[2023-03-15 03:08:16,158] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:08:16,160] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:08:16,160] [INFO] DQC Reference Directory: /var/lib/cwl/stgc93dd7d3-163a-4ff7-ab57-82cee46d6ba5/dqc_reference
[2023-03-15 03:08:22,249] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:08:22,250] [INFO] Task started: Prodigal
[2023-03-15 03:08:22,250] [INFO] Running command: cat /var/lib/cwl/stg568c2068-cc97-48f4-82d9-8e9f4fcbd6a3/OceanDNA-b35076.fa | prodigal -d OceanDNA-b35076/cds.fna -a OceanDNA-b35076/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:08:39,697] [INFO] Task succeeded: Prodigal
[2023-03-15 03:08:39,697] [INFO] Task started: HMMsearch
[2023-03-15 03:08:39,697] [INFO] Running command: hmmsearch --tblout OceanDNA-b35076/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc93dd7d3-163a-4ff7-ab57-82cee46d6ba5/dqc_reference/reference_markers.hmm OceanDNA-b35076/protein.faa > /dev/null
[2023-03-15 03:08:39,985] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:08:39,985] [INFO] Found 6/6 markers.
[2023-03-15 03:08:40,011] [INFO] Query marker FASTA was written to OceanDNA-b35076/markers.fasta
[2023-03-15 03:08:40,013] [INFO] Task started: Blastn
[2023-03-15 03:08:40,013] [INFO] Running command: blastn -query OceanDNA-b35076/markers.fasta -db /var/lib/cwl/stgc93dd7d3-163a-4ff7-ab57-82cee46d6ba5/dqc_reference/reference_markers.fasta -out OceanDNA-b35076/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:08:44,359] [INFO] Task succeeded: Blastn
[2023-03-15 03:08:44,362] [INFO] Selected 11 target genomes.
[2023-03-15 03:08:44,363] [INFO] Target genome list was writen to OceanDNA-b35076/target_genomes.txt
[2023-03-15 03:08:44,367] [INFO] Task started: fastANI
[2023-03-15 03:08:44,367] [INFO] Running command: fastANI --query /var/lib/cwl/stg568c2068-cc97-48f4-82d9-8e9f4fcbd6a3/OceanDNA-b35076.fa --refList OceanDNA-b35076/target_genomes.txt --output OceanDNA-b35076/fastani_result.tsv --threads 1
[2023-03-15 03:08:53,944] [INFO] Task succeeded: fastANI
[2023-03-15 03:08:53,944] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc93dd7d3-163a-4ff7-ab57-82cee46d6ba5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:08:53,945] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc93dd7d3-163a-4ff7-ab57-82cee46d6ba5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:08:53,999] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:08:53,999] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 03:08:54,000] [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
Pseudoalteromonas undina	strain=DSM 6065	GCA_000238275.4	43660	43660	type	True	94.0733	944	1110	95	below_threshold
Pseudoalteromonas tetraodonis	strain=GFC	GCA_002310835.1	43659	43659	suspected-type	True	92.0432	947	1110	95	below_threshold
Pseudoalteromonas tetraodonis	strain=NBRC 103034	GCA_007991235.1	43659	43659	suspected-type	True	92.0145	917	1110	95	below_threshold
Pseudoalteromonas issachenkonii	strain=KCTC 12958	GCA_001455325.1	152297	152297	suspected-type	True	91.9115	944	1110	95	below_threshold
Pseudoalteromonas issachenkonii	strain=KMM 3549	GCA_002310795.1	152297	152297	suspected-type	True	91.8364	950	1110	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	81.5906	675	1110	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	80.5528	527	1110	95	below_threshold
Motilimonas cestriensis	strain=MKS20	GCA_021295315.1	2742685	2742685	type	True	76.7792	59	1110	95	below_threshold
Shewanella schlegeliana	strain=LMG 21406	GCA_023283605.1	190308	190308	type	True	75.953	52	1110	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 03:08:54,002] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35076/tc_result.tsv
[2023-03-15 03:08:54,003] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:08:54,003] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:08:54,003] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc93dd7d3-163a-4ff7-ab57-82cee46d6ba5/dqc_reference/checkm_data
[2023-03-15 03:08:54,004] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:08:54,016] [INFO] Task started: CheckM
[2023-03-15 03:08:54,016] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35076/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35076/checkm_input OceanDNA-b35076/checkm_result
[2023-03-15 03:09:44,098] [INFO] Task succeeded: CheckM
[2023-03-15 03:09:44,098] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:09:44,117] [INFO] ===== Completeness check finished =====
[2023-03-15 03:09:44,117] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:09:44,117] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35076/markers.fasta)
[2023-03-15 03:09:44,119] [INFO] Task started: Blastn
[2023-03-15 03:09:44,119] [INFO] Running command: blastn -query OceanDNA-b35076/markers.fasta -db /var/lib/cwl/stgc93dd7d3-163a-4ff7-ab57-82cee46d6ba5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35076/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:09:45,503] [INFO] Task succeeded: Blastn
[2023-03-15 03:09:45,523] [INFO] Selected 12 target genomes.
[2023-03-15 03:09:45,523] [INFO] Target genome list was writen to OceanDNA-b35076/target_genomes_gtdb.txt
[2023-03-15 03:09:45,532] [INFO] Task started: fastANI
[2023-03-15 03:09:45,532] [INFO] Running command: fastANI --query /var/lib/cwl/stg568c2068-cc97-48f4-82d9-8e9f4fcbd6a3/OceanDNA-b35076.fa --refList OceanDNA-b35076/target_genomes_gtdb.txt --output OceanDNA-b35076/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:09:56,758] [INFO] Task succeeded: fastANI
[2023-03-15 03:09:56,766] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 03:09:56,766] [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_004328665.1	s__Pseudoalteromonas sp001974855	95.5649	954	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.16	95.35	0.86	0.83	5	conclusive
GCF_000238275.3	s__Pseudoalteromonas undina	94.0733	944	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	96.09	0.91	0.86	14	-
GCF_002310835.1	s__Pseudoalteromonas tetraodonis	92.0276	948	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.76	96.28	0.91	0.84	28	-
GCA_018402495.1	s__Pseudoalteromonas sp018402495	89.2515	897	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000238335.3	s__Pseudoalteromonas marina	81.7153	629	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.76	97.57	0.91	0.88	12	-
GCF_018100985.1	s__Pseudoalteromonas sp018100985	81.6067	623	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.38	98.38	0.93	0.93	2	-
GCA_007988745.1	s__Pseudoalteromonas atlantica	81.5607	620	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.93	97.66	0.89	0.85	29	-
GCF_002221525.1	s__Pseudoalteromonas espejiana	81.5432	651	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011378855.1	s__Pseudoalteromonas sp011378855	81.4975	653	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.10	97.06	0.91	0.90	3	-
GCF_001465295.1	s__Pseudoalteromonas translucida	81.4382	655	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.0242	N/A	N/A	N/A	N/A	1	-
GCF_008370255.1	s__Pseudoalteromonas sp008370255	81.3805	669	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014905615.1	s__Pseudoalteromonas aliena	81.1971	636	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.51	97.10	0.91	0.88	7	-
--------------------------------------------------------------------------------
[2023-03-15 03:09:56,775] [INFO] GTDB search result was written to OceanDNA-b35076/result_gtdb.tsv
[2023-03-15 03:09:56,787] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:09:56,795] [INFO] DFAST_QC result json was written to OceanDNA-b35076/dqc_result.json
[2023-03-15 03:09:56,795] [INFO] DFAST_QC completed!
[2023-03-15 03:09:56,795] [INFO] Total running time: 0h1m41s