[2024-01-24 11:12:26,170] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:26,175] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:26,175] [INFO] DQC Reference Directory: /var/lib/cwl/stgd088dcbd-640d-4b47-a30c-3c739ef0388e/dqc_reference
[2024-01-24 11:12:27,501] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:27,502] [INFO] Task started: Prodigal
[2024-01-24 11:12:27,503] [INFO] Running command: gunzip -c /var/lib/cwl/stg58835ba2-9d73-4622-8a60-8cfce9259fa8/GCF_014836505.1_ASM1483650v1_genomic.fna.gz | prodigal -d GCF_014836505.1_ASM1483650v1_genomic.fna/cds.fna -a GCF_014836505.1_ASM1483650v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:34,017] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:34,018] [INFO] Task started: HMMsearch
[2024-01-24 11:12:34,018] [INFO] Running command: hmmsearch --tblout GCF_014836505.1_ASM1483650v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd088dcbd-640d-4b47-a30c-3c739ef0388e/dqc_reference/reference_markers.hmm GCF_014836505.1_ASM1483650v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:34,297] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:34,299] [INFO] Found 6/6 markers.
[2024-01-24 11:12:34,328] [INFO] Query marker FASTA was written to GCF_014836505.1_ASM1483650v1_genomic.fna/markers.fasta
[2024-01-24 11:12:34,329] [INFO] Task started: Blastn
[2024-01-24 11:12:34,329] [INFO] Running command: blastn -query GCF_014836505.1_ASM1483650v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd088dcbd-640d-4b47-a30c-3c739ef0388e/dqc_reference/reference_markers.fasta -out GCF_014836505.1_ASM1483650v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:35,009] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:35,012] [INFO] Selected 14 target genomes.
[2024-01-24 11:12:35,012] [INFO] Target genome list was writen to GCF_014836505.1_ASM1483650v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:35,017] [INFO] Task started: fastANI
[2024-01-24 11:12:35,018] [INFO] Running command: fastANI --query /var/lib/cwl/stg58835ba2-9d73-4622-8a60-8cfce9259fa8/GCF_014836505.1_ASM1483650v1_genomic.fna.gz --refList GCF_014836505.1_ASM1483650v1_genomic.fna/target_genomes.txt --output GCF_014836505.1_ASM1483650v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:12:46,313] [INFO] Task succeeded: fastANI
[2024-01-24 11:12:46,314] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd088dcbd-640d-4b47-a30c-3c739ef0388e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:12:46,314] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd088dcbd-640d-4b47-a30c-3c739ef0388e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:12:46,325] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:12:46,325] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:12:46,325] [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	100.0	932	935	95	inconclusive
Psychrobacter faecalis	strain=DSM 14664	GCA_016107575.1	180588	180588	type	True	96.7098	839	935	95	inconclusive
Psychrobacter luti	strain=CECT 5885	GCA_014192115.1	198481	198481	type	True	85.6976	764	935	95	below_threshold
Psychrobacter cryohalolentis	strain=K5	GCA_000013905.1	330922	330922	type	True	81.8149	664	935	95	below_threshold
Psychrobacter aquimaris	strain=DSM 16329	GCA_016107525.1	292733	292733	type	True	81.568	651	935	95	below_threshold
Psychrobacter arcticus	strain=273-4	GCA_000012305.1	334543	334543	type	True	81.27	587	935	95	below_threshold
Psychrobacter celer	strain=DSM 23510	GCA_016107555.1	306572	306572	type	True	81.0414	559	935	95	below_threshold
Psychrobacter halodurans	strain=F2608	GCA_017498075.1	2818439	2818439	type	True	80.8755	569	935	95	below_threshold
Psychrobacter glaciei	strain=KCTC 42280	GCA_014652895.1	619771	619771	type	True	80.8036	615	935	95	below_threshold
Psychrobacter namhaensis	strain=DSM 16330	GCA_016107545.1	292734	292734	type	True	80.611	590	935	95	below_threshold
Psychrobacter aquaticus	strain=CMS 56	GCA_000471625.1	248452	248452	type	True	80.3286	588	935	95	below_threshold
Psychrobacter frigidicola	strain=ACAM 304	GCA_007997305.1	45611	45611	type	True	79.0182	394	935	95	below_threshold
Psychrobacter coccoides	strain=F1192	GCA_017498085.1	2818440	2818440	type	True	78.665	432	935	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:12:46,330] [INFO] DFAST Taxonomy check result was written to GCF_014836505.1_ASM1483650v1_genomic.fna/tc_result.tsv
[2024-01-24 11:12:46,331] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:12:46,331] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:12:46,331] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd088dcbd-640d-4b47-a30c-3c739ef0388e/dqc_reference/checkm_data
[2024-01-24 11:12:46,333] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:12:46,369] [INFO] Task started: CheckM
[2024-01-24 11:12:46,369] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014836505.1_ASM1483650v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014836505.1_ASM1483650v1_genomic.fna/checkm_input GCF_014836505.1_ASM1483650v1_genomic.fna/checkm_result
[2024-01-24 11:13:13,244] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:13,245] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:13,263] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:13,263] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:13,264] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014836505.1_ASM1483650v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:13,264] [INFO] Task started: Blastn
[2024-01-24 11:13:13,265] [INFO] Running command: blastn -query GCF_014836505.1_ASM1483650v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd088dcbd-640d-4b47-a30c-3c739ef0388e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014836505.1_ASM1483650v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:14,396] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:14,400] [INFO] Selected 12 target genomes.
[2024-01-24 11:13:14,401] [INFO] Target genome list was writen to GCF_014836505.1_ASM1483650v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:14,410] [INFO] Task started: fastANI
[2024-01-24 11:13:14,410] [INFO] Running command: fastANI --query /var/lib/cwl/stg58835ba2-9d73-4622-8a60-8cfce9259fa8/GCF_014836505.1_ASM1483650v1_genomic.fna.gz --refList GCF_014836505.1_ASM1483650v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014836505.1_ASM1483650v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:23,740] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:23,756] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:23,757] [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	96.6834	840	935	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	93.1224	796	935	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	87.4367	802	935	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	87.0047	742	935	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	86.7359	760	935	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	86.4738	785	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904846175.1	s__Psychrobacter immobilis_E	86.3945	777	935	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	85.6976	764	935	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	82.0318	657	935	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	81.7996	667	935	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	81.595	649	935	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	80.6049	591	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	98.25	97.66	0.93	0.91	5	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:23,758] [INFO] GTDB search result was written to GCF_014836505.1_ASM1483650v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:23,759] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:23,764] [INFO] DFAST_QC result json was written to GCF_014836505.1_ASM1483650v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:23,765] [INFO] DFAST_QC completed!
[2024-01-24 11:13:23,765] [INFO] Total running time: 0h0m58s