[2023-06-18 23:43:04,096] [INFO] DFAST_QC pipeline started.
[2023-06-18 23:43:04,099] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 23:43:04,099] [INFO] DQC Reference Directory: /var/lib/cwl/stga29ae793-416f-4bbb-8a47-199868bbcf35/dqc_reference
[2023-06-18 23:43:05,509] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 23:43:05,510] [INFO] Task started: Prodigal
[2023-06-18 23:43:05,510] [INFO] Running command: gunzip -c /var/lib/cwl/stgbb7cc5f4-41cf-466e-b877-2c417f863713/GCA_018055145.1_ASM1805514v1_genomic.fna.gz | prodigal -d GCA_018055145.1_ASM1805514v1_genomic.fna/cds.fna -a GCA_018055145.1_ASM1805514v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 23:43:08,672] [INFO] Task succeeded: Prodigal
[2023-06-18 23:43:08,672] [INFO] Task started: HMMsearch
[2023-06-18 23:43:08,672] [INFO] Running command: hmmsearch --tblout GCA_018055145.1_ASM1805514v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga29ae793-416f-4bbb-8a47-199868bbcf35/dqc_reference/reference_markers.hmm GCA_018055145.1_ASM1805514v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 23:43:08,915] [INFO] Task succeeded: HMMsearch
[2023-06-18 23:43:08,917] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbb7cc5f4-41cf-466e-b877-2c417f863713/GCA_018055145.1_ASM1805514v1_genomic.fna.gz]
[2023-06-18 23:43:08,936] [INFO] Query marker FASTA was written to GCA_018055145.1_ASM1805514v1_genomic.fna/markers.fasta
[2023-06-18 23:43:08,936] [INFO] Task started: Blastn
[2023-06-18 23:43:08,936] [INFO] Running command: blastn -query GCA_018055145.1_ASM1805514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga29ae793-416f-4bbb-8a47-199868bbcf35/dqc_reference/reference_markers.fasta -out GCA_018055145.1_ASM1805514v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 23:43:09,580] [INFO] Task succeeded: Blastn
[2023-06-18 23:43:09,583] [INFO] Selected 13 target genomes.
[2023-06-18 23:43:09,584] [INFO] Target genome list was writen to GCA_018055145.1_ASM1805514v1_genomic.fna/target_genomes.txt
[2023-06-18 23:43:09,586] [INFO] Task started: fastANI
[2023-06-18 23:43:09,586] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb7cc5f4-41cf-466e-b877-2c417f863713/GCA_018055145.1_ASM1805514v1_genomic.fna.gz --refList GCA_018055145.1_ASM1805514v1_genomic.fna/target_genomes.txt --output GCA_018055145.1_ASM1805514v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 23:43:17,750] [INFO] Task succeeded: fastANI
[2023-06-18 23:43:17,751] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga29ae793-416f-4bbb-8a47-199868bbcf35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 23:43:17,751] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga29ae793-416f-4bbb-8a47-199868bbcf35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 23:43:17,763] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2023-06-18 23:43:17,764] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-06-18 23:43:17,764] [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
Psychrobacter communis	strain=Sa4CVA2	GCA_014836505.1	2762238	2762238	type	True	97.2794	400	420	95	inconclusive
Psychrobacter faecalis	strain=DSM 14664	GCA_016107575.1	180588	180588	type	True	96.3019	410	420	95	inconclusive
Psychrobacter luti	strain=CECT 5885	GCA_014192115.1	198481	198481	type	True	85.6479	387	420	95	below_threshold
Psychrobacter cryohalolentis	strain=K5	GCA_000013905.1	330922	330922	type	True	81.4862	334	420	95	below_threshold
Psychrobacter aquimaris	strain=DSM 16329	GCA_016107525.1	292733	292733	type	True	81.3694	326	420	95	below_threshold
Psychrobacter arcticus	strain=273-4	GCA_000012305.1	334543	334543	type	True	80.9901	306	420	95	below_threshold
Psychrobacter celer	strain=DSM 23510	GCA_016107555.1	306572	306572	type	True	80.5046	291	420	95	below_threshold
Psychrobacter glaciei	strain=KCTC 42280	GCA_014652895.1	619771	619771	type	True	80.4477	326	420	95	below_threshold
Psychrobacter halodurans	strain=F2608	GCA_017498075.1	2818439	2818439	type	True	80.3376	298	420	95	below_threshold
Psychrobacter namhaensis	strain=DSM 16330	GCA_016107545.1	292734	292734	type	True	80.2629	292	420	95	below_threshold
Psychrobacter coccoides	strain=F1192	GCA_017498085.1	2818440	2818440	type	True	78.2865	212	420	95	below_threshold
Psychrobacter frigidicola	strain=ACAM 304	GCA_007997305.1	45611	45611	type	True	78.2856	219	420	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 23:43:17,766] [INFO] DFAST Taxonomy check result was written to GCA_018055145.1_ASM1805514v1_genomic.fna/tc_result.tsv
[2023-06-18 23:43:17,767] [INFO] ===== Taxonomy check completed =====
[2023-06-18 23:43:17,767] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 23:43:17,768] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga29ae793-416f-4bbb-8a47-199868bbcf35/dqc_reference/checkm_data
[2023-06-18 23:43:17,769] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 23:43:17,791] [INFO] Task started: CheckM
[2023-06-18 23:43:17,791] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018055145.1_ASM1805514v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018055145.1_ASM1805514v1_genomic.fna/checkm_input GCA_018055145.1_ASM1805514v1_genomic.fna/checkm_result
[2023-06-18 23:43:35,369] [INFO] Task succeeded: CheckM
[2023-06-18 23:43:35,370] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 23:43:35,397] [INFO] ===== Completeness check finished =====
[2023-06-18 23:43:35,397] [INFO] ===== Start GTDB Search =====
[2023-06-18 23:43:35,398] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018055145.1_ASM1805514v1_genomic.fna/markers.fasta)
[2023-06-18 23:43:35,398] [INFO] Task started: Blastn
[2023-06-18 23:43:35,399] [INFO] Running command: blastn -query GCA_018055145.1_ASM1805514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga29ae793-416f-4bbb-8a47-199868bbcf35/dqc_reference/reference_markers_gtdb.fasta -out GCA_018055145.1_ASM1805514v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 23:43:36,384] [INFO] Task succeeded: Blastn
[2023-06-18 23:43:36,389] [INFO] Selected 11 target genomes.
[2023-06-18 23:43:36,390] [INFO] Target genome list was writen to GCA_018055145.1_ASM1805514v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 23:43:36,397] [INFO] Task started: fastANI
[2023-06-18 23:43:36,397] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb7cc5f4-41cf-466e-b877-2c417f863713/GCA_018055145.1_ASM1805514v1_genomic.fna.gz --refList GCA_018055145.1_ASM1805514v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018055145.1_ASM1805514v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 23:43:42,444] [INFO] Task succeeded: fastANI
[2023-06-18 23:43:42,454] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 23:43:42,454] [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_016107575.1	s__Psychrobacter faecalis	96.3019	410	420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	96.81	95.77	0.89	0.85	16	conclusive
GCA_002377905.1	s__Psychrobacter sp002377905	93.3023	399	420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904846345.1	s__Psychrobacter maritimus	87.1643	400	420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	96.41	96.16	0.91	0.90	6	-
GCA_002414005.1	s__Psychrobacter sp002414005	87.0714	372	420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904846285.1	s__Psychrobacter immobilis_D	86.6061	397	420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002453355.1	s__Psychrobacter sp002453355	86.5169	393	420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192115.1	s__Psychrobacter luti	85.6479	387	420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013248965.1	s__Psychrobacter okhotskensis	81.6086	333	420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.29	97.15	0.88	0.85	12	-
GCF_000013905.1	s__Psychrobacter cryohalolentis	81.4862	334	420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.64	96.60	0.93	0.89	9	-
GCF_016107525.1	s__Psychrobacter aquimaris	81.3694	326	420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	98.04	97.20	0.92	0.89	5	-
GCF_016107545.1	s__Psychrobacter namhaensis	80.2629	292	420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	98.25	97.66	0.93	0.91	5	-
--------------------------------------------------------------------------------
[2023-06-18 23:43:42,456] [INFO] GTDB search result was written to GCA_018055145.1_ASM1805514v1_genomic.fna/result_gtdb.tsv
[2023-06-18 23:43:42,457] [INFO] ===== GTDB Search completed =====
[2023-06-18 23:43:42,460] [INFO] DFAST_QC result json was written to GCA_018055145.1_ASM1805514v1_genomic.fna/dqc_result.json
[2023-06-18 23:43:42,460] [INFO] DFAST_QC completed!
[2023-06-18 23:43:42,461] [INFO] Total running time: 0h0m38s