533	808	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.23	97.92	0.94	0.87	4	-
GCF_000235725.1	s__Halomonas sp000235725	81.4881	732	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.32	95.32	0.80	0.80	2	-
GCF_013371085.1	s__Halomonas maris	81.4297	725	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001882345.1	s__Halomonas sp001882345	81.4229	771	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364445.1	s__Halomonas alkaliantarctica	81.2724	780	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.52	96.69	0.85	0.81	3	-
GCA_001507855.1	s__Halomonas sp001507855	81.2555	640	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	0.98	0.98	2	-
GCF_013416325.1	s__Halomonas sedimenti	81.1945	779	1214	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	81.1212	733	1214	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	81.1189	799	1214	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	81.0772	690	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001651035.1	s__Halomonas sp001651035	81.0531	725	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.79	97.57	0.91	0.81	5	-
GCF_002211105.1	s__Halomonas campaniensis_A	80.962	751	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.13	98.13	0.90	0.90	2	-
GCA_011050415.1	s__Halomonas sp011050415	80.8007	730	1214	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	80.7803	648	1214	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 12:07:22,976] [INFO] GTDB search result was written to GCF_019722725.1_ASM1972272v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:22,976] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:22,980] [INFO] DFAST_QC result json was written to GCF_019722725.1_ASM1972272v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:22,981] [INFO] DFAST_QC completed!
[2024-01-24 12:07:22,981] [INFO] Total running time: 0h1m11s