[2024-01-24 13:45:46,703] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:46,706] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:46,707] [INFO] DQC Reference Directory: /var/lib/cwl/stg08cd2fa5-e4c8-4998-8646-d9aac9861c7b/dqc_reference
[2024-01-24 13:45:48,142] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:48,143] [INFO] Task started: Prodigal
[2024-01-24 13:45:48,143] [INFO] Running command: gunzip -c /var/lib/cwl/stg5d861ca1-f6c0-4587-9b0d-bf67401c760e/GCF_014652895.1_ASM1465289v1_genomic.fna.gz | prodigal -d GCF_014652895.1_ASM1465289v1_genomic.fna/cds.fna -a GCF_014652895.1_ASM1465289v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:45:56,217] [INFO] Task succeeded: Prodigal
[2024-01-24 13:45:56,218] [INFO] Task started: HMMsearch
[2024-01-24 13:45:56,218] [INFO] Running command: hmmsearch --tblout GCF_014652895.1_ASM1465289v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg08cd2fa5-e4c8-4998-8646-d9aac9861c7b/dqc_reference/reference_markers.hmm GCF_014652895.1_ASM1465289v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:45:56,584] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:45:56,585] [INFO] Found 6/6 markers.
[2024-01-24 13:45:56,620] [INFO] Query marker FASTA was written to GCF_014652895.1_ASM1465289v1_genomic.fna/markers.fasta
[2024-01-24 13:45:56,620] [INFO] Task started: Blastn
[2024-01-24 13:45:56,620] [INFO] Running command: blastn -query GCF_014652895.1_ASM1465289v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08cd2fa5-e4c8-4998-8646-d9aac9861c7b/dqc_reference/reference_markers.fasta -out GCF_014652895.1_ASM1465289v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:45:57,368] [INFO] Task succeeded: Blastn
[2024-01-24 13:45:57,373] [INFO] Selected 16 target genomes.
[2024-01-24 13:45:57,374] [INFO] Target genome list was writen to GCF_014652895.1_ASM1465289v1_genomic.fna/target_genomes.txt
[2024-01-24 13:45:57,396] [INFO] Task started: fastANI
[2024-01-24 13:45:57,397] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d861ca1-f6c0-4587-9b0d-bf67401c760e/GCF_014652895.1_ASM1465289v1_genomic.fna.gz --refList GCF_014652895.1_ASM1465289v1_genomic.fna/target_genomes.txt --output GCF_014652895.1_ASM1465289v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:09,202] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:09,203] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg08cd2fa5-e4c8-4998-8646-d9aac9861c7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:09,203] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg08cd2fa5-e4c8-4998-8646-d9aac9861c7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:09,217] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:09,217] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:09,217] [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 glaciei	strain=KCTC 42280	GCA_014652895.1	619771	619771	type	True	100.0	1114	1115	95	conclusive
Psychrobacter immobilis	strain=DSM 7229	GCA_003148585.1	498	498	suspected-type	True	83.4197	779	1115	95	below_threshold
Psychrobacter aquimaris	strain=DSM 16329	GCA_016107525.1	292733	292733	type	True	83.1633	775	1115	95	below_threshold
Psychrobacter fozii	strain=CECT 5889	GCA_003217155.1	198480	198480	type	True	83.1479	747	1115	95	below_threshold
Psychrobacter cibarius	strain=DSM 16327	GCA_016107535.1	282669	282669	type	True	83.0603	757	1115	95	below_threshold
Psychrobacter cryohalolentis	strain=K5	GCA_000013905.1	330922	330922	type	True	81.7876	681	1115	95	below_threshold
Psychrobacter pacificensis	strain=DSM 23406	GCA_900101915.1	112002	112002	type	True	81.4608	667	1115	95	below_threshold
Psychrobacter luti	strain=CECT 5885	GCA_014192115.1	198481	198481	type	True	81.448	661	1115	95	below_threshold
Psychrobacter namhaensis	strain=DSM 16330	GCA_016107545.1	292734	292734	type	True	81.3972	654	1115	95	below_threshold
Psychrobacter arcticus	strain=273-4	GCA_000012305.1	334543	334543	type	True	81.0359	584	1115	95	below_threshold
Psychrobacter faecalis	strain=DSM 14664	GCA_016107575.1	180588	180588	type	True	80.9481	616	1115	95	below_threshold
Psychrobacter communis	strain=Sa4CVA2	GCA_014836505.1	2762238	2762238	type	True	80.943	604	1115	95	below_threshold
Psychrobacter celer	strain=DSM 23510	GCA_016107555.1	306572	306572	type	True	80.6417	574	1115	95	below_threshold
Psychrobacter halodurans	strain=F2608	GCA_017498075.1	2818439	2818439	type	True	80.2808	560	1115	95	below_threshold
Psychrobacter coccoides	strain=F1192	GCA_017498085.1	2818440	2818440	type	True	78.6662	431	1115	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:09,243] [INFO] DFAST Taxonomy check result was written to GCF_014652895.1_ASM1465289v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:09,244] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:09,244] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:09,244] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg08cd2fa5-e4c8-4998-8646-d9aac9861c7b/dqc_reference/checkm_data
[2024-01-24 13:46:09,246] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:09,288] [INFO] Task started: CheckM
[2024-01-24 13:46:09,289] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652895.1_ASM1465289v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652895.1_ASM1465289v1_genomic.fna/checkm_input GCF_014652895.1_ASM1465289v1_genomic.fna/checkm_result
[2024-01-24 13:46:41,194] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:41,195] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:41,214] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:41,214] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:41,215] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652895.1_ASM1465289v1_genomic.fna/markers.fasta)
[2024-01-24 13:46:41,215] [INFO] Task started: Blastn
[2024-01-24 13:46:41,215] [INFO] Running command: blastn -query GCF_014652895.1_ASM1465289v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08cd2fa5-e4c8-4998-8646-d9aac9861c7b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652895.1_ASM1465289v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:42,447] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:42,453] [INFO] Selected 21 target genomes.
[2024-01-24 13:46:42,453] [INFO] Target genome list was writen to GCF_014652895.1_ASM1465289v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:42,790] [INFO] Task started: fastANI
[2024-01-24 13:46:42,790] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d861ca1-f6c0-4587-9b0d-bf67401c760e/GCF_014652895.1_ASM1465289v1_genomic.fna.gz --refList GCF_014652895.1_ASM1465289v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652895.1_ASM1465289v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:00,147] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:00,164] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:00,165] [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_014652895.1	s__Psychrobacter glaciei	100.0	1114	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.25	96.04	0.92	0.86	6	conclusive
GCF_013248965.1	s__Psychrobacter okhotskensis	87.0365	859	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.29	97.15	0.88	0.85	12	-
GCF_904846185.1	s__Psychrobacter immobilis_B	83.4023	810	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.3523	99.90	99.90	0.97	0.97	2	-
GCF_015864825.1	s__Psychrobacter sp015864825	83.3064	714	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015234355.1	s__Psychrobacter sp015234355	83.2659	746	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904846075.1	s__Psychrobacter glacincola_C	83.187	797	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.4049	96.53	96.53	0.88	0.88	2	-
GCF_016107525.1	s__Psychrobacter aquimaris	83.1741	775	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	98.04	97.20	0.92	0.89	5	-
GCF_003217155.1	s__Psychrobacter fozii	83.169	745	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	95.56	95.06	0.91	0.88	5	-
GCF_016107535.1	s__Psychrobacter cibarius	83.0584	757	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.3915	99.97	99.97	0.99	0.99	2	-
GCF_015277735.1	s__Psychrobacter sp015277735	82.9848	754	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	95.26	95.15	0.92	0.92	3	-
GCF_904846235.1	s__Psychrobacter immobilis_C	82.8013	719	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836735.1	s__Psychrobacter sp002836735	82.7535	740	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	95.08	95.08	0.86	0.86	2	-
GCF_904846705.1	s__Psychrobacter sp904846705	82.654	709	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009812035.1	s__Psychrobacter nivimaris_A	82.6228	729	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013905.1	s__Psychrobacter cryohalolentis	81.7983	680	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.64	96.60	0.93	0.89	9	-
GCF_904846345.1	s__Psychrobacter maritimus	81.7675	716	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	96.41	96.16	0.91	0.90	6	-
GCF_904846225.1	s__Psychrobacter immobilis_F	81.474	706	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008369115.1	s__Psychrobacter sp008369115	81.2719	650	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001593285.1	s__Psychrobacter sp001593285	81.226	629	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.71	97.71	0.93	0.93	2	-
GCF_900168255.1	s__Psychrobacter sp900168255	80.997	687	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	96.48	96.48	0.91	0.91	2	-
GCF_016107575.1	s__Psychrobacter faecalis	80.9237	617	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	96.81	95.77	0.89	0.85	16	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:00,167] [INFO] GTDB search result was written to GCF_014652895.1_ASM1465289v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:00,167] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:00,172] [INFO] DFAST_QC result json was written to GCF_014652895.1_ASM1465289v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:00,172] [INFO] DFAST_QC completed!
[2024-01-24 13:47:00,172] [INFO] Total running time: 0h1m13s