[2023-03-17 08:11:32,979] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:11:32,979] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:11:32,979] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e344c42-7281-4163-a6e8-0838be2c94d9/dqc_reference
[2023-03-17 08:11:34,670] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:11:34,670] [INFO] Task started: Prodigal
[2023-03-17 08:11:34,670] [INFO] Running command: cat /var/lib/cwl/stg3e4e29e0-a289-4d95-9755-966ba4b84063/OceanDNA-b30005.fa | prodigal -d OceanDNA-b30005/cds.fna -a OceanDNA-b30005/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:11:48,654] [INFO] Task succeeded: Prodigal
[2023-03-17 08:11:48,654] [INFO] Task started: HMMsearch
[2023-03-17 08:11:48,655] [INFO] Running command: hmmsearch --tblout OceanDNA-b30005/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e344c42-7281-4163-a6e8-0838be2c94d9/dqc_reference/reference_markers.hmm OceanDNA-b30005/protein.faa > /dev/null
[2023-03-17 08:11:48,791] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:11:48,792] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg3e4e29e0-a289-4d95-9755-966ba4b84063/OceanDNA-b30005.fa]
[2023-03-17 08:11:48,806] [INFO] Query marker FASTA was written to OceanDNA-b30005/markers.fasta
[2023-03-17 08:11:48,807] [INFO] Task started: Blastn
[2023-03-17 08:11:48,807] [INFO] Running command: blastn -query OceanDNA-b30005/markers.fasta -db /var/lib/cwl/stg6e344c42-7281-4163-a6e8-0838be2c94d9/dqc_reference/reference_markers.fasta -out OceanDNA-b30005/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:11:49,492] [INFO] Task succeeded: Blastn
[2023-03-17 08:11:49,493] [INFO] Selected 8 target genomes.
[2023-03-17 08:11:49,493] [INFO] Target genome list was writen to OceanDNA-b30005/target_genomes.txt
[2023-03-17 08:11:49,498] [INFO] Task started: fastANI
[2023-03-17 08:11:49,498] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e4e29e0-a289-4d95-9755-966ba4b84063/OceanDNA-b30005.fa --refList OceanDNA-b30005/target_genomes.txt --output OceanDNA-b30005/fastani_result.tsv --threads 1
[2023-03-17 08:11:55,927] [INFO] Task succeeded: fastANI
[2023-03-17 08:11:55,928] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e344c42-7281-4163-a6e8-0838be2c94d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:11:55,928] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e344c42-7281-4163-a6e8-0838be2c94d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:11:55,935] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 08:11:55,935] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 08:11:55,935] [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
Pseudopuniceibacterium antarcticum	strain=HQ09	GCA_014899185.1	2613965	2613965	type	True	97.6909	742	757	95	conclusive
Pseudopuniceibacterium sediminis	strain=CY03	GCA_003575965.1	2211117	2211117	type	True	85.443	641	757	95	below_threshold
Pseudooceanicola algae	strain=Lw-13e	GCA_003590145.2	1537215	1537215	type	True	79.9258	432	757	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	79.8439	432	757	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	79.5972	429	757	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	79.5801	421	757	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	79.4684	441	757	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	79.4609	437	757	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 08:11:55,935] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30005/tc_result.tsv
[2023-03-17 08:11:55,935] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:11:55,935] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:11:55,935] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e344c42-7281-4163-a6e8-0838be2c94d9/dqc_reference/checkm_data
[2023-03-17 08:11:55,936] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:11:55,939] [INFO] Task started: CheckM
[2023-03-17 08:11:55,939] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30005/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30005/checkm_input OceanDNA-b30005/checkm_result
[2023-03-17 08:12:33,585] [INFO] Task succeeded: CheckM
[2023-03-17 08:12:33,586] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 08:12:33,588] [INFO] ===== Completeness check finished =====
[2023-03-17 08:12:33,588] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:12:33,588] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30005/markers.fasta)
[2023-03-17 08:12:33,589] [INFO] Task started: Blastn
[2023-03-17 08:12:33,589] [INFO] Running command: blastn -query OceanDNA-b30005/markers.fasta -db /var/lib/cwl/stg6e344c42-7281-4163-a6e8-0838be2c94d9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30005/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:12:34,696] [INFO] Task succeeded: Blastn
[2023-03-17 08:12:34,697] [INFO] Selected 8 target genomes.
[2023-03-17 08:12:34,697] [INFO] Target genome list was writen to OceanDNA-b30005/target_genomes_gtdb.txt
[2023-03-17 08:12:34,706] [INFO] Task started: fastANI
[2023-03-17 08:12:34,706] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e4e29e0-a289-4d95-9755-966ba4b84063/OceanDNA-b30005.fa --refList OceanDNA-b30005/target_genomes_gtdb.txt --output OceanDNA-b30005/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:12:41,291] [INFO] Task succeeded: fastANI
[2023-03-17 08:12:41,297] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 08:12:41,297] [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_014899185.1	s__Pseudooceanicola antarcticus_A	97.6909	742	757	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003575965.1	s__Pseudooceanicola sediminis	85.443	641	757	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.95	99.95	0.93	0.93	2	-
GCF_003590145.2	s__Pseudooceanicola algae	79.9257	432	757	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827095.1	s__Pseudooceanicola sp009827095	79.8329	422	757	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.98	0.98	2	-
GCF_000220565.1	s__Pseudooceanicola sp000220565	79.7129	408	757	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215355.1	s__Pseudooceanicola antarcticus	79.5677	422	757	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011806405.1	s__Pseudooceanicola sp011806405	79.4888	455	757	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002786295.1	s__Pseudooceanicola marinus	79.4609	437	757	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-17 08:12:41,297] [INFO] GTDB search result was written to OceanDNA-b30005/result_gtdb.tsv
[2023-03-17 08:12:41,297] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:12:41,298] [INFO] DFAST_QC result json was written to OceanDNA-b30005/dqc_result.json
[2023-03-17 08:12:41,298] [INFO] DFAST_QC completed!
[2023-03-17 08:12:41,298] [INFO] Total running time: 0h1m8s