[2023-03-15 04:37:12,257] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:37:12,267] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:37:12,268] [INFO] DQC Reference Directory: /var/lib/cwl/stg37fa3c02-305a-4b09-b752-237a394b5e55/dqc_reference
[2023-03-15 04:37:13,395] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:37:13,396] [INFO] Task started: Prodigal
[2023-03-15 04:37:13,396] [INFO] Running command: cat /var/lib/cwl/stg2e532a55-daf3-4be0-9af4-a6e1737f269a/OceanDNA-b4061.fa | prodigal -d OceanDNA-b4061/cds.fna -a OceanDNA-b4061/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:37:31,250] [INFO] Task succeeded: Prodigal
[2023-03-15 04:37:31,251] [INFO] Task started: HMMsearch
[2023-03-15 04:37:31,251] [INFO] Running command: hmmsearch --tblout OceanDNA-b4061/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37fa3c02-305a-4b09-b752-237a394b5e55/dqc_reference/reference_markers.hmm OceanDNA-b4061/protein.faa > /dev/null
[2023-03-15 04:37:31,444] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:37:31,445] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2e532a55-daf3-4be0-9af4-a6e1737f269a/OceanDNA-b4061.fa]
[2023-03-15 04:37:31,527] [INFO] Query marker FASTA was written to OceanDNA-b4061/markers.fasta
[2023-03-15 04:37:31,528] [INFO] Task started: Blastn
[2023-03-15 04:37:31,528] [INFO] Running command: blastn -query OceanDNA-b4061/markers.fasta -db /var/lib/cwl/stg37fa3c02-305a-4b09-b752-237a394b5e55/dqc_reference/reference_markers.fasta -out OceanDNA-b4061/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:37:32,030] [INFO] Task succeeded: Blastn
[2023-03-15 04:37:32,053] [INFO] Selected 13 target genomes.
[2023-03-15 04:37:32,053] [INFO] Target genome list was writen to OceanDNA-b4061/target_genomes.txt
[2023-03-15 04:37:32,061] [INFO] Task started: fastANI
[2023-03-15 04:37:32,061] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e532a55-daf3-4be0-9af4-a6e1737f269a/OceanDNA-b4061.fa --refList OceanDNA-b4061/target_genomes.txt --output OceanDNA-b4061/fastani_result.tsv --threads 1
[2023-03-15 04:37:40,398] [INFO] Task succeeded: fastANI
[2023-03-15 04:37:40,399] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37fa3c02-305a-4b09-b752-237a394b5e55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:37:40,399] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37fa3c02-305a-4b09-b752-237a394b5e55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:37:40,403] [INFO] Found 4 fastANI hits (2 hits with ANI > threshold)
[2023-03-15 04:37:40,403] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 04:37:40,404] [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
Roseivirga pacifica	strain=CGMCC 1.12402	GCA_900111145.1	1267423	1267423	type	True	96.2	505	521	95	conclusive
Roseivirga pacifica	strain=DSM 100771	GCA_003633845.1	1267423	1267423	type	True	96.1896	504	521	95	conclusive
Roseivirga spongicola	strain=UST030701-084	GCA_001592965.1	333140	333140	type	True	77.2686	79	521	95	below_threshold
Roseivirga seohaensis subsp. aquiponti	strain=D-25	GCA_001267955.1	1566026	1914963	type	True	76.5087	56	521	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 04:37:40,410] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4061/tc_result.tsv
[2023-03-15 04:37:40,418] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:37:40,418] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:37:40,418] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37fa3c02-305a-4b09-b752-237a394b5e55/dqc_reference/checkm_data
[2023-03-15 04:37:40,419] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:37:40,428] [INFO] Task started: CheckM
[2023-03-15 04:37:40,428] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4061/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4061/checkm_input OceanDNA-b4061/checkm_result
[2023-03-15 04:38:28,215] [INFO] Task succeeded: CheckM
[2023-03-15 04:38:28,216] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 04:38:28,239] [INFO] ===== Completeness check finished =====
[2023-03-15 04:38:28,239] [INFO] ===== Start GTDB Search =====
[2023-03-15 04:38:28,239] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4061/markers.fasta)
[2023-03-15 04:38:28,240] [INFO] Task started: Blastn
[2023-03-15 04:38:28,240] [INFO] Running command: blastn -query OceanDNA-b4061/markers.fasta -db /var/lib/cwl/stg37fa3c02-305a-4b09-b752-237a394b5e55/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4061/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:38:28,877] [INFO] Task succeeded: Blastn
[2023-03-15 04:38:28,885] [INFO] Selected 15 target genomes.
[2023-03-15 04:38:28,885] [INFO] Target genome list was writen to OceanDNA-b4061/target_genomes_gtdb.txt
[2023-03-15 04:38:28,901] [INFO] Task started: fastANI
[2023-03-15 04:38:28,901] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e532a55-daf3-4be0-9af4-a6e1737f269a/OceanDNA-b4061.fa --refList OceanDNA-b4061/target_genomes_gtdb.txt --output OceanDNA-b4061/fastani_result_gtdb.tsv --threads 1
[2023-03-15 04:38:39,162] [INFO] Task succeeded: fastANI
[2023-03-15 04:38:39,166] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 04:38:39,166] [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_900111145.1	s__Fabibacter pacificus	96.2	505	521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001592965.1	s__Fabibacter spongicola	77.2686	79	521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	97.73	96.54	0.93	0.88	5	-
GCA_013373005.1	s__Fabibacter sp013373005	77.0854	57	521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592945.1	s__Roseivirga seohaensis	76.4049	50	521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Roseivirga	95.0	97.29	97.29	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-03-15 04:38:39,169] [INFO] GTDB search result was written to OceanDNA-b4061/result_gtdb.tsv
[2023-03-15 04:38:39,175] [INFO] ===== GTDB Search completed =====
[2023-03-15 04:38:39,179] [INFO] DFAST_QC result json was written to OceanDNA-b4061/dqc_result.json
[2023-03-15 04:38:39,179] [INFO] DFAST_QC completed!
[2023-03-15 04:38:39,179] [INFO] Total running time: 0h1m27s