[2024-01-25 17:51:50,766] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:51:50,767] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:51:50,767] [INFO] DQC Reference Directory: /var/lib/cwl/stgd093f4e4-2e1f-4d46-9998-81f5d663431e/dqc_reference
[2024-01-25 17:51:51,916] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:51:51,917] [INFO] Task started: Prodigal
[2024-01-25 17:51:51,917] [INFO] Running command: gunzip -c /var/lib/cwl/stg9bdbbcb0-9213-4495-a3bf-660bfc981a92/GCF_030160475.1_ASM3016047v1_genomic.fna.gz | prodigal -d GCF_030160475.1_ASM3016047v1_genomic.fna/cds.fna -a GCF_030160475.1_ASM3016047v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:51:58,378] [INFO] Task succeeded: Prodigal
[2024-01-25 17:51:58,378] [INFO] Task started: HMMsearch
[2024-01-25 17:51:58,378] [INFO] Running command: hmmsearch --tblout GCF_030160475.1_ASM3016047v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd093f4e4-2e1f-4d46-9998-81f5d663431e/dqc_reference/reference_markers.hmm GCF_030160475.1_ASM3016047v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:51:58,600] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:51:58,601] [INFO] Found 6/6 markers.
[2024-01-25 17:51:58,624] [INFO] Query marker FASTA was written to GCF_030160475.1_ASM3016047v1_genomic.fna/markers.fasta
[2024-01-25 17:51:58,625] [INFO] Task started: Blastn
[2024-01-25 17:51:58,625] [INFO] Running command: blastn -query GCF_030160475.1_ASM3016047v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd093f4e4-2e1f-4d46-9998-81f5d663431e/dqc_reference/reference_markers.fasta -out GCF_030160475.1_ASM3016047v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:59,240] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:59,242] [INFO] Selected 14 target genomes.
[2024-01-25 17:51:59,243] [INFO] Target genome list was writen to GCF_030160475.1_ASM3016047v1_genomic.fna/target_genomes.txt
[2024-01-25 17:51:59,251] [INFO] Task started: fastANI
[2024-01-25 17:51:59,251] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bdbbcb0-9213-4495-a3bf-660bfc981a92/GCF_030160475.1_ASM3016047v1_genomic.fna.gz --refList GCF_030160475.1_ASM3016047v1_genomic.fna/target_genomes.txt --output GCF_030160475.1_ASM3016047v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:52:09,021] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:09,021] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd093f4e4-2e1f-4d46-9998-81f5d663431e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:52:09,021] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd093f4e4-2e1f-4d46-9998-81f5d663431e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:52:09,031] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:52:09,032] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:52:09,032] [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 pacificensis	strain=DSM 23406	GCA_900101915.1	112002	112002	type	True	99.9909	984	1009	95	conclusive
Psychrobacter celer	strain=DSM 23510	GCA_016107555.1	306572	306572	type	True	82.9184	602	1009	95	below_threshold
Psychrobacter aquimaris	strain=DSM 16329	GCA_016107525.1	292733	292733	type	True	82.2247	689	1009	95	below_threshold
Psychrobacter glaciei	strain=KCTC 42280	GCA_014652895.1	619771	619771	type	True	81.6132	666	1009	95	below_threshold
Psychrobacter namhaensis	strain=DSM 16330	GCA_016107545.1	292734	292734	type	True	81.4139	638	1009	95	below_threshold
Psychrobacter aquaticus	strain=CMS 56	GCA_000471625.1	248452	248452	type	True	81.3216	618	1009	95	below_threshold
Psychrobacter halodurans	strain=F2608	GCA_017498075.1	2818439	2818439	type	True	81.31	550	1009	95	below_threshold
Psychrobacter immobilis	strain=DSM 7229	GCA_003148585.1	498	498	suspected-type	True	81.2763	646	1009	95	below_threshold
Psychrobacter fozii	strain=CECT 5889	GCA_003217155.1	198480	198480	type	True	81.0913	642	1009	95	below_threshold
Psychrobacter cibarius	strain=DSM 16327	GCA_016107535.1	282669	282669	type	True	81.045	649	1009	95	below_threshold
Psychrobacter communis	strain=Sa4CVA2	GCA_014836505.1	2762238	2762238	type	True	80.0784	542	1009	95	below_threshold
Psychrobacter arcticus	strain=273-4	GCA_000012305.1	334543	334543	type	True	79.9415	511	1009	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:52:09,033] [INFO] DFAST Taxonomy check result was written to GCF_030160475.1_ASM3016047v1_genomic.fna/tc_result.tsv
[2024-01-25 17:52:09,033] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:52:09,033] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:52:09,034] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd093f4e4-2e1f-4d46-9998-81f5d663431e/dqc_reference/checkm_data
[2024-01-25 17:52:09,034] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:52:09,066] [INFO] Task started: CheckM
[2024-01-25 17:52:09,067] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030160475.1_ASM3016047v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030160475.1_ASM3016047v1_genomic.fna/checkm_input GCF_030160475.1_ASM3016047v1_genomic.fna/checkm_result
[2024-01-25 17:52:33,090] [INFO] Task succeeded: CheckM
[2024-01-25 17:52:33,091] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:52:33,130] [INFO] ===== Completeness check finished =====
[2024-01-25 17:52:33,131] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:52:33,131] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030160475.1_ASM3016047v1_genomic.fna/markers.fasta)
[2024-01-25 17:52:33,131] [INFO] Task started: Blastn
[2024-01-25 17:52:33,131] [INFO] Running command: blastn -query GCF_030160475.1_ASM3016047v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd093f4e4-2e1f-4d46-9998-81f5d663431e/dqc_reference/reference_markers_gtdb.fasta -out GCF_030160475.1_ASM3016047v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:34,213] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:34,215] [INFO] Selected 12 target genomes.
[2024-01-25 17:52:34,215] [INFO] Target genome list was writen to GCF_030160475.1_ASM3016047v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:52:34,225] [INFO] Task started: fastANI
[2024-01-25 17:52:34,225] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bdbbcb0-9213-4495-a3bf-660bfc981a92/GCF_030160475.1_ASM3016047v1_genomic.fna.gz --refList GCF_030160475.1_ASM3016047v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030160475.1_ASM3016047v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:52:43,413] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:43,421] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:52:43,421] [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_900101915.1	s__Psychrobacter pacificensis	99.9909	984	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.2282	98.35	97.54	0.93	0.90	8	conclusive
GCF_001444505.1	s__Psychrobacter piscatorii	96.1724	833	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.2282	97.27	96.69	0.93	0.91	3	-
GCF_904846415.1	s__Psychrobacter piscatorii_A	92.3624	851	1009	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	84.9861	772	1009	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	84.9615	788	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	95.08	95.08	0.86	0.86	2	-
GCF_013414195.1	s__Psychrobacter sp013414195	84.4943	788	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000586435.1	s__Psychrobacter sp000586435	84.3324	749	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014770435.1	s__Psychrobacter sp014770435	84.3167	771	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350005.1	s__Psychrobacter proteolyticus_A	84.2948	781	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	99.98	99.95	0.99	0.99	4	-
GCF_001435845.1	s__Psychrobacter sp001435845	84.2743	776	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900163785.1	s__Psychrobacter alimentarius	81.9257	621	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.11	97.08	0.93	0.93	3	-
GCA_001411745.2	s__Psychrobacter glacincola_A	81.0401	640	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.4049	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:52:43,425] [INFO] GTDB search result was written to GCF_030160475.1_ASM3016047v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:52:43,425] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:52:43,432] [INFO] DFAST_QC result json was written to GCF_030160475.1_ASM3016047v1_genomic.fna/dqc_result.json
[2024-01-25 17:52:43,432] [INFO] DFAST_QC completed!
[2024-01-25 17:52:43,432] [INFO] Total running time: 0h0m53s