[2024-01-24 14:46:55,038] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:55,041] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:55,041] [INFO] DQC Reference Directory: /var/lib/cwl/stga925da58-1520-4806-bea5-d3955bae33cf/dqc_reference
[2024-01-24 14:46:58,012] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:58,018] [INFO] Task started: Prodigal
[2024-01-24 14:46:58,018] [INFO] Running command: gunzip -c /var/lib/cwl/stge46c0245-a5c2-4f9c-a7d4-ca16d2201729/GCF_001614315.2_ASM161431v2_genomic.fna.gz | prodigal -d GCF_001614315.2_ASM161431v2_genomic.fna/cds.fna -a GCF_001614315.2_ASM161431v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:08,959] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:08,959] [INFO] Task started: HMMsearch
[2024-01-24 14:47:08,959] [INFO] Running command: hmmsearch --tblout GCF_001614315.2_ASM161431v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga925da58-1520-4806-bea5-d3955bae33cf/dqc_reference/reference_markers.hmm GCF_001614315.2_ASM161431v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:09,245] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:09,246] [INFO] Found 6/6 markers.
[2024-01-24 14:47:09,281] [INFO] Query marker FASTA was written to GCF_001614315.2_ASM161431v2_genomic.fna/markers.fasta
[2024-01-24 14:47:09,282] [INFO] Task started: Blastn
[2024-01-24 14:47:09,282] [INFO] Running command: blastn -query GCF_001614315.2_ASM161431v2_genomic.fna/markers.fasta -db /var/lib/cwl/stga925da58-1520-4806-bea5-d3955bae33cf/dqc_reference/reference_markers.fasta -out GCF_001614315.2_ASM161431v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:10,317] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:10,322] [INFO] Selected 24 target genomes.
[2024-01-24 14:47:10,322] [INFO] Target genome list was writen to GCF_001614315.2_ASM161431v2_genomic.fna/target_genomes.txt
[2024-01-24 14:47:10,338] [INFO] Task started: fastANI
[2024-01-24 14:47:10,339] [INFO] Running command: fastANI --query /var/lib/cwl/stge46c0245-a5c2-4f9c-a7d4-ca16d2201729/GCF_001614315.2_ASM161431v2_genomic.fna.gz --refList GCF_001614315.2_ASM161431v2_genomic.fna/target_genomes.txt --output GCF_001614315.2_ASM161431v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:26,461] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:26,461] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga925da58-1520-4806-bea5-d3955bae33cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:26,462] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga925da58-1520-4806-bea5-d3955bae33cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:26,479] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:26,479] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:26,480] [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
Halofilum ochraceum	strain=XJ16	GCA_001614315.2	1611323	1611323	type	True	100.0	1194	1196	95	conclusive
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.8679	124	1196	95	below_threshold
Acidihalobacter aeolianus	strain=V6	GCA_001753165.1	2792603	2792603	type	True	76.7601	92	1196	95	below_threshold
Thioalkalivibrio paradoxus	strain=ARh 1	GCA_000227685.3	108010	108010	type	True	76.7414	110	1196	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	76.677	84	1196	95	below_threshold
Halochromatium salexigens	strain=DSM 4395	GCA_016653295.1	49447	49447	type	True	76.6637	92	1196	95	below_threshold
Thioalkalivibrio versutus	strain=AL 2	GCA_001999325.1	106634	106634	type	True	76.6579	94	1196	95	below_threshold
Thioalkalivibrio nitratireducens	strain=DSM 14787	GCA_000321415.2	186931	186931	type	True	76.6579	112	1196	95	below_threshold
Spiribacter vilamensis	strain=DSM 21056	GCA_004217415.1	531306	531306	type	True	76.6416	85	1196	95	below_threshold
Spiribacter vilamensis	strain=DSM 21056	GCA_007625165.1	531306	531306	type	True	76.5614	83	1196	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	76.543	82	1196	95	below_threshold
Methylohalomonas lacus	strain=HMT 1	GCA_024808875.1	398773	398773	type	True	76.4501	97	1196	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.2848	185	1196	95	below_threshold
Rhodanobacter denitrificans	strain=2APBS1	GCA_000230695.3	666685	666685	type	True	76.2825	113	1196	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	76.1386	150	1196	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	76.1214	144	1196	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.0985	125	1196	95	below_threshold
Plasticicumulans acidivorans	strain=DSM 23606	GCA_003182095.1	886464	886464	type	True	76.0893	138	1196	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.0576	127	1196	95	below_threshold
Pseudomonas xanthosomae	strain=COR54	GCA_019139835.1	2842356	2842356	type	True	75.8663	85	1196	95	below_threshold
Hydrogenophaga taeniospiralis	strain=NBRC 102512	GCA_001592305.1	65656	65656	type	True	75.8474	73	1196	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	75.8014	103	1196	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:26,482] [INFO] DFAST Taxonomy check result was written to GCF_001614315.2_ASM161431v2_genomic.fna/tc_result.tsv
[2024-01-24 14:47:26,482] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:26,482] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:26,483] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga925da58-1520-4806-bea5-d3955bae33cf/dqc_reference/checkm_data
[2024-01-24 14:47:26,484] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:26,525] [INFO] Task started: CheckM
[2024-01-24 14:47:26,526] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001614315.2_ASM161431v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001614315.2_ASM161431v2_genomic.fna/checkm_input GCF_001614315.2_ASM161431v2_genomic.fna/checkm_result
[2024-01-24 14:48:02,131] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:02,133] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:02,152] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:02,152] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:02,153] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001614315.2_ASM161431v2_genomic.fna/markers.fasta)
[2024-01-24 14:48:02,153] [INFO] Task started: Blastn
[2024-01-24 14:48:02,153] [INFO] Running command: blastn -query GCF_001614315.2_ASM161431v2_genomic.fna/markers.fasta -db /var/lib/cwl/stga925da58-1520-4806-bea5-d3955bae33cf/dqc_reference/reference_markers_gtdb.fasta -out GCF_001614315.2_ASM161431v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:03,866] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:03,871] [INFO] Selected 23 target genomes.
[2024-01-24 14:48:03,871] [INFO] Target genome list was writen to GCF_001614315.2_ASM161431v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:03,912] [INFO] Task started: fastANI
[2024-01-24 14:48:03,913] [INFO] Running command: fastANI --query /var/lib/cwl/stge46c0245-a5c2-4f9c-a7d4-ca16d2201729/GCF_001614315.2_ASM161431v2_genomic.fna.gz --refList GCF_001614315.2_ASM161431v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001614315.2_ASM161431v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:17,719] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:17,743] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:17,743] [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_001614315.2	s__Halofilum ochraceum	100.0	1194	1196	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__XJ16;f__Halofilaceae;g__Halofilum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_007134775.1	s__SLKC01 sp007134775	77.5535	227	1196	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__XJ16;f__Halofilaceae;g__SLKC01	95.0	99.71	99.64	0.89	0.87	3	-
GCA_014762505.1	s__SpSt-1174 sp014762505	77.0712	125	1196	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002356355.1	s__Thiohalobacter thiocyanaticus_A	76.8874	134	1196	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	98.53	98.53	0.93	0.93	2	-
GCF_003932505.1	s__Thiohalobacter thiocyanaticus	76.8679	124	1196	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377405.1	s__Thioalkalivibrio sp000377405	76.8656	130	1196	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	97.90	97.79	0.93	0.92	11	-
GCF_000378605.1	s__Thioalkalivibrio sp000378605	76.7851	115	1196	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	100.00	99.99	1.00	1.00	3	-
GCF_001753165.1	s__Acidihalobacter aeolianus	76.7601	92	1196	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Acidihalobacteraceae;g__Acidihalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000227685.2	s__Thioalkalivibrio_B paradoxus	76.7414	110	1196	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025545.1	s__Thioalkalivibrio sp000025545	76.6869	102	1196	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	97.34	97.34	0.93	0.93	2	-
GCF_016653295.1	s__Halochromatium salexigens	76.6637	92	1196	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000321415.2	s__Thioalkalivibrio_B nitratireducens	76.6579	112	1196	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217415.1	s__Spiribacter vilamensis	76.6416	85	1196	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__Spiribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900961225.1	s__Halomonas_C sp900961225	76.5836	109	1196	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004001245.1	s__Sulfurivermis fontis	76.5466	83	1196	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011321775.1	s__Thiogranum sp011321775	76.3415	102	1196	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001830245.1	s__Lysobacter sp001830245	76.1651	94	1196	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.71	99.71	0.92	0.92	2	-
GCA_003695825.1	s__J048 sp003695825	76.1206	84	1196	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__J048;f__J048;g__J048	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007127715.1	s__PWYM01 sp007127715	76.0907	83	1196	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PWYM01;f__PWYM01;g__PWYM01	95.0	99.45	99.43	0.90	0.89	3	-
GCF_019097855.1	s__Pseudomonas_K sp019097855	76.0865	126	1196	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003562815.1	s__Halochromatium sp003562815	75.9662	86	1196	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	99.58	99.39	0.91	0.88	4	-
GCF_019139835.1	s__Pseudomonas_E sp019139835	75.8331	87	1196	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.50	95.50	0.87	0.87	2	-
GCA_004298385.1	s__2-12-FULL-64-23 sp004298385	75.8026	63	1196	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__2-12-FULL-64-23	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:17,745] [INFO] GTDB search result was written to GCF_001614315.2_ASM161431v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:17,746] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:17,750] [INFO] DFAST_QC result json was written to GCF_001614315.2_ASM161431v2_genomic.fna/dqc_result.json
[2024-01-24 14:48:17,751] [INFO] DFAST_QC completed!
[2024-01-24 14:48:17,751] [INFO] Total running time: 0h1m23s