[2023-03-18 01:26:26,394] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:26:26,394] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:26:26,394] [INFO] DQC Reference Directory: /var/lib/cwl/stg863a6f37-48c2-4592-ba77-0d8cf2ae3f9d/dqc_reference
[2023-03-18 01:26:27,566] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:26:27,566] [INFO] Task started: Prodigal
[2023-03-18 01:26:27,567] [INFO] Running command: cat /var/lib/cwl/stg496bac3a-5cfd-4c76-b0cb-128f5d738963/OceanDNA-b22335.fa | prodigal -d OceanDNA-b22335/cds.fna -a OceanDNA-b22335/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:26:47,205] [INFO] Task succeeded: Prodigal
[2023-03-18 01:26:47,206] [INFO] Task started: HMMsearch
[2023-03-18 01:26:47,206] [INFO] Running command: hmmsearch --tblout OceanDNA-b22335/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg863a6f37-48c2-4592-ba77-0d8cf2ae3f9d/dqc_reference/reference_markers.hmm OceanDNA-b22335/protein.faa > /dev/null
[2023-03-18 01:26:47,452] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:26:47,452] [INFO] Found 6/6 markers.
[2023-03-18 01:26:47,475] [INFO] Query marker FASTA was written to OceanDNA-b22335/markers.fasta
[2023-03-18 01:26:47,476] [INFO] Task started: Blastn
[2023-03-18 01:26:47,476] [INFO] Running command: blastn -query OceanDNA-b22335/markers.fasta -db /var/lib/cwl/stg863a6f37-48c2-4592-ba77-0d8cf2ae3f9d/dqc_reference/reference_markers.fasta -out OceanDNA-b22335/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:26:48,002] [INFO] Task succeeded: Blastn
[2023-03-18 01:26:48,003] [INFO] Selected 19 target genomes.
[2023-03-18 01:26:48,003] [INFO] Target genome list was writen to OceanDNA-b22335/target_genomes.txt
[2023-03-18 01:26:48,046] [INFO] Task started: fastANI
[2023-03-18 01:26:48,046] [INFO] Running command: fastANI --query /var/lib/cwl/stg496bac3a-5cfd-4c76-b0cb-128f5d738963/OceanDNA-b22335.fa --refList OceanDNA-b22335/target_genomes.txt --output OceanDNA-b22335/fastani_result.tsv --threads 1
[2023-03-18 01:27:05,930] [INFO] Task succeeded: fastANI
[2023-03-18 01:27:05,930] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg863a6f37-48c2-4592-ba77-0d8cf2ae3f9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:27:05,931] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg863a6f37-48c2-4592-ba77-0d8cf2ae3f9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:27:05,938] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:27:05,938] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:27:05,938] [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
Bythopirellula goksoeyrii	strain=Pr1d	GCA_008065115.1	1400387	1400387	type	True	76.0748	50	1067	95	below_threshold
Bythopirellula polymerisocia	strain=Pla144	GCA_007860015.1	2528003	2528003	type	True	76.0557	51	1067	95	below_threshold
Aeoliella mucimassa	strain=Pan181	GCA_007748035.1	2527972	2527972	type	True	75.8888	51	1067	95	below_threshold
Lacipirellula parvula	strain=PX69	GCA_009177095.1	2650471	2650471	type	True	75.7653	64	1067	95	below_threshold
Adhaeretor mobilis	strain=HG15A2	GCA_007741515.1	1930276	1930276	type	True	75.7502	58	1067	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:27:05,938] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22335/tc_result.tsv
[2023-03-18 01:27:05,938] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:27:05,939] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:27:05,939] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg863a6f37-48c2-4592-ba77-0d8cf2ae3f9d/dqc_reference/checkm_data
[2023-03-18 01:27:05,940] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:27:05,948] [INFO] Task started: CheckM
[2023-03-18 01:27:05,948] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22335/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22335/checkm_input OceanDNA-b22335/checkm_result
[2023-03-18 01:27:58,654] [INFO] Task succeeded: CheckM
[2023-03-18 01:27:58,654] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.70%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:27:58,656] [INFO] ===== Completeness check finished =====
[2023-03-18 01:27:58,656] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:27:58,657] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22335/markers.fasta)
[2023-03-18 01:27:58,657] [INFO] Task started: Blastn
[2023-03-18 01:27:58,657] [INFO] Running command: blastn -query OceanDNA-b22335/markers.fasta -db /var/lib/cwl/stg863a6f37-48c2-4592-ba77-0d8cf2ae3f9d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22335/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:27:59,366] [INFO] Task succeeded: Blastn
[2023-03-18 01:27:59,367] [INFO] Selected 21 target genomes.
[2023-03-18 01:27:59,367] [INFO] Target genome list was writen to OceanDNA-b22335/target_genomes_gtdb.txt
[2023-03-18 01:27:59,442] [INFO] Task started: fastANI
[2023-03-18 01:27:59,443] [INFO] Running command: fastANI --query /var/lib/cwl/stg496bac3a-5cfd-4c76-b0cb-128f5d738963/OceanDNA-b22335.fa --refList OceanDNA-b22335/target_genomes_gtdb.txt --output OceanDNA-b22335/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:28:15,985] [INFO] Task succeeded: fastANI
[2023-03-18 01:28:15,991] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:28:15,991] [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_002713555.1	s__Bythopirellula sp002713555	76.934	171	1067	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Bythopirellula	95.0	99.19	98.89	0.81	0.78	3	-
GCA_013151315.1	s__Bythopirellula sp013151315	76.5725	63	1067	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Bythopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013152515.1	s__Bythopirellula sp013152515	76.4913	76	1067	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Bythopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013152205.1	s__Bythopirellula sp013152205	76.1612	88	1067	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Bythopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002702655.1	s__GCA-2702655 sp002702655	75.9144	77	1067	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__GCA-2702655	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007748035.1	s__Aeoliella mucimassa	75.8888	51	1067	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Aeoliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009177095.1	s__Lacipirellula parvula	75.7653	64	1067	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007741515.1	s__HG15A2 sp007741515	75.7502	58	1067	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__HG15A2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576855.1	s__Lacipirellula sp003576855	75.6919	52	1067	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:28:15,992] [INFO] GTDB search result was written to OceanDNA-b22335/result_gtdb.tsv
[2023-03-18 01:28:15,992] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:28:15,993] [INFO] DFAST_QC result json was written to OceanDNA-b22335/dqc_result.json
[2023-03-18 01:28:15,993] [INFO] DFAST_QC completed!
[2023-03-18 01:28:15,993] [INFO] Total running time: 0h1m50s