[2023-03-16 06:24:41,096] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:24:41,096] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:24:41,096] [INFO] DQC Reference Directory: /var/lib/cwl/stg0484e195-7f23-4dd9-b4c9-dc1728110f8c/dqc_reference
[2023-03-16 06:24:42,190] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:24:42,191] [INFO] Task started: Prodigal
[2023-03-16 06:24:42,191] [INFO] Running command: cat /var/lib/cwl/stgd91237de-dd0d-4dad-9ed5-592474cd4d5a/OceanDNA-b38598.fa | prodigal -d OceanDNA-b38598/cds.fna -a OceanDNA-b38598/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:24:54,908] [INFO] Task succeeded: Prodigal
[2023-03-16 06:24:54,908] [INFO] Task started: HMMsearch
[2023-03-16 06:24:54,908] [INFO] Running command: hmmsearch --tblout OceanDNA-b38598/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0484e195-7f23-4dd9-b4c9-dc1728110f8c/dqc_reference/reference_markers.hmm OceanDNA-b38598/protein.faa > /dev/null
[2023-03-16 06:24:55,073] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:24:55,074] [INFO] Found 6/6 markers.
[2023-03-16 06:24:55,089] [INFO] Query marker FASTA was written to OceanDNA-b38598/markers.fasta
[2023-03-16 06:24:55,090] [INFO] Task started: Blastn
[2023-03-16 06:24:55,090] [INFO] Running command: blastn -query OceanDNA-b38598/markers.fasta -db /var/lib/cwl/stg0484e195-7f23-4dd9-b4c9-dc1728110f8c/dqc_reference/reference_markers.fasta -out OceanDNA-b38598/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:24:55,675] [INFO] Task succeeded: Blastn
[2023-03-16 06:24:55,676] [INFO] Selected 12 target genomes.
[2023-03-16 06:24:55,676] [INFO] Target genome list was writen to OceanDNA-b38598/target_genomes.txt
[2023-03-16 06:24:55,683] [INFO] Task started: fastANI
[2023-03-16 06:24:55,684] [INFO] Running command: fastANI --query /var/lib/cwl/stgd91237de-dd0d-4dad-9ed5-592474cd4d5a/OceanDNA-b38598.fa --refList OceanDNA-b38598/target_genomes.txt --output OceanDNA-b38598/fastani_result.tsv --threads 1
[2023-03-16 06:25:03,544] [INFO] Task succeeded: fastANI
[2023-03-16 06:25:03,544] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0484e195-7f23-4dd9-b4c9-dc1728110f8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:25:03,544] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0484e195-7f23-4dd9-b4c9-dc1728110f8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:25:03,553] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:25:03,553] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 06:25:03,553] [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 cryohalolentis	strain=K5	GCA_000013905.1	330922	330922	type	True	89.0567	689	769	95	below_threshold
Psychrobacter arcticus	strain=273-4	GCA_000012305.1	334543	334543	type	True	88.6468	604	769	95	below_threshold
Psychrobacter luti	strain=CECT 5885	GCA_014192115.1	198481	198481	type	True	82.2527	565	769	95	below_threshold
Psychrobacter cibarius	strain=DSM 16327	GCA_016107535.1	282669	282669	type	True	81.3769	550	769	95	below_threshold
Psychrobacter immobilis	strain=DSM 7229	GCA_003148585.1	498	498	suspected-type	True	81.3354	555	769	95	below_threshold
Psychrobacter faecalis	strain=DSM 14664	GCA_016107575.1	180588	180588	type	True	81.2005	558	769	95	below_threshold
Psychrobacter communis	strain=Sa4CVA2	GCA_014836505.1	2762238	2762238	type	True	81.1208	544	769	95	below_threshold
Psychrobacter aquimaris	strain=DSM 16329	GCA_016107525.1	292733	292733	type	True	80.9202	546	769	95	below_threshold
Psychrobacter glaciei	strain=KCTC 42280	GCA_014652895.1	619771	619771	type	True	80.8404	533	769	95	below_threshold
Psychrobacter aquaticus	strain=CMS 56	GCA_000471625.1	248452	248452	type	True	80.087	504	769	95	below_threshold
Psychrobacter namhaensis	strain=DSM 16330	GCA_016107545.1	292734	292734	type	True	80.0039	479	769	95	below_threshold
Psychrobacter pacificensis	strain=DSM 23406	GCA_900101915.1	112002	112002	type	True	79.6541	458	769	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 06:25:03,553] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38598/tc_result.tsv
[2023-03-16 06:25:03,553] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:25:03,553] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:25:03,553] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0484e195-7f23-4dd9-b4c9-dc1728110f8c/dqc_reference/checkm_data
[2023-03-16 06:25:03,554] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:25:03,758] [INFO] Task started: CheckM
[2023-03-16 06:25:03,758] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38598/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38598/checkm_input OceanDNA-b38598/checkm_result
[2023-03-16 06:25:39,196] [INFO] Task succeeded: CheckM
[2023-03-16 06:25:39,197] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.73%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:25:39,199] [INFO] ===== Completeness check finished =====
[2023-03-16 06:25:39,199] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:25:39,199] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38598/markers.fasta)
[2023-03-16 06:25:39,200] [INFO] Task started: Blastn
[2023-03-16 06:25:39,200] [INFO] Running command: blastn -query OceanDNA-b38598/markers.fasta -db /var/lib/cwl/stg0484e195-7f23-4dd9-b4c9-dc1728110f8c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38598/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:25:39,994] [INFO] Task succeeded: Blastn
[2023-03-16 06:25:39,995] [INFO] Selected 13 target genomes.
[2023-03-16 06:25:39,995] [INFO] Target genome list was writen to OceanDNA-b38598/target_genomes_gtdb.txt
[2023-03-16 06:25:40,006] [INFO] Task started: fastANI
[2023-03-16 06:25:40,006] [INFO] Running command: fastANI --query /var/lib/cwl/stgd91237de-dd0d-4dad-9ed5-592474cd4d5a/OceanDNA-b38598.fa --refList OceanDNA-b38598/target_genomes_gtdb.txt --output OceanDNA-b38598/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:25:50,838] [INFO] Task succeeded: fastANI
[2023-03-16 06:25:50,846] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 06:25:50,846] [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_904846215.1	s__Psychrobacter glacincola_B	97.3129	736	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	96.12	96.12	0.93	0.93	2	conclusive
GCF_000013905.1	s__Psychrobacter cryohalolentis	89.0678	688	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.64	96.60	0.93	0.89	9	-
GCF_000012305.1	s__Psychrobacter arcticus	88.6468	604	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900168255.1	s__Psychrobacter sp900168255	84.1848	614	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	96.48	96.48	0.91	0.91	2	-
GCF_904846285.1	s__Psychrobacter immobilis_D	82.4305	572	769	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	82.2844	579	769	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	82.2789	596	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	96.41	96.16	0.91	0.90	6	-
GCF_014192115.1	s__Psychrobacter luti	82.2623	564	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_904846175.1	s__Psychrobacter immobilis_E	82.2459	572	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018448495.1	s__Psychrobacter sp018448495	81.3485	548	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.24	97.46	97.46	0.95	0.95	2	-
GCF_014861365.1	s__Psychrobacter sp014861365	80.9645	526	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	98.77	98.77	0.85	0.85	2	-
GCF_014652895.1	s__Psychrobacter glaciei	80.8524	532	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.25	96.04	0.92	0.86	6	-
GCF_002836735.1	s__Psychrobacter sp002836735	79.746	472	769	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	95.08	95.08	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-03-16 06:25:50,847] [INFO] GTDB search result was written to OceanDNA-b38598/result_gtdb.tsv
[2023-03-16 06:25:50,847] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:25:50,848] [INFO] DFAST_QC result json was written to OceanDNA-b38598/dqc_result.json
[2023-03-16 06:25:50,848] [INFO] DFAST_QC completed!
[2023-03-16 06:25:50,848] [INFO] Total running time: 0h1m10s