[2024-01-24 13:56:12,906] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:12,909] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:12,909] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c57f011-2f3a-4965-b30c-102281933191/dqc_reference
[2024-01-24 13:56:14,423] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:14,424] [INFO] Task started: Prodigal
[2024-01-24 13:56:14,425] [INFO] Running command: gunzip -c /var/lib/cwl/stgac62ab80-41e4-446b-b27e-a515ec5b54b2/GCF_031451755.1_ASM3145175v1_genomic.fna.gz | prodigal -d GCF_031451755.1_ASM3145175v1_genomic.fna/cds.fna -a GCF_031451755.1_ASM3145175v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:24,156] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:24,156] [INFO] Task started: HMMsearch
[2024-01-24 13:56:24,156] [INFO] Running command: hmmsearch --tblout GCF_031451755.1_ASM3145175v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c57f011-2f3a-4965-b30c-102281933191/dqc_reference/reference_markers.hmm GCF_031451755.1_ASM3145175v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:24,455] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:24,456] [INFO] Found 6/6 markers.
[2024-01-24 13:56:24,491] [INFO] Query marker FASTA was written to GCF_031451755.1_ASM3145175v1_genomic.fna/markers.fasta
[2024-01-24 13:56:24,491] [INFO] Task started: Blastn
[2024-01-24 13:56:24,491] [INFO] Running command: blastn -query GCF_031451755.1_ASM3145175v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c57f011-2f3a-4965-b30c-102281933191/dqc_reference/reference_markers.fasta -out GCF_031451755.1_ASM3145175v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:25,245] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:25,249] [INFO] Selected 23 target genomes.
[2024-01-24 13:56:25,250] [INFO] Target genome list was writen to GCF_031451755.1_ASM3145175v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:25,266] [INFO] Task started: fastANI
[2024-01-24 13:56:25,267] [INFO] Running command: fastANI --query /var/lib/cwl/stgac62ab80-41e4-446b-b27e-a515ec5b54b2/GCF_031451755.1_ASM3145175v1_genomic.fna.gz --refList GCF_031451755.1_ASM3145175v1_genomic.fna/target_genomes.txt --output GCF_031451755.1_ASM3145175v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:40,537] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:40,537] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c57f011-2f3a-4965-b30c-102281933191/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:40,538] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c57f011-2f3a-4965-b30c-102281933191/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:40,554] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:56:40,554] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:56:40,555] [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 salicampi	strain=BH103	GCA_013415105.1	1449798	1449798	type	True	86.5478	816	1123	95	below_threshold
Halomonas massiliensis	strain=Marseille-P2426	GCA_900155385.1	1816686	1816686	type	True	81.6976	733	1123	95	below_threshold
Halomonas arcis	strain=CGMCC 1.6494	GCA_900103865.1	416873	416873	type	True	79.1323	350	1123	95	below_threshold
Halomonas meridiana	strain=NBRC 15608	GCA_006540125.1	29570	29570	type	True	79.0407	331	1123	95	below_threshold
Halomonas meridiana	strain=ACAM 246	GCA_900129255.1	29570	29570	type	True	78.9935	348	1123	95	below_threshold
Halomonas aquamarina	strain=558	GCA_900110265.1	77097	77097	type	True	78.8957	328	1123	95	below_threshold
Halomonas piezotolerans	strain=NBT06E8	GCA_012427705.1	2609667	2609667	type	True	78.876	308	1123	95	below_threshold
Halomonas piezotolerans	strain=NBT06E8	GCA_009660035.1	2609667	2609667	type	True	78.8379	301	1123	95	below_threshold
Halomonas lionensis	strain=RHS90	GCA_002087295.1	1144478	1144478	type	True	78.7739	307	1123	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019722725.1	2852117	2852117	type	True	78.5126	272	1123	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019504685.1	2852117	2852117	type	True	78.5046	268	1123	95	below_threshold
Halomonas azerica	strain=TBZ9	GCA_013112225.1	2732867	2732867	type	True	78.5007	326	1123	95	below_threshold
Halomonas zhaodongensis	strain=NEAU-ST10-25	GCA_013415115.1	1176240	1176240	type	True	78.4866	253	1123	95	below_threshold
Halomonas subglaciescola	strain=ACAM 12	GCA_900142895.1	29571	29571	type	True	78.4757	305	1123	95	below_threshold
Halomonas zhanjiangensis	strain=DSM 21076	GCA_000377665.1	1121960	1121960	type	True	78.4589	264	1123	95	below_threshold
Halomonas nanhaiensis	strain=JCM 18142	GCA_003990185.1	1258546	1258546	type	True	78.3446	262	1123	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	77.7058	250	1123	95	below_threshold
Halomonas antri	strain=Y3S6	GCA_019430905.1	2846777	2846777	type	True	77.7033	183	1123	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	77.6314	198	1123	95	below_threshold
Halomonas cupida	strain=NBRC 102219	GCA_007991155.1	44933	44933	type	True	77.4546	122	1123	95	below_threshold
Halomonas cupida	strain=DSM 4740	GCA_900142755.1	44933	44933	type	True	77.3375	127	1123	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:40,556] [INFO] DFAST Taxonomy check result was written to GCF_031451755.1_ASM3145175v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:40,557] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:40,557] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:40,557] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c57f011-2f3a-4965-b30c-102281933191/dqc_reference/checkm_data
[2024-01-24 13:56:40,559] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:40,595] [INFO] Task started: CheckM
[2024-01-24 13:56:40,596] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031451755.1_ASM3145175v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031451755.1_ASM3145175v1_genomic.fna/checkm_input GCF_031451755.1_ASM3145175v1_genomic.fna/checkm_result
[2024-01-24 13:57:14,076] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:14,078] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:14,097] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:14,097] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:14,097] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031451755.1_ASM3145175v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:14,098] [INFO] Task started: Blastn
[2024-01-24 13:57:14,098] [INFO] Running command: blastn -query GCF_031451755.1_ASM3145175v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c57f011-2f3a-4965-b30c-102281933191/dqc_reference/reference_markers_gtdb.fasta -out GCF_031451755.1_ASM3145175v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:15,081] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:15,085] [INFO] Selected 19 target genomes.
[2024-01-24 13:57:15,085] [INFO] Target genome list was writen to GCF_031451755.1_ASM3145175v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:15,100] [INFO] Task started: fastANI
[2024-01-24 13:57:15,100] [INFO] Running command: fastANI --query /var/lib/cwl/stgac62ab80-41e4-446b-b27e-a515ec5b54b2/GCF_031451755.1_ASM3145175v1_genomic.fna.gz --refList GCF_031451755.1_ASM3145175v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031451755.1_ASM3145175v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:28,338] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:28,359] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:57:28,360] [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_013415105.1	s__Halomonas salicampi	86.5478	816	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155385.1	s__Halomonas massiliensis	81.71	732	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.38	98.38	0.88	0.88	2	-
GCF_014263395.1	s__Halomonas sp014263395	79.9678	344	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103865.1	s__Halomonas arcis	79.1293	349	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002966495.1	s__Halomonas sp002966495	79.0476	292	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012427705.1	s__Halomonas piezotolerans	78.8873	306	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.35	98.70	0.97	0.94	3	-
GCF_900110265.1	s__Halomonas aquamarina	78.8819	329	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.65	97.09	0.84	0.80	25	-
GCF_001651035.1	s__Halomonas sp001651035	78.8495	314	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.79	97.57	0.91	0.81	5	-
GCF_009846525.1	s__Halomonas sp002696125	78.8152	325	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.53	98.53	0.95	0.95	2	-
GCF_002087295.1	s__Halomonas lionensis	78.7739	307	1123	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	78.6753	371	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.23	97.92	0.94	0.87	4	-
GCA_001507855.1	s__Halomonas sp001507855	78.6092	354	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	0.98	0.98	2	-
GCA_004295565.1	s__Halomonas olivaria	78.5922	338	1123	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	78.5378	343	1123	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	78.5156	348	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377665.1	s__Halomonas zhanjiangensis	78.4651	263	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142755.1	s__Halomonas cupida	77.3375	127	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:28,361] [INFO] GTDB search result was written to GCF_031451755.1_ASM3145175v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:28,362] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:28,366] [INFO] DFAST_QC result json was written to GCF_031451755.1_ASM3145175v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:28,366] [INFO] DFAST_QC completed!
[2024-01-24 13:57:28,366] [INFO] Total running time: 0h1m15s