[2023-03-17 05:34:58,157] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:34:58,157] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:34:58,157] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f18102f-f76d-45c9-b0c5-9cb632475f00/dqc_reference
[2023-03-17 05:34:59,268] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:34:59,269] [INFO] Task started: Prodigal
[2023-03-17 05:34:59,269] [INFO] Running command: cat /var/lib/cwl/stg5522b7c0-46ea-4788-b500-775f44fc95d3/OceanDNA-b34840.fa | prodigal -d OceanDNA-b34840/cds.fna -a OceanDNA-b34840/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:35:12,203] [INFO] Task succeeded: Prodigal
[2023-03-17 05:35:12,203] [INFO] Task started: HMMsearch
[2023-03-17 05:35:12,203] [INFO] Running command: hmmsearch --tblout OceanDNA-b34840/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f18102f-f76d-45c9-b0c5-9cb632475f00/dqc_reference/reference_markers.hmm OceanDNA-b34840/protein.faa > /dev/null
[2023-03-17 05:35:12,386] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:35:12,387] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5522b7c0-46ea-4788-b500-775f44fc95d3/OceanDNA-b34840.fa]
[2023-03-17 05:35:12,412] [INFO] Query marker FASTA was written to OceanDNA-b34840/markers.fasta
[2023-03-17 05:35:12,414] [INFO] Task started: Blastn
[2023-03-17 05:35:12,414] [INFO] Running command: blastn -query OceanDNA-b34840/markers.fasta -db /var/lib/cwl/stg8f18102f-f76d-45c9-b0c5-9cb632475f00/dqc_reference/reference_markers.fasta -out OceanDNA-b34840/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:35:13,050] [INFO] Task succeeded: Blastn
[2023-03-17 05:35:13,052] [INFO] Selected 21 target genomes.
[2023-03-17 05:35:13,052] [INFO] Target genome list was writen to OceanDNA-b34840/target_genomes.txt
[2023-03-17 05:35:13,063] [INFO] Task started: fastANI
[2023-03-17 05:35:13,063] [INFO] Running command: fastANI --query /var/lib/cwl/stg5522b7c0-46ea-4788-b500-775f44fc95d3/OceanDNA-b34840.fa --refList OceanDNA-b34840/target_genomes.txt --output OceanDNA-b34840/fastani_result.tsv --threads 1
[2023-03-17 05:35:23,789] [INFO] Task succeeded: fastANI
[2023-03-17 05:35:23,790] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f18102f-f76d-45c9-b0c5-9cb632475f00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:35:23,790] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f18102f-f76d-45c9-b0c5-9cb632475f00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:35:23,798] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 05:35:23,798] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 05:35:23,798] [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 baltica	strain=OS145	GCA_000152885.1	190892	190892	type	True	98.5961	709	749	95	conclusive
Idiomarina fontislapidosi	strain=F23	GCA_003987025.1	263723	263723	type	True	83.3091	553	749	95	below_threshold
Idiomarina fontislapidosi	strain=CECT 5859	GCA_003226255.1	263723	263723	type	True	83.222	551	749	95	below_threshold
Idiomarina aquatica	strain=SN-14	GCA_003987185.1	1327752	1327752	type	True	78.6267	132	749	95	below_threshold
Idiomarina zobellii	strain=KMM 231	GCA_900100855.1	86103	86103	type	True	78.5	105	749	95	below_threshold
Idiomarina zobellii	strain=KMM 231	GCA_001294745.1	86103	86103	type	True	78.4673	105	749	95	below_threshold
Idiomarina loihiensis	strain=L2TR	GCA_000008465.1	135577	135577	type	True	78.2233	95	749	95	below_threshold
Idiomarina piscisalsi	strain=TPS4-2	GCA_003987095.1	1096243	1096243	type	True	78.06	99	749	95	below_threshold
Idiomarina seosinensis	strain=CL-SP19	GCA_003987275.1	281739	281739	type	True	77.8907	127	749	95	below_threshold
Pseudidiomarina atlantica	strain=MCCC 1A10513	GCA_000753735.1	1517416	1517416	type	True	77.443	59	749	95	below_threshold
Idiomarina xiamenensis	strain=10-D-4	GCA_000299895.1	1207041	1207041	type	True	77.2946	72	749	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:35:23,799] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34840/tc_result.tsv
[2023-03-17 05:35:23,801] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:35:23,801] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:35:23,801] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f18102f-f76d-45c9-b0c5-9cb632475f00/dqc_reference/checkm_data
[2023-03-17 05:35:23,802] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:35:23,847] [INFO] Task started: CheckM
[2023-03-17 05:35:23,847] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34840/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34840/checkm_input OceanDNA-b34840/checkm_result
[2023-03-17 05:35:59,667] [INFO] Task succeeded: CheckM
[2023-03-17 05:35:59,667] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:35:59,737] [INFO] ===== Completeness check finished =====
[2023-03-17 05:35:59,738] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:35:59,738] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34840/markers.fasta)
[2023-03-17 05:35:59,739] [INFO] Task started: Blastn
[2023-03-17 05:35:59,739] [INFO] Running command: blastn -query OceanDNA-b34840/markers.fasta -db /var/lib/cwl/stg8f18102f-f76d-45c9-b0c5-9cb632475f00/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34840/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:36:00,630] [INFO] Task succeeded: Blastn
[2023-03-17 05:36:00,634] [INFO] Selected 10 target genomes.
[2023-03-17 05:36:00,634] [INFO] Target genome list was writen to OceanDNA-b34840/target_genomes_gtdb.txt
[2023-03-17 05:36:00,678] [INFO] Task started: fastANI
[2023-03-17 05:36:00,678] [INFO] Running command: fastANI --query /var/lib/cwl/stg5522b7c0-46ea-4788-b500-775f44fc95d3/OceanDNA-b34840.fa --refList OceanDNA-b34840/target_genomes_gtdb.txt --output OceanDNA-b34840/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:36:06,015] [INFO] Task succeeded: fastANI
[2023-03-17 05:36:06,021] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:36:06,021] [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_000152885.1	s__Idiomarina baltica	98.5813	710	749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	98.48	98.19	0.90	0.79	8	conclusive
GCA_002685255.1	s__Idiomarina sp002685255	89.508	615	749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	99.23	98.54	0.93	0.91	3	-
GCF_001870515.1	s__Idiomarina sp001870515	89.4976	635	749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003226255.1	s__Idiomarina fontislapidosi	83.2378	550	749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003987185.1	s__Idiomarina aquatica	78.6267	132	749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	99.08	99.08	0.91	0.91	2	-
GCF_002808045.1	s__Idiomarina sp002808045	78.4122	102	749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.72	96.72	0.95	0.95	2	-
GCF_002211765.1	s__Idiomarina piscisalsi_A	78.0516	109	749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.69	97.69	0.90	0.90	2	-
GCF_000299895.1	s__Idiomarina xiamenensis	77.2946	72	749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:36:06,022] [INFO] GTDB search result was written to OceanDNA-b34840/result_gtdb.tsv
[2023-03-17 05:36:06,023] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:36:06,026] [INFO] DFAST_QC result json was written to OceanDNA-b34840/dqc_result.json
[2023-03-17 05:36:06,026] [INFO] DFAST_QC completed!
[2023-03-17 05:36:06,026] [INFO] Total running time: 0h1m8s