[2023-03-15 16:28:44,760] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:28:44,762] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:28:44,762] [INFO] DQC Reference Directory: /var/lib/cwl/stg76208f34-3af8-45d7-b9eb-934b31bf9db5/dqc_reference
[2023-03-15 16:28:45,896] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:28:45,896] [INFO] Task started: Prodigal
[2023-03-15 16:28:45,896] [INFO] Running command: cat /var/lib/cwl/stgf705bcc8-8481-46ad-b7f9-eb829c03e014/OceanDNA-b40951.fa | prodigal -d OceanDNA-b40951/cds.fna -a OceanDNA-b40951/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:29:06,421] [INFO] Task succeeded: Prodigal
[2023-03-15 16:29:06,421] [INFO] Task started: HMMsearch
[2023-03-15 16:29:06,421] [INFO] Running command: hmmsearch --tblout OceanDNA-b40951/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76208f34-3af8-45d7-b9eb-934b31bf9db5/dqc_reference/reference_markers.hmm OceanDNA-b40951/protein.faa > /dev/null
[2023-03-15 16:29:06,637] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:29:06,638] [INFO] Found 6/6 markers.
[2023-03-15 16:29:06,669] [INFO] Query marker FASTA was written to OceanDNA-b40951/markers.fasta
[2023-03-15 16:29:06,670] [INFO] Task started: Blastn
[2023-03-15 16:29:06,670] [INFO] Running command: blastn -query OceanDNA-b40951/markers.fasta -db /var/lib/cwl/stg76208f34-3af8-45d7-b9eb-934b31bf9db5/dqc_reference/reference_markers.fasta -out OceanDNA-b40951/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:29:07,617] [INFO] Task succeeded: Blastn
[2023-03-15 16:29:07,619] [INFO] Selected 15 target genomes.
[2023-03-15 16:29:07,619] [INFO] Target genome list was writen to OceanDNA-b40951/target_genomes.txt
[2023-03-15 16:29:07,626] [INFO] Task started: fastANI
[2023-03-15 16:29:07,627] [INFO] Running command: fastANI --query /var/lib/cwl/stgf705bcc8-8481-46ad-b7f9-eb829c03e014/OceanDNA-b40951.fa --refList OceanDNA-b40951/target_genomes.txt --output OceanDNA-b40951/fastani_result.tsv --threads 1
[2023-03-15 16:29:20,943] [INFO] Task succeeded: fastANI
[2023-03-15 16:29:20,943] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76208f34-3af8-45d7-b9eb-934b31bf9db5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:29:20,943] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76208f34-3af8-45d7-b9eb-934b31bf9db5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:29:20,953] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2023-03-15 16:29:20,953] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 16:29:20,953] [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
Stutzerimonas balearica	strain=DSM 6083	GCA_900103375.1	74829	74829	type	True	98.4407	972	1069	95	conclusive
Stutzerimonas balearica	strain=DSM6083 (=SP1402)	GCA_000818015.1	74829	74829	type	True	98.4057	977	1069	95	conclusive
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	84.0875	798	1069	95	below_threshold
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	84.0821	791	1069	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	83.7225	774	1069	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	83.7198	777	1069	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	83.7062	777	1069	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	83.7046	788	1069	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	83.6924	775	1069	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	83.4424	739	1069	95	below_threshold
Pseudomonas songnenensis	strain=DSM 27560T	GCA_024448495.1	1176259	1176259	type	True	83.2773	750	1069	95	below_threshold
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	81.4104	644	1069	95	below_threshold
Pseudomonas carbonaria	strain=CIP 111764	GCA_904061905.1	2762745	2762745	type	True	81.1291	597	1069	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_900155995.1	706570	706570	type	True	80.5988	536	1069	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	80.4662	552	1069	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 16:29:20,953] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40951/tc_result.tsv
[2023-03-15 16:29:20,954] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:29:20,954] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:29:20,954] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76208f34-3af8-45d7-b9eb-934b31bf9db5/dqc_reference/checkm_data
[2023-03-15 16:29:20,955] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:29:20,964] [INFO] Task started: CheckM
[2023-03-15 16:29:20,964] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40951/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40951/checkm_input OceanDNA-b40951/checkm_result
[2023-03-15 16:30:13,382] [INFO] Task succeeded: CheckM
[2023-03-15 16:30:13,382] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 16:30:13,388] [INFO] ===== Completeness check finished =====
[2023-03-15 16:30:13,388] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:30:13,388] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40951/markers.fasta)
[2023-03-15 16:30:13,389] [INFO] Task started: Blastn
[2023-03-15 16:30:13,389] [INFO] Running command: blastn -query OceanDNA-b40951/markers.fasta -db /var/lib/cwl/stg76208f34-3af8-45d7-b9eb-934b31bf9db5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40951/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:30:15,102] [INFO] Task succeeded: Blastn
[2023-03-15 16:30:15,103] [INFO] Selected 18 target genomes.
[2023-03-15 16:30:15,103] [INFO] Target genome list was writen to OceanDNA-b40951/target_genomes_gtdb.txt
[2023-03-15 16:30:15,146] [INFO] Task started: fastANI
[2023-03-15 16:30:15,146] [INFO] Running command: fastANI --query /var/lib/cwl/stgf705bcc8-8481-46ad-b7f9-eb829c03e014/OceanDNA-b40951.fa --refList OceanDNA-b40951/target_genomes_gtdb.txt --output OceanDNA-b40951/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:30:33,867] [INFO] Task succeeded: fastANI
[2023-03-15 16:30:33,878] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 16:30:33,878] [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_000818015.1	s__Pseudomonas_A balearica	98.4301	976	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.54	98.20	0.91	0.86	18	conclusive
GCF_002890915.1	s__Pseudomonas_A stutzeri_AF	84.3184	789	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.35	98.08	0.91	0.89	3	-
GCF_000219605.1	s__Pseudomonas_A stutzeri	84.1083	796	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.69	96.98	0.90	0.83	156	-
GCF_003205815.1	s__Pseudomonas_A sp003205815	83.8823	790	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.18	96.58	0.91	0.87	27	-
GCF_000263395.1	s__Pseudomonas_A stutzeri_C	83.8529	730	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_907163115.1	s__Pseudomonas_A stutzeri_AL	83.6893	763	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.05	96.55	0.94	0.91	6	-
GCF_015070855.1	s__Pseudomonas_A lopnurensis	83.5481	763	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.76	98.41	0.83	0.83	4	-
GCF_005844005.1	s__Pseudomonas_A sp000765155	83.5458	755	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.19	98.01	0.92	0.89	5	-
GCF_003696315.1	s__Pseudomonas_A songnenensis	83.4211	741	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.36	98.32	0.94	0.90	4	-
GCF_000307775.2	s__Pseudomonas_A stutzeri_B	83.3533	752	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.65	98.65	0.90	0.90	2	-
GCF_000935215.1	s__Pseudomonas_A stutzeri_AD	83.2458	725	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	96.8359	97.48	96.93	0.86	0.84	3	-
GCF_000327065.1	s__Pseudomonas_A stutzeri_AE	83.0197	766	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.70	97.56	0.93	0.91	3	-
GCF_000425625.1	s__Pseudomonas_N azotifigens	82.1687	684	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003696305.1	s__Pseudomonas_E sp003696305	81.2959	611	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009799925.1	s__Pseudomonas_E sp009799925	81.1618	568	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904061905.1	s__Pseudomonas_E carbonaria	81.1581	594	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014490745.1	s__Pseudomonas_E alcaligenes_C	80.6628	552	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003595175.1	s__Pseudomonas_E sp003595175	80.4762	552	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 16:30:33,878] [INFO] GTDB search result was written to OceanDNA-b40951/result_gtdb.tsv
[2023-03-15 16:30:33,878] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:30:33,880] [INFO] DFAST_QC result json was written to OceanDNA-b40951/dqc_result.json
[2023-03-15 16:30:33,881] [INFO] DFAST_QC completed!
[2023-03-15 16:30:33,881] [INFO] Total running time: 0h1m49s