[2023-03-19 05:32:20,809] [INFO] DFAST_QC pipeline started.
[2023-03-19 05:32:20,809] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 05:32:20,809] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5812ba1-5c7a-493c-8220-833a56de3478/dqc_reference
[2023-03-19 05:32:22,377] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 05:32:22,378] [INFO] Task started: Prodigal
[2023-03-19 05:32:22,379] [INFO] Running command: cat /var/lib/cwl/stga03842e3-4ec3-4f0b-9ed8-c67e42af7661/OceanDNA-b41178.fa | prodigal -d OceanDNA-b41178/cds.fna -a OceanDNA-b41178/protein.faa -g 11 -q > /dev/null
[2023-03-19 05:32:42,848] [INFO] Task succeeded: Prodigal
[2023-03-19 05:32:42,848] [INFO] Task started: HMMsearch
[2023-03-19 05:32:42,848] [INFO] Running command: hmmsearch --tblout OceanDNA-b41178/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5812ba1-5c7a-493c-8220-833a56de3478/dqc_reference/reference_markers.hmm OceanDNA-b41178/protein.faa > /dev/null
[2023-03-19 05:32:43,044] [INFO] Task succeeded: HMMsearch
[2023-03-19 05:32:43,044] [INFO] Found 6/6 markers.
[2023-03-19 05:32:43,067] [INFO] Query marker FASTA was written to OceanDNA-b41178/markers.fasta
[2023-03-19 05:32:43,068] [INFO] Task started: Blastn
[2023-03-19 05:32:43,068] [INFO] Running command: blastn -query OceanDNA-b41178/markers.fasta -db /var/lib/cwl/stgf5812ba1-5c7a-493c-8220-833a56de3478/dqc_reference/reference_markers.fasta -out OceanDNA-b41178/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:32:43,886] [INFO] Task succeeded: Blastn
[2023-03-19 05:32:43,886] [INFO] Selected 11 target genomes.
[2023-03-19 05:32:43,887] [INFO] Target genome list was writen to OceanDNA-b41178/target_genomes.txt
[2023-03-19 05:32:43,893] [INFO] Task started: fastANI
[2023-03-19 05:32:43,893] [INFO] Running command: fastANI --query /var/lib/cwl/stga03842e3-4ec3-4f0b-9ed8-c67e42af7661/OceanDNA-b41178.fa --refList OceanDNA-b41178/target_genomes.txt --output OceanDNA-b41178/fastani_result.tsv --threads 1
[2023-03-19 05:32:52,216] [INFO] Task succeeded: fastANI
[2023-03-19 05:32:52,217] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5812ba1-5c7a-493c-8220-833a56de3478/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 05:32:52,217] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5812ba1-5c7a-493c-8220-833a56de3478/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 05:32:52,224] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 05:32:52,225] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 05:32:52,225] [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 pachastrellae	strain=CCUG 46540	GCA_001989375.1	254161	254161	type	True	89.1413	893	1108	95	below_threshold
Halopseudomonas pachastrellae	strain=JCM 12285	GCA_900114765.1	254161	254161	type	True	89.0872	930	1108	95	below_threshold
Halopseudomonas aestusnigri	strain=CECT 8317	GCA_900108005.1	857252	857252	type	True	83.0533	745	1108	95	below_threshold
Halopseudomonas aestusnigri	strain=VGXO14	GCA_002197985.1	857252	857252	type	True	83.0531	747	1108	95	below_threshold
Halopseudomonas oceani	strain=CGMCC 1.15195	GCA_014641295.1	1708783	1708783	type	True	82.779	740	1108	95	below_threshold
Halopseudomonas oceani	strain=DSM 100277	GCA_002903165.1	1708783	1708783	type	True	82.7216	736	1108	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	77.8344	275	1108	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	77.8288	272	1108	95	below_threshold
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	77.7807	275	1108	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	77.7488	304	1108	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	77.5856	305	1108	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 05:32:52,225] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41178/tc_result.tsv
[2023-03-19 05:32:52,225] [INFO] ===== Taxonomy check completed =====
[2023-03-19 05:32:52,225] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 05:32:52,225] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5812ba1-5c7a-493c-8220-833a56de3478/dqc_reference/checkm_data
[2023-03-19 05:32:52,226] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 05:32:52,231] [INFO] Task started: CheckM
[2023-03-19 05:32:52,231] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41178/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41178/checkm_input OceanDNA-b41178/checkm_result
[2023-03-19 05:33:43,797] [INFO] Task succeeded: CheckM
[2023-03-19 05:33:43,798] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 05:33:43,800] [INFO] ===== Completeness check finished =====
[2023-03-19 05:33:43,801] [INFO] ===== Start GTDB Search =====
[2023-03-19 05:33:43,801] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41178/markers.fasta)
[2023-03-19 05:33:43,801] [INFO] Task started: Blastn
[2023-03-19 05:33:43,801] [INFO] Running command: blastn -query OceanDNA-b41178/markers.fasta -db /var/lib/cwl/stgf5812ba1-5c7a-493c-8220-833a56de3478/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41178/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:33:45,253] [INFO] Task succeeded: Blastn
[2023-03-19 05:33:45,254] [INFO] Selected 8 target genomes.
[2023-03-19 05:33:45,254] [INFO] Target genome list was writen to OceanDNA-b41178/target_genomes_gtdb.txt
[2023-03-19 05:33:45,259] [INFO] Task started: fastANI
[2023-03-19 05:33:45,260] [INFO] Running command: fastANI --query /var/lib/cwl/stga03842e3-4ec3-4f0b-9ed8-c67e42af7661/OceanDNA-b41178.fa --refList OceanDNA-b41178/target_genomes_gtdb.txt --output OceanDNA-b41178/fastani_result_gtdb.tsv --threads 1
[2023-03-19 05:33:51,772] [INFO] Task succeeded: fastANI
[2023-03-19 05:33:51,778] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 05:33:51,778] [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
GCA_002296055.1	s__Pseudomonas_D sp002296055	99.6525	914	1108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900114765.1	s__Pseudomonas_D pachastrellae	89.0872	930	1108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	96.15	95.72	0.86	0.72	17	-
GCF_003444685.1	s__Pseudomonas_D gallaeciensis	86.497	931	1108	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_002197985.1	s__Pseudomonas_D aestusnigri	83.0646	746	1108	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_002903165.1	s__Pseudomonas_D oceani	82.7216	736	1108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900105255.1	s__Pseudomonas_D sabulinigri	80.5307	618	1108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840055.1	s__Pseudomonas_D sp002840055	78.7218	275	1108	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_008365385.1	s__Pseudomonas_D laoshanensis	78.302	380	1108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	96.00	95.95	0.96	0.95	3	-
--------------------------------------------------------------------------------
[2023-03-19 05:33:51,778] [INFO] GTDB search result was written to OceanDNA-b41178/result_gtdb.tsv
[2023-03-19 05:33:51,778] [INFO] ===== GTDB Search completed =====
[2023-03-19 05:33:51,780] [INFO] DFAST_QC result json was written to OceanDNA-b41178/dqc_result.json
[2023-03-19 05:33:51,780] [INFO] DFAST_QC completed!
[2023-03-19 05:33:51,780] [INFO] Total running time: 0h1m31s