[2023-03-15 16:25:56,993] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:25:57,003] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:25:57,003] [INFO] DQC Reference Directory: /var/lib/cwl/stg3aaae1e6-2378-42f2-abc9-b874326da003/dqc_reference
[2023-03-15 16:25:58,595] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:25:58,595] [INFO] Task started: Prodigal
[2023-03-15 16:25:58,596] [INFO] Running command: cat /var/lib/cwl/stg4d52f17e-90e7-4fcc-a940-e9dd72faf044/OceanDNA-b6173.fa | prodigal -d OceanDNA-b6173/cds.fna -a OceanDNA-b6173/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:26:15,625] [INFO] Task succeeded: Prodigal
[2023-03-15 16:26:15,626] [INFO] Task started: HMMsearch
[2023-03-15 16:26:15,626] [INFO] Running command: hmmsearch --tblout OceanDNA-b6173/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3aaae1e6-2378-42f2-abc9-b874326da003/dqc_reference/reference_markers.hmm OceanDNA-b6173/protein.faa > /dev/null
[2023-03-15 16:26:15,825] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:26:15,825] [INFO] Found 6/6 markers.
[2023-03-15 16:26:15,884] [INFO] Query marker FASTA was written to OceanDNA-b6173/markers.fasta
[2023-03-15 16:26:15,886] [INFO] Task started: Blastn
[2023-03-15 16:26:15,886] [INFO] Running command: blastn -query OceanDNA-b6173/markers.fasta -db /var/lib/cwl/stg3aaae1e6-2378-42f2-abc9-b874326da003/dqc_reference/reference_markers.fasta -out OceanDNA-b6173/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:26:16,433] [INFO] Task succeeded: Blastn
[2023-03-15 16:26:16,444] [INFO] Selected 26 target genomes.
[2023-03-15 16:26:16,444] [INFO] Target genome list was writen to OceanDNA-b6173/target_genomes.txt
[2023-03-15 16:26:16,459] [INFO] Task started: fastANI
[2023-03-15 16:26:16,460] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d52f17e-90e7-4fcc-a940-e9dd72faf044/OceanDNA-b6173.fa --refList OceanDNA-b6173/target_genomes.txt --output OceanDNA-b6173/fastani_result.tsv --threads 1
[2023-03-15 16:26:32,015] [INFO] Task succeeded: fastANI
[2023-03-15 16:26:32,016] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3aaae1e6-2378-42f2-abc9-b874326da003/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:26:32,016] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3aaae1e6-2378-42f2-abc9-b874326da003/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:26:32,019] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:26:32,019] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 16:26:32,019] [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	76.1584	60	837	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 16:26:32,022] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6173/tc_result.tsv
[2023-03-15 16:26:32,024] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:26:32,024] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:26:32,025] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3aaae1e6-2378-42f2-abc9-b874326da003/dqc_reference/checkm_data
[2023-03-15 16:26:32,025] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:26:32,032] [INFO] Task started: CheckM
[2023-03-15 16:26:32,032] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6173/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6173/checkm_input OceanDNA-b6173/checkm_result
[2023-03-15 16:27:16,675] [INFO] Task succeeded: CheckM
[2023-03-15 16:27:16,675] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 16:27:16,741] [INFO] ===== Completeness check finished =====
[2023-03-15 16:27:16,741] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:27:16,741] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6173/markers.fasta)
[2023-03-15 16:27:16,741] [INFO] Task started: Blastn
[2023-03-15 16:27:16,741] [INFO] Running command: blastn -query OceanDNA-b6173/markers.fasta -db /var/lib/cwl/stg3aaae1e6-2378-42f2-abc9-b874326da003/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6173/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:27:17,488] [INFO] Task succeeded: Blastn
[2023-03-15 16:27:17,500] [INFO] Selected 34 target genomes.
[2023-03-15 16:27:17,500] [INFO] Target genome list was writen to OceanDNA-b6173/target_genomes_gtdb.txt
[2023-03-15 16:27:17,531] [INFO] Task started: fastANI
[2023-03-15 16:27:17,531] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d52f17e-90e7-4fcc-a940-e9dd72faf044/OceanDNA-b6173.fa --refList OceanDNA-b6173/target_genomes_gtdb.txt --output OceanDNA-b6173/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:27:38,285] [INFO] Task succeeded: fastANI
[2023-03-15 16:27:38,289] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 16:27:38,290] [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_018401735.1	s__Croceimicrobium sp018401735	78.2761	316	837	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	78.2016	324	837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Croceimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014524565.1	s__Croceimicrobium hydrocarbonivorans	76.1584	60	837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Croceimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002501205.1	s__Croceimicrobium sp002501205	76.1232	60	837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Croceimicrobium	95.0	99.91	99.91	0.95	0.95	2	-
GCA_017795025.1	s__Croceimicrobium sp017795025	75.9168	64	837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Croceimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 16:27:38,294] [INFO] GTDB search result was written to OceanDNA-b6173/result_gtdb.tsv
[2023-03-15 16:27:38,294] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:27:38,302] [INFO] DFAST_QC result json was written to OceanDNA-b6173/dqc_result.json
[2023-03-15 16:27:38,302] [INFO] DFAST_QC completed!
[2023-03-15 16:27:38,303] [INFO] Total running time: 0h1m41s