[2023-03-17 11:19:47,574] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:19:47,574] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:19:47,574] [INFO] DQC Reference Directory: /var/lib/cwl/stg583d2127-80c2-47b8-987d-99767b83b6ef/dqc_reference
[2023-03-17 11:19:48,710] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:19:48,710] [INFO] Task started: Prodigal
[2023-03-17 11:19:48,710] [INFO] Running command: cat /var/lib/cwl/stg73f63b74-ec8f-485a-b8fa-d64fe229d397/OceanDNA-b9778.fa | prodigal -d OceanDNA-b9778/cds.fna -a OceanDNA-b9778/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:20:24,483] [INFO] Task succeeded: Prodigal
[2023-03-17 11:20:24,483] [INFO] Task started: HMMsearch
[2023-03-17 11:20:24,483] [INFO] Running command: hmmsearch --tblout OceanDNA-b9778/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg583d2127-80c2-47b8-987d-99767b83b6ef/dqc_reference/reference_markers.hmm OceanDNA-b9778/protein.faa > /dev/null
[2023-03-17 11:20:24,689] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:20:24,690] [INFO] Found 6/6 markers.
[2023-03-17 11:20:24,714] [INFO] Query marker FASTA was written to OceanDNA-b9778/markers.fasta
[2023-03-17 11:20:24,715] [INFO] Task started: Blastn
[2023-03-17 11:20:24,715] [INFO] Running command: blastn -query OceanDNA-b9778/markers.fasta -db /var/lib/cwl/stg583d2127-80c2-47b8-987d-99767b83b6ef/dqc_reference/reference_markers.fasta -out OceanDNA-b9778/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:20:25,256] [INFO] Task succeeded: Blastn
[2023-03-17 11:20:25,257] [INFO] Selected 12 target genomes.
[2023-03-17 11:20:25,257] [INFO] Target genome list was writen to OceanDNA-b9778/target_genomes.txt
[2023-03-17 11:20:25,269] [INFO] Task started: fastANI
[2023-03-17 11:20:25,269] [INFO] Running command: fastANI --query /var/lib/cwl/stg73f63b74-ec8f-485a-b8fa-d64fe229d397/OceanDNA-b9778.fa --refList OceanDNA-b9778/target_genomes.txt --output OceanDNA-b9778/fastani_result.tsv --threads 1
[2023-03-17 11:20:34,114] [INFO] Task succeeded: fastANI
[2023-03-17 11:20:34,115] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg583d2127-80c2-47b8-987d-99767b83b6ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:20:34,115] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg583d2127-80c2-47b8-987d-99767b83b6ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:20:34,122] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:20:34,122] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 11:20:34,122] [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
Muricauda lutimaris	strain=KCTC 22173	GCA_003581615.1	475082	475082	type	True	81.852	743	1399	95	below_threshold
Muricauda ruestringensis	strain=DSM 13258	GCA_000224085.1	111501	111501	type	True	81.7916	733	1399	95	below_threshold
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	81.238	688	1399	95	below_threshold
Muricauda oceanensis	strain=40DY170	GCA_003992595.1	2499163	2499163	type	True	81.0231	694	1399	95	below_threshold
Muricauda oceani	strain=501str8	GCA_019457985.1	2698672	2698672	type	True	80.8113	665	1399	95	below_threshold
Muricauda oceani	strain=501str8	GCA_011068285.1	2698672	2698672	type	True	80.7663	675	1399	95	below_threshold
Muricauda aurea	strain=BC31-1-A7	GCA_017313785.1	2915619	2915619	type	True	80.489	671	1399	95	below_threshold
Muricauda chongwuensis	strain=HICW	GCA_013376415.1	2697365	2697365	type	True	80.2465	608	1399	95	below_threshold
Muricauda brasiliensis	strain=K001	GCA_003057865.1	2162892	2162892	type	True	80.2306	611	1399	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:20:34,122] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9778/tc_result.tsv
[2023-03-17 11:20:34,123] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:20:34,123] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:20:34,123] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg583d2127-80c2-47b8-987d-99767b83b6ef/dqc_reference/checkm_data
[2023-03-17 11:20:34,124] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:20:34,133] [INFO] Task started: CheckM
[2023-03-17 11:20:34,133] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9778/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9778/checkm_input OceanDNA-b9778/checkm_result
[2023-03-17 11:22:00,107] [INFO] Task succeeded: CheckM
[2023-03-17 11:22:00,107] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 11:22:00,110] [INFO] ===== Completeness check finished =====
[2023-03-17 11:22:00,110] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:22:00,111] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9778/markers.fasta)
[2023-03-17 11:22:00,112] [INFO] Task started: Blastn
[2023-03-17 11:22:00,112] [INFO] Running command: blastn -query OceanDNA-b9778/markers.fasta -db /var/lib/cwl/stg583d2127-80c2-47b8-987d-99767b83b6ef/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9778/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:22:00,902] [INFO] Task succeeded: Blastn
[2023-03-17 11:22:00,903] [INFO] Selected 10 target genomes.
[2023-03-17 11:22:00,903] [INFO] Target genome list was writen to OceanDNA-b9778/target_genomes_gtdb.txt
[2023-03-17 11:22:01,098] [INFO] Task started: fastANI
[2023-03-17 11:22:01,098] [INFO] Running command: fastANI --query /var/lib/cwl/stg73f63b74-ec8f-485a-b8fa-d64fe229d397/OceanDNA-b9778.fa --refList OceanDNA-b9778/target_genomes_gtdb.txt --output OceanDNA-b9778/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:22:10,237] [INFO] Task succeeded: fastANI
[2023-03-17 11:22:10,243] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 11:22:10,243] [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_002699205.1	s__Muricauda sp002699205	99.9481	1275	1399	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.91	99.91	0.89	0.89	2	conclusive
GCA_013911645.1	s__Muricauda sp013911645	81.9446	747	1399	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813125.1	s__Muricauda sp002813125	81.9432	791	1399	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167435.2	s__Muricauda sp002167435	81.9279	690	1399	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003581615.1	s__Muricauda lutimaris	81.8349	745	1399	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000224085.1	s__Muricauda ruestringensis	81.7647	736	1399	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010468565.1	s__Muricauda sp010468565	81.5826	713	1399	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313275.1	s__Muricauda lutimaris_A	81.2478	687	1399	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313105.1	s__Muricauda sp017313105	81.0123	632	1399	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011068285.1	s__Muricauda sp011068285	80.7549	677	1399	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:22:10,244] [INFO] GTDB search result was written to OceanDNA-b9778/result_gtdb.tsv
[2023-03-17 11:22:10,244] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:22:10,245] [INFO] DFAST_QC result json was written to OceanDNA-b9778/dqc_result.json
[2023-03-17 11:22:10,245] [INFO] DFAST_QC completed!
[2023-03-17 11:22:10,245] [INFO] Total running time: 0h2m23s