[2023-03-18 00:58:44,625] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:58:44,625] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:58:44,626] [INFO] DQC Reference Directory: /var/lib/cwl/stg0523caf2-3d54-4dae-9e94-272bd537ba88/dqc_reference
[2023-03-18 00:58:46,296] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:58:46,296] [INFO] Task started: Prodigal
[2023-03-18 00:58:46,296] [INFO] Running command: cat /var/lib/cwl/stgfb07525d-dee7-4fed-a189-82c86d60a4d3/OceanDNA-b41140.fa | prodigal -d OceanDNA-b41140/cds.fna -a OceanDNA-b41140/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:59:00,542] [INFO] Task succeeded: Prodigal
[2023-03-18 00:59:00,542] [INFO] Task started: HMMsearch
[2023-03-18 00:59:00,542] [INFO] Running command: hmmsearch --tblout OceanDNA-b41140/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0523caf2-3d54-4dae-9e94-272bd537ba88/dqc_reference/reference_markers.hmm OceanDNA-b41140/protein.faa > /dev/null
[2023-03-18 00:59:00,743] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:59:00,744] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgfb07525d-dee7-4fed-a189-82c86d60a4d3/OceanDNA-b41140.fa]
[2023-03-18 00:59:00,765] [INFO] Query marker FASTA was written to OceanDNA-b41140/markers.fasta
[2023-03-18 00:59:00,766] [INFO] Task started: Blastn
[2023-03-18 00:59:00,766] [INFO] Running command: blastn -query OceanDNA-b41140/markers.fasta -db /var/lib/cwl/stg0523caf2-3d54-4dae-9e94-272bd537ba88/dqc_reference/reference_markers.fasta -out OceanDNA-b41140/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:59:01,366] [INFO] Task succeeded: Blastn
[2023-03-18 00:59:01,367] [INFO] Selected 10 target genomes.
[2023-03-18 00:59:01,367] [INFO] Target genome list was writen to OceanDNA-b41140/target_genomes.txt
[2023-03-18 00:59:01,374] [INFO] Task started: fastANI
[2023-03-18 00:59:01,374] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb07525d-dee7-4fed-a189-82c86d60a4d3/OceanDNA-b41140.fa --refList OceanDNA-b41140/target_genomes.txt --output OceanDNA-b41140/fastani_result.tsv --threads 1
[2023-03-18 00:59:07,696] [INFO] Task succeeded: fastANI
[2023-03-18 00:59:07,697] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0523caf2-3d54-4dae-9e94-272bd537ba88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:59:07,697] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0523caf2-3d54-4dae-9e94-272bd537ba88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:59:07,704] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2023-03-18 00:59:07,704] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 00:59:07,704] [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
Halopseudomonas oceani	strain=DSM 100277	GCA_002903165.1	1708783	1708783	type	True	98.6747	725	750	95	conclusive
Halopseudomonas oceani	strain=CGMCC 1.15195	GCA_014641295.1	1708783	1708783	type	True	98.653	725	750	95	conclusive
Halopseudomonas aestusnigri	strain=CECT 8317	GCA_900108005.1	857252	857252	type	True	86.3309	635	750	95	below_threshold
Halopseudomonas aestusnigri	strain=VGXO14	GCA_002197985.1	857252	857252	type	True	86.3014	642	750	95	below_threshold
Halopseudomonas pachastrellae	strain=JCM 12285	GCA_900114765.1	254161	254161	type	True	82.2904	557	750	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	77.5698	177	750	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	77.5678	177	750	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	77.5432	190	750	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	77.5256	194	750	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	77.5168	199	750	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:59:07,705] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41140/tc_result.tsv
[2023-03-18 00:59:07,705] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:59:07,705] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:59:07,705] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0523caf2-3d54-4dae-9e94-272bd537ba88/dqc_reference/checkm_data
[2023-03-18 00:59:07,706] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:59:07,785] [INFO] Task started: CheckM
[2023-03-18 00:59:07,785] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41140/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41140/checkm_input OceanDNA-b41140/checkm_result
[2023-03-18 00:59:45,906] [INFO] Task succeeded: CheckM
[2023-03-18 00:59:45,907] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:59:45,911] [INFO] ===== Completeness check finished =====
[2023-03-18 00:59:45,911] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:59:45,912] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41140/markers.fasta)
[2023-03-18 00:59:45,912] [INFO] Task started: Blastn
[2023-03-18 00:59:45,913] [INFO] Running command: blastn -query OceanDNA-b41140/markers.fasta -db /var/lib/cwl/stg0523caf2-3d54-4dae-9e94-272bd537ba88/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41140/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:59:46,852] [INFO] Task succeeded: Blastn
[2023-03-18 00:59:46,855] [INFO] Selected 6 target genomes.
[2023-03-18 00:59:46,855] [INFO] Target genome list was writen to OceanDNA-b41140/target_genomes_gtdb.txt
[2023-03-18 00:59:46,862] [INFO] Task started: fastANI
[2023-03-18 00:59:46,862] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb07525d-dee7-4fed-a189-82c86d60a4d3/OceanDNA-b41140.fa --refList OceanDNA-b41140/target_genomes_gtdb.txt --output OceanDNA-b41140/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:59:51,320] [INFO] Task succeeded: fastANI
[2023-03-18 00:59:51,324] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:59:51,325] [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_002903165.1	s__Pseudomonas_D oceani	98.6747	725	750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_002197985.1	s__Pseudomonas_D aestusnigri	86.3014	642	750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.11	96.74	0.91	0.81	25	-
GCF_003444685.1	s__Pseudomonas_D gallaeciensis	82.5255	572	750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.87	97.82	0.88	0.85	8	-
GCF_900114765.1	s__Pseudomonas_D pachastrellae	82.2937	557	750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	96.15	95.72	0.86	0.72	17	-
GCA_002296055.1	s__Pseudomonas_D sp002296055	81.4235	457	750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105255.1	s__Pseudomonas_D sabulinigri	79.6517	409	750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:59:51,326] [INFO] GTDB search result was written to OceanDNA-b41140/result_gtdb.tsv
[2023-03-18 00:59:51,326] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:59:51,328] [INFO] DFAST_QC result json was written to OceanDNA-b41140/dqc_result.json
[2023-03-18 00:59:51,328] [INFO] DFAST_QC completed!
[2023-03-18 00:59:51,328] [INFO] Total running time: 0h1m7s