[2023-03-15 18:39:12,205] [INFO] DFAST_QC pipeline started.
[2023-03-15 18:39:12,205] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 18:39:12,205] [INFO] DQC Reference Directory: /var/lib/cwl/stg597992ef-214f-4204-81d7-86cc5a690ca9/dqc_reference
[2023-03-15 18:39:13,657] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 18:39:13,658] [INFO] Task started: Prodigal
[2023-03-15 18:39:13,658] [INFO] Running command: cat /var/lib/cwl/stg638b286b-0eba-4d03-a0bb-25b06ebf6966/OceanDNA-b22492.fa | prodigal -d OceanDNA-b22492/cds.fna -a OceanDNA-b22492/protein.faa -g 11 -q > /dev/null
[2023-03-15 18:39:42,634] [INFO] Task succeeded: Prodigal
[2023-03-15 18:39:42,634] [INFO] Task started: HMMsearch
[2023-03-15 18:39:42,634] [INFO] Running command: hmmsearch --tblout OceanDNA-b22492/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg597992ef-214f-4204-81d7-86cc5a690ca9/dqc_reference/reference_markers.hmm OceanDNA-b22492/protein.faa > /dev/null
[2023-03-15 18:39:42,897] [INFO] Task succeeded: HMMsearch
[2023-03-15 18:39:42,897] [INFO] Found 6/6 markers.
[2023-03-15 18:39:42,927] [INFO] Query marker FASTA was written to OceanDNA-b22492/markers.fasta
[2023-03-15 18:39:42,928] [INFO] Task started: Blastn
[2023-03-15 18:39:42,928] [INFO] Running command: blastn -query OceanDNA-b22492/markers.fasta -db /var/lib/cwl/stg597992ef-214f-4204-81d7-86cc5a690ca9/dqc_reference/reference_markers.fasta -out OceanDNA-b22492/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:39:43,455] [INFO] Task succeeded: Blastn
[2023-03-15 18:39:43,455] [INFO] Selected 22 target genomes.
[2023-03-15 18:39:43,456] [INFO] Target genome list was writen to OceanDNA-b22492/target_genomes.txt
[2023-03-15 18:39:43,468] [INFO] Task started: fastANI
[2023-03-15 18:39:43,468] [INFO] Running command: fastANI --query /var/lib/cwl/stg638b286b-0eba-4d03-a0bb-25b06ebf6966/OceanDNA-b22492.fa --refList OceanDNA-b22492/target_genomes.txt --output OceanDNA-b22492/fastani_result.tsv --threads 1
[2023-03-15 18:40:04,366] [INFO] Task succeeded: fastANI
[2023-03-15 18:40:04,366] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg597992ef-214f-4204-81d7-86cc5a690ca9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 18:40:04,367] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg597992ef-214f-4204-81d7-86cc5a690ca9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 18:40:04,372] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 18:40:04,372] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 18:40:04,372] [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
Rubripirellula lacrimiformis	strain=K22.7	GCA_007741535.1	1930273	1930273	type	True	76.4155	68	1563	95	below_threshold
Rubripirellula amarantea	strain=Pla22	GCA_007859865.1	2527999	2527999	type	True	75.7877	56	1563	95	below_threshold
Rubripirellula obstinata	strain=CECT 8602	GCA_001642955.1	406547	406547	type	True	75.6683	59	1563	95	below_threshold
Rubripirellula obstinata	strain=LF1	GCA_008374075.1	406547	406547	type	True	75.6495	60	1563	95	below_threshold
Crateriforma spongiae	strain=JC647	GCA_012290005.1	2724528	2724528	type	True	75.6492	51	1563	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 18:40:04,372] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22492/tc_result.tsv
[2023-03-15 18:40:04,372] [INFO] ===== Taxonomy check completed =====
[2023-03-15 18:40:04,372] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 18:40:04,372] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg597992ef-214f-4204-81d7-86cc5a690ca9/dqc_reference/checkm_data
[2023-03-15 18:40:04,373] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 18:40:04,379] [INFO] Task started: CheckM
[2023-03-15 18:40:04,379] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22492/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22492/checkm_input OceanDNA-b22492/checkm_result
[2023-03-15 18:41:16,431] [INFO] Task succeeded: CheckM
[2023-03-15 18:41:16,432] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 18:41:16,435] [INFO] ===== Completeness check finished =====
[2023-03-15 18:41:16,435] [INFO] ===== Start GTDB Search =====
[2023-03-15 18:41:16,435] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22492/markers.fasta)
[2023-03-15 18:41:16,437] [INFO] Task started: Blastn
[2023-03-15 18:41:16,437] [INFO] Running command: blastn -query OceanDNA-b22492/markers.fasta -db /var/lib/cwl/stg597992ef-214f-4204-81d7-86cc5a690ca9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22492/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:41:17,156] [INFO] Task succeeded: Blastn
[2023-03-15 18:41:17,157] [INFO] Selected 27 target genomes.
[2023-03-15 18:41:17,157] [INFO] Target genome list was writen to OceanDNA-b22492/target_genomes_gtdb.txt
[2023-03-15 18:41:17,790] [INFO] Task started: fastANI
[2023-03-15 18:41:17,790] [INFO] Running command: fastANI --query /var/lib/cwl/stg638b286b-0eba-4d03-a0bb-25b06ebf6966/OceanDNA-b22492.fa --refList OceanDNA-b22492/target_genomes_gtdb.txt --output OceanDNA-b22492/fastani_result_gtdb.tsv --threads 1
[2023-03-15 18:41:43,369] [INFO] Task succeeded: fastANI
[2023-03-15 18:41:43,376] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 18:41:43,376] [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_016779185.1	s__Rubripirellula sp016779185	77.2218	161	1563	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012270385.1	s__Rubripirellula sp012270385	76.654	165	1563	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007741535.1	s__Rubripirellula sp007741535	76.4155	68	1563	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862205.1	s__Rubripirellula sp002862205	75.8017	57	1563	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859865.1	s__Rubripirellula amarantea	75.7877	56	1563	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001642955.1	s__Rubripirellula obstinata	75.6683	59	1563	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	99.93	99.93	1.00	1.00	2	-
GCF_012290005.1	s__Crateriforma spongiae	75.6492	51	1563	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.43	98.43	0.93	0.93	2	-
GCF_002901265.1	s__Stieleria baltica_A	75.5998	55	1563	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	99.97	99.97	0.98	0.98	2	-
GCF_002289565.1	s__Stieleria sp002289565	75.5756	50	1563	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007859835.1	s__Novipirellula sp007859835	75.4636	64	1563	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 18:41:43,377] [INFO] GTDB search result was written to OceanDNA-b22492/result_gtdb.tsv
[2023-03-15 18:41:43,377] [INFO] ===== GTDB Search completed =====
[2023-03-15 18:41:43,378] [INFO] DFAST_QC result json was written to OceanDNA-b22492/dqc_result.json
[2023-03-15 18:41:43,378] [INFO] DFAST_QC completed!
[2023-03-15 18:41:43,378] [INFO] Total running time: 0h2m31s