[2023-03-18 09:53:10,294] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:53:10,294] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:53:10,294] [INFO] DQC Reference Directory: /var/lib/cwl/stg928585c0-d8d6-42a2-b0d3-ad3e26f2526e/dqc_reference
[2023-03-18 09:53:11,401] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:53:11,401] [INFO] Task started: Prodigal
[2023-03-18 09:53:11,401] [INFO] Running command: cat /var/lib/cwl/stg32a5fa85-135c-476e-bddd-f1a15b3cf868/OceanDNA-b7000.fa | prodigal -d OceanDNA-b7000/cds.fna -a OceanDNA-b7000/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:53:18,713] [INFO] Task succeeded: Prodigal
[2023-03-18 09:53:18,713] [INFO] Task started: HMMsearch
[2023-03-18 09:53:18,713] [INFO] Running command: hmmsearch --tblout OceanDNA-b7000/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg928585c0-d8d6-42a2-b0d3-ad3e26f2526e/dqc_reference/reference_markers.hmm OceanDNA-b7000/protein.faa > /dev/null
[2023-03-18 09:53:18,875] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:53:18,876] [INFO] Found 6/6 markers.
[2023-03-18 09:53:18,888] [INFO] Query marker FASTA was written to OceanDNA-b7000/markers.fasta
[2023-03-18 09:53:18,888] [INFO] Task started: Blastn
[2023-03-18 09:53:18,888] [INFO] Running command: blastn -query OceanDNA-b7000/markers.fasta -db /var/lib/cwl/stg928585c0-d8d6-42a2-b0d3-ad3e26f2526e/dqc_reference/reference_markers.fasta -out OceanDNA-b7000/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:53:19,429] [INFO] Task succeeded: Blastn
[2023-03-18 09:53:19,429] [INFO] Selected 29 target genomes.
[2023-03-18 09:53:19,430] [INFO] Target genome list was writen to OceanDNA-b7000/target_genomes.txt
[2023-03-18 09:53:19,448] [INFO] Task started: fastANI
[2023-03-18 09:53:19,448] [INFO] Running command: fastANI --query /var/lib/cwl/stg32a5fa85-135c-476e-bddd-f1a15b3cf868/OceanDNA-b7000.fa --refList OceanDNA-b7000/target_genomes.txt --output OceanDNA-b7000/fastani_result.tsv --threads 1
[2023-03-18 09:53:34,637] [INFO] Task succeeded: fastANI
[2023-03-18 09:53:34,637] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg928585c0-d8d6-42a2-b0d3-ad3e26f2526e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:53:34,637] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg928585c0-d8d6-42a2-b0d3-ad3e26f2526e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:53:34,641] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:53:34,642] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 09:53:34,642] [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
Ulvibacter litoralis	strain=KCTC 12104	GCA_014651275.1	227084	227084	type	True	76.455	57	337	95	below_threshold
Ulvibacter litoralis	strain=DSM 16195	GCA_900102055.1	227084	227084	type	True	76.4458	56	337	95	below_threshold
Lacinutrix algicola	strain=AKS293	GCA_001418085.1	342954	342954	type	True	75.9046	54	337	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 09:53:34,642] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7000/tc_result.tsv
[2023-03-18 09:53:34,642] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:53:34,642] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:53:34,642] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg928585c0-d8d6-42a2-b0d3-ad3e26f2526e/dqc_reference/checkm_data
[2023-03-18 09:53:34,643] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:53:34,650] [INFO] Task started: CheckM
[2023-03-18 09:53:34,650] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7000/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7000/checkm_input OceanDNA-b7000/checkm_result
[2023-03-18 09:53:58,236] [INFO] Task succeeded: CheckM
[2023-03-18 09:53:58,236] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.97%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:53:58,238] [INFO] ===== Completeness check finished =====
[2023-03-18 09:53:58,238] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:53:58,238] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7000/markers.fasta)
[2023-03-18 09:53:58,239] [INFO] Task started: Blastn
[2023-03-18 09:53:58,239] [INFO] Running command: blastn -query OceanDNA-b7000/markers.fasta -db /var/lib/cwl/stg928585c0-d8d6-42a2-b0d3-ad3e26f2526e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7000/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:53:58,969] [INFO] Task succeeded: Blastn
[2023-03-18 09:53:58,970] [INFO] Selected 13 target genomes.
[2023-03-18 09:53:58,970] [INFO] Target genome list was writen to OceanDNA-b7000/target_genomes_gtdb.txt
[2023-03-18 09:53:58,980] [INFO] Task started: fastANI
[2023-03-18 09:53:58,980] [INFO] Running command: fastANI --query /var/lib/cwl/stg32a5fa85-135c-476e-bddd-f1a15b3cf868/OceanDNA-b7000.fa --refList OceanDNA-b7000/target_genomes_gtdb.txt --output OceanDNA-b7000/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:54:04,697] [INFO] Task succeeded: fastANI
[2023-03-18 09:54:04,702] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 09:54:04,703] [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_905181835.1	s__GCA-002733185 sp905181835	95.496	331	337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004214175.1	s__GCA-002733185 sp004214175	89.136	232	337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004213605.1	s__GCA-002733185 sp004213605	84.6641	230	337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	95.79	95.79	0.89	0.89	2	-
GCA_002713705.1	s__GCA-002733185 sp002713705	78.3703	175	337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	97.32	97.11	0.93	0.92	3	-
GCA_018669795.1	s__GCA-002733185 sp018669795	78.1539	192	337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	98.54	95.82	0.94	0.91	4	-
GCA_002733185.1	s__GCA-002733185 sp002733185	77.1564	119	337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102055.1	s__Ulvibacter litoralis	76.4458	56	337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_003610635.1	s__Ichthyenterobacterium magnum	76.2374	54	337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ichthyenterobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:54:04,703] [INFO] GTDB search result was written to OceanDNA-b7000/result_gtdb.tsv
[2023-03-18 09:54:04,703] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:54:04,704] [INFO] DFAST_QC result json was written to OceanDNA-b7000/dqc_result.json
[2023-03-18 09:54:04,704] [INFO] DFAST_QC completed!
[2023-03-18 09:54:04,704] [INFO] Total running time: 0h0m54s