[2023-03-16 06:31:19,236] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:31:19,236] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:31:19,236] [INFO] DQC Reference Directory: /var/lib/cwl/stgae855555-84ab-416e-8ade-4af77306aa68/dqc_reference
[2023-03-16 06:31:20,366] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:31:20,367] [INFO] Task started: Prodigal
[2023-03-16 06:31:20,367] [INFO] Running command: cat /var/lib/cwl/stg56b6e876-e060-44ec-921c-f35c5eac23bc/OceanDNA-b34866.fa | prodigal -d OceanDNA-b34866/cds.fna -a OceanDNA-b34866/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:31:34,576] [INFO] Task succeeded: Prodigal
[2023-03-16 06:31:34,576] [INFO] Task started: HMMsearch
[2023-03-16 06:31:34,576] [INFO] Running command: hmmsearch --tblout OceanDNA-b34866/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae855555-84ab-416e-8ade-4af77306aa68/dqc_reference/reference_markers.hmm OceanDNA-b34866/protein.faa > /dev/null
[2023-03-16 06:31:34,783] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:31:34,783] [INFO] Found 6/6 markers.
[2023-03-16 06:31:34,801] [INFO] Query marker FASTA was written to OceanDNA-b34866/markers.fasta
[2023-03-16 06:31:34,801] [INFO] Task started: Blastn
[2023-03-16 06:31:34,801] [INFO] Running command: blastn -query OceanDNA-b34866/markers.fasta -db /var/lib/cwl/stgae855555-84ab-416e-8ade-4af77306aa68/dqc_reference/reference_markers.fasta -out OceanDNA-b34866/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:31:35,465] [INFO] Task succeeded: Blastn
[2023-03-16 06:31:35,466] [INFO] Selected 16 target genomes.
[2023-03-16 06:31:35,466] [INFO] Target genome list was writen to OceanDNA-b34866/target_genomes.txt
[2023-03-16 06:31:35,477] [INFO] Task started: fastANI
[2023-03-16 06:31:35,477] [INFO] Running command: fastANI --query /var/lib/cwl/stg56b6e876-e060-44ec-921c-f35c5eac23bc/OceanDNA-b34866.fa --refList OceanDNA-b34866/target_genomes.txt --output OceanDNA-b34866/fastani_result.tsv --threads 1
[2023-03-16 06:31:44,454] [INFO] Task succeeded: fastANI
[2023-03-16 06:31:44,455] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae855555-84ab-416e-8ade-4af77306aa68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:31:44,455] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae855555-84ab-416e-8ade-4af77306aa68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:31:44,462] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2023-03-16 06:31:44,462] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 06:31:44,462] [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
Idiomarina zobellii	strain=KMM 231	GCA_001294745.1	86103	86103	type	True	96.6917	748	831	95	conclusive
Idiomarina zobellii	strain=KMM 231	GCA_900100855.1	86103	86103	type	True	96.6156	748	831	95	conclusive
Idiomarina piscisalsi	strain=TPS4-2	GCA_003987095.1	1096243	1096243	type	True	94.6056	731	831	95	below_threshold
Idiomarina abyssalis	strain=KMM 227	GCA_900116625.1	86102	86102	type	True	82.1935	419	831	95	below_threshold
Idiomarina abyssalis	strain=KMM 227	GCA_001294685.1	86102	86102	type	True	82.0342	432	831	95	below_threshold
Idiomarina loihiensis	strain=L2TR	GCA_000008465.1	135577	135577	type	True	80.72	417	831	95	below_threshold
Idiomarina baltica	strain=OS145	GCA_000152885.1	190892	190892	type	True	80.0326	123	831	95	below_threshold
Idiomarina aquatica	strain=SN-14	GCA_003987185.1	1327752	1327752	type	True	79.9295	202	831	95	below_threshold
Idiomarina fontislapidosi	strain=F23	GCA_003987025.1	263723	263723	type	True	78.2156	128	831	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 06:31:44,463] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34866/tc_result.tsv
[2023-03-16 06:31:44,463] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:31:44,463] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:31:44,463] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae855555-84ab-416e-8ade-4af77306aa68/dqc_reference/checkm_data
[2023-03-16 06:31:44,464] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:31:44,469] [INFO] Task started: CheckM
[2023-03-16 06:31:44,469] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34866/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34866/checkm_input OceanDNA-b34866/checkm_result
[2023-03-16 06:32:22,947] [INFO] Task succeeded: CheckM
[2023-03-16 06:32:22,948] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:32:22,992] [INFO] ===== Completeness check finished =====
[2023-03-16 06:32:22,992] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:32:22,992] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34866/markers.fasta)
[2023-03-16 06:32:22,994] [INFO] Task started: Blastn
[2023-03-16 06:32:22,994] [INFO] Running command: blastn -query OceanDNA-b34866/markers.fasta -db /var/lib/cwl/stgae855555-84ab-416e-8ade-4af77306aa68/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34866/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:32:24,053] [INFO] Task succeeded: Blastn
[2023-03-16 06:32:24,066] [INFO] Selected 11 target genomes.
[2023-03-16 06:32:24,066] [INFO] Target genome list was writen to OceanDNA-b34866/target_genomes_gtdb.txt
[2023-03-16 06:32:24,075] [INFO] Task started: fastANI
[2023-03-16 06:32:24,076] [INFO] Running command: fastANI --query /var/lib/cwl/stg56b6e876-e060-44ec-921c-f35c5eac23bc/OceanDNA-b34866.fa --refList OceanDNA-b34866/target_genomes_gtdb.txt --output OceanDNA-b34866/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:32:31,138] [INFO] Task succeeded: fastANI
[2023-03-16 06:32:31,143] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 06:32:31,143] [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_900100855.1	s__Idiomarina zobellii	96.6156	748	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.93	96.27	0.89	0.85	9	conclusive
GCF_003987095.1	s__Idiomarina piscisalsi	94.6056	731	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002211765.1	s__Idiomarina piscisalsi_A	87.975	718	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.69	97.69	0.90	0.90	2	-
GCF_002808045.1	s__Idiomarina sp002808045	87.7709	725	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.72	96.72	0.95	0.95	2	-
GCF_900116625.1	s__Idiomarina abyssalis	82.1935	419	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.70	97.34	0.91	0.79	25	-
GCF_004362895.1	s__Idiomarina sp002729675	81.8759	210	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.61	97.37	0.88	0.80	5	-
GCF_000008465.1	s__Idiomarina loihiensis	80.7058	418	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.95	95.80	0.91	0.86	17	-
GCF_003987065.1	s__Pseudidiomarina insulisalsae	77.4793	80	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 06:32:31,148] [INFO] GTDB search result was written to OceanDNA-b34866/result_gtdb.tsv
[2023-03-16 06:32:31,150] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:32:31,155] [INFO] DFAST_QC result json was written to OceanDNA-b34866/dqc_result.json
[2023-03-16 06:32:31,155] [INFO] DFAST_QC completed!
[2023-03-16 06:32:31,155] [INFO] Total running time: 0h1m12s