[2023-03-19 01:50:01,528] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:50:01,528] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:50:01,528] [INFO] DQC Reference Directory: /var/lib/cwl/stg19d3b76f-0fd7-4d26-bcbf-de813317e6d0/dqc_reference
[2023-03-19 01:50:02,652] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:50:02,653] [INFO] Task started: Prodigal
[2023-03-19 01:50:02,653] [INFO] Running command: cat /var/lib/cwl/stg5c9f5f10-22b0-4725-b1f5-48d4bc0c386d/OceanDNA-b38650.fa | prodigal -d OceanDNA-b38650/cds.fna -a OceanDNA-b38650/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:50:20,491] [INFO] Task succeeded: Prodigal
[2023-03-19 01:50:20,492] [INFO] Task started: HMMsearch
[2023-03-19 01:50:20,492] [INFO] Running command: hmmsearch --tblout OceanDNA-b38650/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19d3b76f-0fd7-4d26-bcbf-de813317e6d0/dqc_reference/reference_markers.hmm OceanDNA-b38650/protein.faa > /dev/null
[2023-03-19 01:50:20,704] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:50:20,704] [INFO] Found 6/6 markers.
[2023-03-19 01:50:20,723] [INFO] Query marker FASTA was written to OceanDNA-b38650/markers.fasta
[2023-03-19 01:50:20,725] [INFO] Task started: Blastn
[2023-03-19 01:50:20,725] [INFO] Running command: blastn -query OceanDNA-b38650/markers.fasta -db /var/lib/cwl/stg19d3b76f-0fd7-4d26-bcbf-de813317e6d0/dqc_reference/reference_markers.fasta -out OceanDNA-b38650/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:50:21,333] [INFO] Task succeeded: Blastn
[2023-03-19 01:50:21,334] [INFO] Selected 15 target genomes.
[2023-03-19 01:50:21,334] [INFO] Target genome list was writen to OceanDNA-b38650/target_genomes.txt
[2023-03-19 01:50:21,344] [INFO] Task started: fastANI
[2023-03-19 01:50:21,345] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c9f5f10-22b0-4725-b1f5-48d4bc0c386d/OceanDNA-b38650.fa --refList OceanDNA-b38650/target_genomes.txt --output OceanDNA-b38650/fastani_result.tsv --threads 1
[2023-03-19 01:50:31,923] [INFO] Task succeeded: fastANI
[2023-03-19 01:50:31,924] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19d3b76f-0fd7-4d26-bcbf-de813317e6d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:50:31,924] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19d3b76f-0fd7-4d26-bcbf-de813317e6d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:50:31,933] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:50:31,933] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 01:50:31,933] [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	84.6641	756	1017	95	below_threshold
Psychrobacter fozii	strain=CECT 5889	GCA_003217155.1	198480	198480	type	True	82.5634	724	1017	95	below_threshold
Psychrobacter glaciei	strain=KCTC 42280	GCA_014652895.1	619771	619771	type	True	82.3376	718	1017	95	below_threshold
Psychrobacter aquimaris	strain=DSM 16329	GCA_016107525.1	292733	292733	type	True	81.8934	702	1017	95	below_threshold
Psychrobacter immobilis	strain=DSM 7229	GCA_003148585.1	498	498	suspected-type	True	81.3901	680	1017	95	below_threshold
Psychrobacter cibarius	strain=DSM 16327	GCA_016107535.1	282669	282669	type	True	81.3639	642	1017	95	below_threshold
Psychrobacter namhaensis	strain=DSM 16330	GCA_016107545.1	292734	292734	type	True	81.349	601	1017	95	below_threshold
Psychrobacter aquaticus	strain=CMS 56	GCA_000471625.1	248452	248452	type	True	80.9227	638	1017	95	below_threshold
Psychrobacter luti	strain=CECT 5885	GCA_014192115.1	198481	198481	type	True	80.4091	561	1017	95	below_threshold
Psychrobacter celer	strain=DSM 23510	GCA_016107555.1	306572	306572	type	True	80.3323	572	1017	95	below_threshold
Psychrobacter cryohalolentis	strain=K5	GCA_000013905.1	330922	330922	type	True	80.2801	562	1017	95	below_threshold
Psychrobacter communis	strain=Sa4CVA2	GCA_014836505.1	2762238	2762238	type	True	80.2268	547	1017	95	below_threshold
Psychrobacter halodurans	strain=F2608	GCA_017498075.1	2818439	2818439	type	True	80.0951	535	1017	95	below_threshold
Psychrobacter coccoides	strain=F1192	GCA_017498085.1	2818440	2818440	type	True	78.5631	387	1017	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 01:50:31,934] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38650/tc_result.tsv
[2023-03-19 01:50:31,934] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:50:31,934] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:50:31,934] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19d3b76f-0fd7-4d26-bcbf-de813317e6d0/dqc_reference/checkm_data
[2023-03-19 01:50:31,935] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:50:31,940] [INFO] Task started: CheckM
[2023-03-19 01:50:31,940] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38650/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38650/checkm_input OceanDNA-b38650/checkm_result
[2023-03-19 01:51:16,641] [INFO] Task succeeded: CheckM
[2023-03-19 01:51:16,642] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:51:16,644] [INFO] ===== Completeness check finished =====
[2023-03-19 01:51:16,644] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:51:16,644] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38650/markers.fasta)
[2023-03-19 01:51:16,645] [INFO] Task started: Blastn
[2023-03-19 01:51:16,645] [INFO] Running command: blastn -query OceanDNA-b38650/markers.fasta -db /var/lib/cwl/stg19d3b76f-0fd7-4d26-bcbf-de813317e6d0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38650/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:51:17,631] [INFO] Task succeeded: Blastn
[2023-03-19 01:51:17,632] [INFO] Selected 13 target genomes.
[2023-03-19 01:51:17,632] [INFO] Target genome list was writen to OceanDNA-b38650/target_genomes_gtdb.txt
[2023-03-19 01:51:17,640] [INFO] Task started: fastANI
[2023-03-19 01:51:17,640] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c9f5f10-22b0-4725-b1f5-48d4bc0c386d/OceanDNA-b38650.fa --refList OceanDNA-b38650/target_genomes_gtdb.txt --output OceanDNA-b38650/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:51:27,177] [INFO] Task succeeded: fastANI
[2023-03-19 01:51:27,184] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 01:51:27,185] [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_002836505.1	s__Psychrobacter sp002836505	99.301	969	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.96	95.05	0.93	0.86	11	conclusive
GCF_904846235.1	s__Psychrobacter immobilis_C	94.9693	903	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013414195.1	s__Psychrobacter sp013414195	94.8694	899	1017	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	94.8589	891	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	95.08	95.08	0.86	0.86	2	-
GCA_000586435.1	s__Psychrobacter sp000586435	94.8164	868	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836715.1	s__Psychrobacter sp002836715	94.7535	864	1017	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	94.7006	901	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904846705.1	s__Psychrobacter sp904846705	94.5982	888	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002377945.1	s__Psychrobacter sp002377945	94.3375	904	1017	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	94.3312	896	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904846625.1	s__Psychrobacter sp000586415	94.1678	897	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	99.91	99.91	1.00	1.00	2	-
GCF_001435845.1	s__Psychrobacter sp001435845	94.0998	902	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904846645.1	s__Psychrobacter sp904846645	93.8924	888	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:51:27,185] [INFO] GTDB search result was written to OceanDNA-b38650/result_gtdb.tsv
[2023-03-19 01:51:27,185] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:51:27,186] [INFO] DFAST_QC result json was written to OceanDNA-b38650/dqc_result.json
[2023-03-19 01:51:27,186] [INFO] DFAST_QC completed!
[2023-03-19 01:51:27,186] [INFO] Total running time: 0h1m26s