[2023-03-16 17:59:31,064] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:59:31,064] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:59:31,064] [INFO] DQC Reference Directory: /var/lib/cwl/stg5aeb23df-4108-4379-a7a4-368cd25e1468/dqc_reference
[2023-03-16 17:59:32,267] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:59:32,268] [INFO] Task started: Prodigal
[2023-03-16 17:59:32,269] [INFO] Running command: cat /var/lib/cwl/stgd419c75a-14d6-46c0-aedf-45201a5e1245/OceanDNA-b6163.fa | prodigal -d OceanDNA-b6163/cds.fna -a OceanDNA-b6163/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:59:54,056] [INFO] Task succeeded: Prodigal
[2023-03-16 17:59:54,056] [INFO] Task started: HMMsearch
[2023-03-16 17:59:54,056] [INFO] Running command: hmmsearch --tblout OceanDNA-b6163/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5aeb23df-4108-4379-a7a4-368cd25e1468/dqc_reference/reference_markers.hmm OceanDNA-b6163/protein.faa > /dev/null
[2023-03-16 17:59:54,243] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:59:54,244] [INFO] Found 6/6 markers.
[2023-03-16 17:59:54,268] [INFO] Query marker FASTA was written to OceanDNA-b6163/markers.fasta
[2023-03-16 17:59:54,270] [INFO] Task started: Blastn
[2023-03-16 17:59:54,270] [INFO] Running command: blastn -query OceanDNA-b6163/markers.fasta -db /var/lib/cwl/stg5aeb23df-4108-4379-a7a4-368cd25e1468/dqc_reference/reference_markers.fasta -out OceanDNA-b6163/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:59:54,841] [INFO] Task succeeded: Blastn
[2023-03-16 17:59:54,843] [INFO] Selected 28 target genomes.
[2023-03-16 17:59:54,843] [INFO] Target genome list was writen to OceanDNA-b6163/target_genomes.txt
[2023-03-16 17:59:54,860] [INFO] Task started: fastANI
[2023-03-16 17:59:54,860] [INFO] Running command: fastANI --query /var/lib/cwl/stgd419c75a-14d6-46c0-aedf-45201a5e1245/OceanDNA-b6163.fa --refList OceanDNA-b6163/target_genomes.txt --output OceanDNA-b6163/fastani_result.tsv --threads 1
[2023-03-16 18:00:10,614] [INFO] Task succeeded: fastANI
[2023-03-16 18:00:10,615] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5aeb23df-4108-4379-a7a4-368cd25e1468/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:00:10,615] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5aeb23df-4108-4379-a7a4-368cd25e1468/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:00:10,618] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:00:10,618] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 18:00:10,618] [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
Croceimicrobium hydrocarbonivorans	strain=A20-9	GCA_014524565.1	2761580	2761580	type	True	77.4358	260	1027	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 18:00:10,619] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6163/tc_result.tsv
[2023-03-16 18:00:10,619] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:00:10,620] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:00:10,620] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5aeb23df-4108-4379-a7a4-368cd25e1468/dqc_reference/checkm_data
[2023-03-16 18:00:10,620] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:00:10,626] [INFO] Task started: CheckM
[2023-03-16 18:00:10,626] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6163/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6163/checkm_input OceanDNA-b6163/checkm_result
[2023-03-16 18:01:16,289] [INFO] Task succeeded: CheckM
[2023-03-16 18:01:16,290] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:01:16,294] [INFO] ===== Completeness check finished =====
[2023-03-16 18:01:16,295] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:01:16,295] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6163/markers.fasta)
[2023-03-16 18:01:16,297] [INFO] Task started: Blastn
[2023-03-16 18:01:16,297] [INFO] Running command: blastn -query OceanDNA-b6163/markers.fasta -db /var/lib/cwl/stg5aeb23df-4108-4379-a7a4-368cd25e1468/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6163/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:01:17,068] [INFO] Task succeeded: Blastn
[2023-03-16 18:01:17,070] [INFO] Selected 26 target genomes.
[2023-03-16 18:01:17,070] [INFO] Target genome list was writen to OceanDNA-b6163/target_genomes_gtdb.txt
[2023-03-16 18:01:17,349] [INFO] Task started: fastANI
[2023-03-16 18:01:17,350] [INFO] Running command: fastANI --query /var/lib/cwl/stgd419c75a-14d6-46c0-aedf-45201a5e1245/OceanDNA-b6163.fa --refList OceanDNA-b6163/target_genomes_gtdb.txt --output OceanDNA-b6163/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:01:44,070] [INFO] Task succeeded: fastANI
[2023-03-16 18:01:44,075] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 18:01:44,075] [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_002501205.1	s__Croceimicrobium sp002501205	77.5428	219	1027	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Croceimicrobium	95.0	99.91	99.91	0.95	0.95	2	-
GCF_014524565.1	s__Croceimicrobium hydrocarbonivorans	77.4358	260	1027	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Croceimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017795025.1	s__Croceimicrobium sp017795025	77.2775	230	1027	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Croceimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003045865.1	s__Croceimicrobium sp003045865	76.2182	103	1027	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Croceimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401735.1	s__Croceimicrobium sp018401735	76.1209	97	1027	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Croceimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 18:01:44,077] [INFO] GTDB search result was written to OceanDNA-b6163/result_gtdb.tsv
[2023-03-16 18:01:44,077] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:01:44,078] [INFO] DFAST_QC result json was written to OceanDNA-b6163/dqc_result.json
[2023-03-16 18:01:44,079] [INFO] DFAST_QC completed!
[2023-03-16 18:01:44,079] [INFO] Total running time: 0h2m13s