[2023-03-17 09:59:01,183] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:59:01,184] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:59:01,184] [INFO] DQC Reference Directory: /var/lib/cwl/stga239595f-66db-4cbf-8cf9-0f7c87706d1d/dqc_reference
[2023-03-17 09:59:02,530] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:59:02,530] [INFO] Task started: Prodigal
[2023-03-17 09:59:02,531] [INFO] Running command: cat /var/lib/cwl/stg2cacb83f-4f23-4653-a7d2-76d669394756/OceanDNA-b38606.fa | prodigal -d OceanDNA-b38606/cds.fna -a OceanDNA-b38606/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:59:15,119] [INFO] Task succeeded: Prodigal
[2023-03-17 09:59:15,120] [INFO] Task started: HMMsearch
[2023-03-17 09:59:15,120] [INFO] Running command: hmmsearch --tblout OceanDNA-b38606/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga239595f-66db-4cbf-8cf9-0f7c87706d1d/dqc_reference/reference_markers.hmm OceanDNA-b38606/protein.faa > /dev/null
[2023-03-17 09:59:15,306] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:59:15,307] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg2cacb83f-4f23-4653-a7d2-76d669394756/OceanDNA-b38606.fa]
[2023-03-17 09:59:15,321] [INFO] Query marker FASTA was written to OceanDNA-b38606/markers.fasta
[2023-03-17 09:59:15,322] [INFO] Task started: Blastn
[2023-03-17 09:59:15,322] [INFO] Running command: blastn -query OceanDNA-b38606/markers.fasta -db /var/lib/cwl/stga239595f-66db-4cbf-8cf9-0f7c87706d1d/dqc_reference/reference_markers.fasta -out OceanDNA-b38606/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:59:15,872] [INFO] Task succeeded: Blastn
[2023-03-17 09:59:15,872] [INFO] Selected 12 target genomes.
[2023-03-17 09:59:15,873] [INFO] Target genome list was writen to OceanDNA-b38606/target_genomes.txt
[2023-03-17 09:59:15,906] [INFO] Task started: fastANI
[2023-03-17 09:59:15,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cacb83f-4f23-4653-a7d2-76d669394756/OceanDNA-b38606.fa --refList OceanDNA-b38606/target_genomes.txt --output OceanDNA-b38606/fastani_result.tsv --threads 1
[2023-03-17 09:59:23,729] [INFO] Task succeeded: fastANI
[2023-03-17 09:59:23,729] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga239595f-66db-4cbf-8cf9-0f7c87706d1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:59:23,729] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga239595f-66db-4cbf-8cf9-0f7c87706d1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:59:23,964] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 09:59:23,965] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 09:59:23,965] [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	96.9381	732	765	95	conclusive
Psychrobacter arcticus	strain=273-4	GCA_000012305.1	334543	334543	type	True	88.6256	604	765	95	below_threshold
Psychrobacter luti	strain=CECT 5885	GCA_014192115.1	198481	198481	type	True	82.6692	582	765	95	below_threshold
Psychrobacter immobilis	strain=DSM 7229	GCA_003148585.1	498	498	suspected-type	True	82.0207	550	765	95	below_threshold
Psychrobacter cibarius	strain=DSM 16327	GCA_016107535.1	282669	282669	type	True	82.0089	548	765	95	below_threshold
Psychrobacter aquimaris	strain=DSM 16329	GCA_016107525.1	292733	292733	type	True	81.4447	545	765	95	below_threshold
Psychrobacter communis	strain=Sa4CVA2	GCA_014836505.1	2762238	2762238	type	True	81.2216	537	765	95	below_threshold
Psychrobacter namhaensis	strain=DSM 16330	GCA_016107545.1	292734	292734	type	True	79.9502	462	765	95	below_threshold
Psychrobacter halodurans	strain=F2608	GCA_017498075.1	2818439	2818439	type	True	79.3364	410	765	95	below_threshold
Psychrobacter celer	strain=DSM 23510	GCA_016107555.1	306572	306572	type	True	79.06	414	765	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 09:59:23,965] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38606/tc_result.tsv
[2023-03-17 09:59:23,965] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:59:23,965] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:59:23,965] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga239595f-66db-4cbf-8cf9-0f7c87706d1d/dqc_reference/checkm_data
[2023-03-17 09:59:23,966] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:59:23,970] [INFO] Task started: CheckM
[2023-03-17 09:59:23,970] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38606/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38606/checkm_input OceanDNA-b38606/checkm_result
[2023-03-17 09:59:59,090] [INFO] Task succeeded: CheckM
[2023-03-17 09:59:59,091] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.88%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:59:59,092] [INFO] ===== Completeness check finished =====
[2023-03-17 09:59:59,093] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:59:59,093] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38606/markers.fasta)
[2023-03-17 09:59:59,094] [INFO] Task started: Blastn
[2023-03-17 09:59:59,094] [INFO] Running command: blastn -query OceanDNA-b38606/markers.fasta -db /var/lib/cwl/stga239595f-66db-4cbf-8cf9-0f7c87706d1d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38606/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:59:59,918] [INFO] Task succeeded: Blastn
[2023-03-17 09:59:59,919] [INFO] Selected 12 target genomes.
[2023-03-17 09:59:59,919] [INFO] Target genome list was writen to OceanDNA-b38606/target_genomes_gtdb.txt
[2023-03-17 10:00:00,164] [INFO] Task started: fastANI
[2023-03-17 10:00:00,164] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cacb83f-4f23-4653-a7d2-76d669394756/OceanDNA-b38606.fa --refList OceanDNA-b38606/target_genomes_gtdb.txt --output OceanDNA-b38606/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:00:08,377] [INFO] Task succeeded: fastANI
[2023-03-17 10:00:08,384] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 10:00:08,385] [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_000013905.1	s__Psychrobacter cryohalolentis	96.9653	731	765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.64	96.60	0.93	0.89	9	conclusive
GCF_904846215.1	s__Psychrobacter glacincola_B	89.0378	670	765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	96.12	96.12	0.93	0.93	2	-
GCF_000012305.1	s__Psychrobacter arcticus	88.6256	604	765	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	83.1247	616	765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	96.48	96.48	0.91	0.91	2	-
GCF_904846345.1	s__Psychrobacter maritimus	82.4526	604	765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	96.41	96.16	0.91	0.90	6	-
GCF_904846285.1	s__Psychrobacter immobilis_D	82.3421	561	765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904846615.1	s__Psychrobacter sp000586455	82.143	550	765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.4083	99.93	99.93	1.00	1.00	2	-
GCF_000586475.1	s__Psychrobacter sp000586475	82.1055	547	765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.2677	98.16	96.39	0.95	0.90	3	-
GCF_001435295.1	s__Psychrobacter sp001435295	82.006	565	765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.4083	N/A	N/A	N/A	N/A	1	-
GCF_904846185.1	s__Psychrobacter immobilis_B	81.9946	578	765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.3523	99.90	99.90	0.97	0.97	2	-
GCA_018448495.1	s__Psychrobacter sp018448495	81.9421	559	765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.24	97.46	97.46	0.95	0.95	2	-
GCF_016107525.1	s__Psychrobacter aquimaris	81.4447	545	765	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	98.04	97.20	0.92	0.89	5	-
--------------------------------------------------------------------------------
[2023-03-17 10:00:08,386] [INFO] GTDB search result was written to OceanDNA-b38606/result_gtdb.tsv
[2023-03-17 10:00:08,388] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:00:08,394] [INFO] DFAST_QC result json was written to OceanDNA-b38606/dqc_result.json
[2023-03-17 10:00:08,394] [INFO] DFAST_QC completed!
[2023-03-17 10:00:08,394] [INFO] Total running time: 0h1m7s