[2024-01-24 13:19:26,356] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:26,357] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:26,358] [INFO] DQC Reference Directory: /var/lib/cwl/stgdde9c829-cc16-48f2-9137-6d473f00d291/dqc_reference
[2024-01-24 13:19:27,550] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:27,551] [INFO] Task started: Prodigal
[2024-01-24 13:19:27,551] [INFO] Running command: gunzip -c /var/lib/cwl/stg90c7a1b0-a4e9-4057-b819-47f4ee2dcbcb/GCF_031451775.1_ASM3145177v1_genomic.fna.gz | prodigal -d GCF_031451775.1_ASM3145177v1_genomic.fna/cds.fna -a GCF_031451775.1_ASM3145177v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:37,232] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:37,233] [INFO] Task started: HMMsearch
[2024-01-24 13:19:37,233] [INFO] Running command: hmmsearch --tblout GCF_031451775.1_ASM3145177v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdde9c829-cc16-48f2-9137-6d473f00d291/dqc_reference/reference_markers.hmm GCF_031451775.1_ASM3145177v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:37,502] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:37,504] [INFO] Found 6/6 markers.
[2024-01-24 13:19:37,534] [INFO] Query marker FASTA was written to GCF_031451775.1_ASM3145177v1_genomic.fna/markers.fasta
[2024-01-24 13:19:37,534] [INFO] Task started: Blastn
[2024-01-24 13:19:37,535] [INFO] Running command: blastn -query GCF_031451775.1_ASM3145177v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdde9c829-cc16-48f2-9137-6d473f00d291/dqc_reference/reference_markers.fasta -out GCF_031451775.1_ASM3145177v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:38,391] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:38,397] [INFO] Selected 22 target genomes.
[2024-01-24 13:19:38,397] [INFO] Target genome list was writen to GCF_031451775.1_ASM3145177v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:38,453] [INFO] Task started: fastANI
[2024-01-24 13:19:38,454] [INFO] Running command: fastANI --query /var/lib/cwl/stg90c7a1b0-a4e9-4057-b819-47f4ee2dcbcb/GCF_031451775.1_ASM3145177v1_genomic.fna.gz --refList GCF_031451775.1_ASM3145177v1_genomic.fna/target_genomes.txt --output GCF_031451775.1_ASM3145177v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:52,225] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:52,226] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdde9c829-cc16-48f2-9137-6d473f00d291/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:52,227] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdde9c829-cc16-48f2-9137-6d473f00d291/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:52,255] [INFO] Found 22 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:19:52,256] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:19:52,256] [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
Larsenimonas suaedae	strain=DSM 22428	GCA_023712105.1	1851019	1851019	type	True	99.9997	1066	1066	95	inconclusive
Larsenimonas salina	strain=CCM 8464	GCA_023736155.1	1295565	1295565	type	True	95.5195	957	1066	95	inconclusive
Kushneria konosiri	strain=X49	GCA_002155145.1	698828	698828	type	True	78.1255	242	1066	95	below_threshold
Kushneria indalinina	strain=DSM 14324	GCA_003385845.1	184067	184067	type	True	78.0407	262	1066	95	below_threshold
Salinicola aestuarinus	strain=CPA62	GCA_003206645.1	1949082	1949082	type	True	77.8648	199	1066	95	below_threshold
Kushneria marisflavi	strain=DSM 15357	GCA_003610515.1	157779	157779	type	True	77.8306	242	1066	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	77.7705	192	1066	95	below_threshold
Halomonas zincidurans	strain=B6	GCA_000731955.1	1178777	1178777	type	True	77.7646	212	1066	95	below_threshold
Kushneria avicenniae	strain=DSM 23439	GCA_900112585.1	402385	402385	type	True	77.7505	262	1066	95	below_threshold
Halomonas aestuarii	strain=Hb3	GCA_001886615.1	1897729	1897729	type	True	77.7205	164	1066	95	below_threshold
Kushneria phosphatilytica	strain=YCWA18	GCA_001854625.1	657387	657387	type	True	77.6637	160	1066	95	below_threshold
Kushneria phosphatilytica	strain=YCWA18	GCA_008247605.1	657387	657387	type	True	77.6531	166	1066	95	below_threshold
Halomonas alkalisoli	strain=M5N1S17	GCA_021412585.1	2907158	2907158	type	True	77.6393	171	1066	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	77.6333	206	1066	95	below_threshold
Salinicola halophilus	strain=CECT 5903	GCA_003206155.1	184065	184065	type	True	77.5789	218	1066	95	below_threshold
Halomonas songnenensis	strain=CGMCC 1.12152	GCA_003002925.1	1176243	1176243	type	True	77.4043	166	1066	95	below_threshold
Salinicola tamaricis	strain=F01	GCA_003006155.1	1771309	1771309	type	True	77.3372	258	1066	95	below_threshold
Halomonas urumqiensis	strain=BZ-SZ-XJ27	GCA_002879635.1	1684789	1684789	type	True	77.3023	152	1066	95	below_threshold
Halomonas urumqiensis	strain=BZ-SZ-XJ27	GCA_003028575.1	1684789	1684789	type	True	77.1992	153	1066	95	below_threshold
Halomonas urumqiensis	strain=CGMCC 1.12917	GCA_014653135.1	1684789	1684789	type	True	77.1149	155	1066	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	76.9492	169	1066	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	76.4875	107	1066	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:52,257] [INFO] DFAST Taxonomy check result was written to GCF_031451775.1_ASM3145177v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:52,258] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:52,258] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:52,258] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdde9c829-cc16-48f2-9137-6d473f00d291/dqc_reference/checkm_data
[2024-01-24 13:19:52,259] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:52,292] [INFO] Task started: CheckM
[2024-01-24 13:19:52,292] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031451775.1_ASM3145177v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031451775.1_ASM3145177v1_genomic.fna/checkm_input GCF_031451775.1_ASM3145177v1_genomic.fna/checkm_result
[2024-01-24 13:20:25,706] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:25,707] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:25,728] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:25,729] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:25,729] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031451775.1_ASM3145177v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:25,729] [INFO] Task started: Blastn
[2024-01-24 13:20:25,730] [INFO] Running command: blastn -query GCF_031451775.1_ASM3145177v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdde9c829-cc16-48f2-9137-6d473f00d291/dqc_reference/reference_markers_gtdb.fasta -out GCF_031451775.1_ASM3145177v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:27,187] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:27,192] [INFO] Selected 32 target genomes.
[2024-01-24 13:20:27,192] [INFO] Target genome list was writen to GCF_031451775.1_ASM3145177v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:27,480] [INFO] Task started: fastANI
[2024-01-24 13:20:27,481] [INFO] Running command: fastANI --query /var/lib/cwl/stg90c7a1b0-a4e9-4057-b819-47f4ee2dcbcb/GCF_031451775.1_ASM3145177v1_genomic.fna.gz --refList GCF_031451775.1_ASM3145177v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031451775.1_ASM3145177v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:46,226] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:46,262] [INFO] Found 32 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:20:46,263] [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_002155145.1	s__Kushneria konosiri	78.1107	243	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385845.1	s__Kushneria indalinina	78.0407	262	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007989465.1	s__Halomonas halophila	77.8927	231	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.43	97.59	0.92	0.89	4	-
GCF_003206645.1	s__Salinicola aestuarinus	77.88	198	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014840935.1	s__Halomonas_E sp014840935	77.8773	212	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265245.1	s__Halomonas smyrnensis	77.8559	232	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.45	98.45	0.89	0.89	2	-
GCA_001577635.1	s__Halomonas_C sp001577635	77.7902	224	1066	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_001937195.1	s__Salinicola socius	77.7867	197	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	99.48	98.96	0.96	0.93	3	-
GCF_004798905.1	s__Halomonas borealis	77.7668	190	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112585.1	s__Kushneria avicenniae	77.7587	260	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056305.1	s__Halomonas denitrificans	77.7579	196	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000737985.1	s__Salinicola sp000737985	77.7442	262	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	96.18	96.18	0.88	0.88	2	-
GCF_001886615.1	s__Halomonas aestuarii	77.7204	164	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004117855.1	s__Halomonas_C coralii	77.6955	239	1066	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_003206575.1	s__Salinicola endophyticus	77.6647	250	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	99.06	99.06	0.96	0.96	2	-
GCF_008247605.1	s__Kushneria phosphatilytica	77.626	166	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_900961225.1	s__Halomonas_C sp900961225	77.5936	239	1066	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_013349955.1	s__Halomonas_E taeanensis_B	77.576	203	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003206155.1	s__Salinicola halophilus	77.5734	217	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363755.1	s__Halomonas sp009363755	77.4803	199	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003206045.1	s__Salinicola lusitanus	77.462	232	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	96.87	96.87	0.93	0.93	2	-
GCF_000686925.1	s__Halomonas sp000686925	77.4453	140	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003002925.1	s__Halomonas songnenensis	77.4211	165	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113605.1	s__Halomonas_C xianhensis	77.4147	193	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	96.25	96.25	0.87	0.87	2	-
GCF_003206065.1	s__Salinicola halimionae	77.3712	173	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003006155.1	s__Salinicola tamaricis	77.3697	254	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	99.82	99.82	0.99	0.99	2	-
GCA_003012345.1	s__Phytohalomonas tamaricis	77.328	152	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Phytohalomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003028575.1	s__Halomonas urumqiensis	77.1996	152	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.97	1.00	0.99	3	-
GCF_004361885.1	s__Halomonas ventosae_C	77.1859	163	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902500215.1	s__Halomonas sp902500215	76.9637	168	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001457615.1	s__Pseudomonas aeruginosa	76.4319	110	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.12	97.38	0.94	0.84	5623	-
GCF_003205295.1	s__Pseudomonas_E mosselii_B	76.2136	103	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.3017	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:46,265] [INFO] GTDB search result was written to GCF_031451775.1_ASM3145177v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:46,265] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:46,270] [INFO] DFAST_QC result json was written to GCF_031451775.1_ASM3145177v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:46,270] [INFO] DFAST_QC completed!
[2024-01-24 13:20:46,270] [INFO] Total running time: 0h1m20s