[2023-03-16 05:50:18,332] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:50:18,332] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:50:18,332] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3e4c595-8bb8-4a68-9264-c0f811e10c14/dqc_reference
[2023-03-16 05:50:20,130] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:50:20,130] [INFO] Task started: Prodigal
[2023-03-16 05:50:20,130] [INFO] Running command: cat /var/lib/cwl/stg9b218c2e-a43e-48a1-a464-b5ab9a97383a/OceanDNA-b5244.fa | prodigal -d OceanDNA-b5244/cds.fna -a OceanDNA-b5244/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:50:43,781] [INFO] Task succeeded: Prodigal
[2023-03-16 05:50:43,782] [INFO] Task started: HMMsearch
[2023-03-16 05:50:43,782] [INFO] Running command: hmmsearch --tblout OceanDNA-b5244/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3e4c595-8bb8-4a68-9264-c0f811e10c14/dqc_reference/reference_markers.hmm OceanDNA-b5244/protein.faa > /dev/null
[2023-03-16 05:50:44,005] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:50:44,006] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg9b218c2e-a43e-48a1-a464-b5ab9a97383a/OceanDNA-b5244.fa]
[2023-03-16 05:50:44,028] [INFO] Query marker FASTA was written to OceanDNA-b5244/markers.fasta
[2023-03-16 05:50:44,029] [INFO] Task started: Blastn
[2023-03-16 05:50:44,029] [INFO] Running command: blastn -query OceanDNA-b5244/markers.fasta -db /var/lib/cwl/stgb3e4c595-8bb8-4a68-9264-c0f811e10c14/dqc_reference/reference_markers.fasta -out OceanDNA-b5244/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:50:44,627] [INFO] Task succeeded: Blastn
[2023-03-16 05:50:44,628] [INFO] Selected 14 target genomes.
[2023-03-16 05:50:44,628] [INFO] Target genome list was writen to OceanDNA-b5244/target_genomes.txt
[2023-03-16 05:50:44,638] [INFO] Task started: fastANI
[2023-03-16 05:50:44,638] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b218c2e-a43e-48a1-a464-b5ab9a97383a/OceanDNA-b5244.fa --refList OceanDNA-b5244/target_genomes.txt --output OceanDNA-b5244/fastani_result.tsv --threads 1
[2023-03-16 05:50:53,216] [INFO] Task succeeded: fastANI
[2023-03-16 05:50:53,216] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3e4c595-8bb8-4a68-9264-c0f811e10c14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:50:53,217] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3e4c595-8bb8-4a68-9264-c0f811e10c14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:50:53,222] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:50:53,222] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 05:50:53,222] [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
Crocinitomix catalasitica	strain=ATCC 23190	GCA_000621625.1	184607	184607	type	True	76.2253	99	1154	95	below_threshold
Putridiphycobacter roseus	strain=SM1701	GCA_003234935.1	2219161	2219161	type	True	76.105	59	1154	95	below_threshold
Crocinitomix algicola	strain=0182	GCA_001661595.2	1740263	1740263	type	True	75.9439	62	1154	95	below_threshold
Brumimicrobium glaciale	strain=IC156	GCA_004152935.1	200475	200475	type	True	75.6887	50	1154	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 05:50:53,222] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5244/tc_result.tsv
[2023-03-16 05:50:53,222] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:50:53,222] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:50:53,222] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3e4c595-8bb8-4a68-9264-c0f811e10c14/dqc_reference/checkm_data
[2023-03-16 05:50:53,223] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:50:53,782] [INFO] Task started: CheckM
[2023-03-16 05:50:53,782] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5244/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5244/checkm_input OceanDNA-b5244/checkm_result
[2023-03-16 05:51:55,139] [INFO] Task succeeded: CheckM
[2023-03-16 05:51:55,139] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 05:51:55,141] [INFO] ===== Completeness check finished =====
[2023-03-16 05:51:55,141] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:51:55,141] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5244/markers.fasta)
[2023-03-16 05:51:55,143] [INFO] Task started: Blastn
[2023-03-16 05:51:55,143] [INFO] Running command: blastn -query OceanDNA-b5244/markers.fasta -db /var/lib/cwl/stgb3e4c595-8bb8-4a68-9264-c0f811e10c14/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5244/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:51:56,070] [INFO] Task succeeded: Blastn
[2023-03-16 05:51:56,071] [INFO] Selected 16 target genomes.
[2023-03-16 05:51:56,071] [INFO] Target genome list was writen to OceanDNA-b5244/target_genomes_gtdb.txt
[2023-03-16 05:51:56,084] [INFO] Task started: fastANI
[2023-03-16 05:51:56,084] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b218c2e-a43e-48a1-a464-b5ab9a97383a/OceanDNA-b5244.fa --refList OceanDNA-b5244/target_genomes_gtdb.txt --output OceanDNA-b5244/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:52:06,006] [INFO] Task succeeded: fastANI
[2023-03-16 05:52:06,011] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 05:52:06,012] [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_905478225.1	s__Crocinitomix sp905478225	76.8503	95	1154	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Crocinitomix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013138735.1	s__Crocinitomix sp013138735	76.5573	95	1154	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Crocinitomix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762645.1	s__JABURP01 sp014762645	76.541	103	1154	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__JABURP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000621625.1	s__Crocinitomix catalasitica	76.2253	99	1154	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Crocinitomix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003234935.1	s__Putridiphycobacter roseus	76.105	59	1154	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Putridiphycobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001661595.2	s__Crocinitomix algicola	75.9439	62	1154	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Crocinitomix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004152935.1	s__Brumimicrobium glaciale	75.6887	50	1154	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 05:52:06,012] [INFO] GTDB search result was written to OceanDNA-b5244/result_gtdb.tsv
[2023-03-16 05:52:06,012] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:52:06,013] [INFO] DFAST_QC result json was written to OceanDNA-b5244/dqc_result.json
[2023-03-16 05:52:06,013] [INFO] DFAST_QC completed!
[2023-03-16 05:52:06,013] [INFO] Total running time: 0h1m48s