[2023-03-19 02:05:11,578] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:05:11,578] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:05:11,578] [INFO] DQC Reference Directory: /var/lib/cwl/stg90bacac2-a6d2-441e-bb01-502ba86655c4/dqc_reference
[2023-03-19 02:05:13,260] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:05:13,261] [INFO] Task started: Prodigal
[2023-03-19 02:05:13,261] [INFO] Running command: cat /var/lib/cwl/stg1e3d33c5-b60c-4eb4-9380-708178ad9099/OceanDNA-b6186.fa | prodigal -d OceanDNA-b6186/cds.fna -a OceanDNA-b6186/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:05:27,688] [INFO] Task succeeded: Prodigal
[2023-03-19 02:05:27,689] [INFO] Task started: HMMsearch
[2023-03-19 02:05:27,689] [INFO] Running command: hmmsearch --tblout OceanDNA-b6186/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90bacac2-a6d2-441e-bb01-502ba86655c4/dqc_reference/reference_markers.hmm OceanDNA-b6186/protein.faa > /dev/null
[2023-03-19 02:05:27,911] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:05:27,912] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1e3d33c5-b60c-4eb4-9380-708178ad9099/OceanDNA-b6186.fa]
[2023-03-19 02:05:27,932] [INFO] Query marker FASTA was written to OceanDNA-b6186/markers.fasta
[2023-03-19 02:05:27,932] [INFO] Task started: Blastn
[2023-03-19 02:05:27,932] [INFO] Running command: blastn -query OceanDNA-b6186/markers.fasta -db /var/lib/cwl/stg90bacac2-a6d2-441e-bb01-502ba86655c4/dqc_reference/reference_markers.fasta -out OceanDNA-b6186/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:05:28,497] [INFO] Task succeeded: Blastn
[2023-03-19 02:05:28,498] [INFO] Selected 28 target genomes.
[2023-03-19 02:05:28,498] [INFO] Target genome list was writen to OceanDNA-b6186/target_genomes.txt
[2023-03-19 02:05:28,517] [INFO] Task started: fastANI
[2023-03-19 02:05:28,517] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e3d33c5-b60c-4eb4-9380-708178ad9099/OceanDNA-b6186.fa --refList OceanDNA-b6186/target_genomes.txt --output OceanDNA-b6186/fastani_result.tsv --threads 1
[2023-03-19 02:05:45,325] [INFO] Task succeeded: fastANI
[2023-03-19 02:05:45,325] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90bacac2-a6d2-441e-bb01-502ba86655c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:05:45,325] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90bacac2-a6d2-441e-bb01-502ba86655c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:05:45,329] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:05:45,329] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 02:05:45,329] [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
Dokdonia sinensis	strain=SH27	GCA_003688895.1	2479847	2479847	type	True	76.8732	142	706	95	below_threshold
Dokdonia pacifica	strain=CGMCC 1.12184	GCA_014636685.1	1627892	1627892	type	True	76.0529	119	706	95	below_threshold
Dokdonia pacifica	strain=DSM 25597	GCA_900188275.1	1627892	1627892	type	True	76.0321	122	706	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	75.8239	51	706	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 02:05:45,330] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6186/tc_result.tsv
[2023-03-19 02:05:45,330] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:05:45,330] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:05:45,330] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90bacac2-a6d2-441e-bb01-502ba86655c4/dqc_reference/checkm_data
[2023-03-19 02:05:45,331] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:05:45,335] [INFO] Task started: CheckM
[2023-03-19 02:05:45,335] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6186/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6186/checkm_input OceanDNA-b6186/checkm_result
[2023-03-19 02:06:24,542] [INFO] Task succeeded: CheckM
[2023-03-19 02:06:24,543] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:06:24,545] [INFO] ===== Completeness check finished =====
[2023-03-19 02:06:24,545] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:06:24,546] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6186/markers.fasta)
[2023-03-19 02:06:24,547] [INFO] Task started: Blastn
[2023-03-19 02:06:24,547] [INFO] Running command: blastn -query OceanDNA-b6186/markers.fasta -db /var/lib/cwl/stg90bacac2-a6d2-441e-bb01-502ba86655c4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6186/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:06:25,296] [INFO] Task succeeded: Blastn
[2023-03-19 02:06:25,297] [INFO] Selected 31 target genomes.
[2023-03-19 02:06:25,297] [INFO] Target genome list was writen to OceanDNA-b6186/target_genomes_gtdb.txt
[2023-03-19 02:06:25,978] [INFO] Task started: fastANI
[2023-03-19 02:06:25,979] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e3d33c5-b60c-4eb4-9380-708178ad9099/OceanDNA-b6186.fa --refList OceanDNA-b6186/target_genomes_gtdb.txt --output OceanDNA-b6186/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:06:42,474] [INFO] Task succeeded: fastANI
[2023-03-19 02:06:42,479] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:06:42,480] [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
GCF_003688895.1	s__Dokdonia sinensis	76.8732	142	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000212355.1	s__Dokdonia sp000212355	76.8022	153	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	98.49	98.49	0.97	0.97	2	-
GCF_003095655.1	s__Dokdonia sp003095655	76.6798	148	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000355805.1	s__Dokdonia sp000355805	76.6464	153	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827465.1	s__Dokdonia sp007827465	76.4553	91	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188275.1	s__Dokdonia pacifica	76.0457	121	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001418105.1	s__Oceanihabitans himadriensis	75.8239	51	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:06:42,480] [INFO] GTDB search result was written to OceanDNA-b6186/result_gtdb.tsv
[2023-03-19 02:06:42,480] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:06:42,481] [INFO] DFAST_QC result json was written to OceanDNA-b6186/dqc_result.json
[2023-03-19 02:06:42,481] [INFO] DFAST_QC completed!
[2023-03-19 02:06:42,481] [INFO] Total running time: 0h1m31s