[2023-03-17 02:31:12,683] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:31:12,683] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:31:12,684] [INFO] DQC Reference Directory: /var/lib/cwl/stgee1df070-ae72-4e62-bd0c-4923ca2cc55e/dqc_reference
[2023-03-17 02:31:13,850] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:31:13,850] [INFO] Task started: Prodigal
[2023-03-17 02:31:13,850] [INFO] Running command: cat /var/lib/cwl/stg11e221ed-7598-45e4-9bc4-0a6133befd53/OceanDNA-b4249.fa | prodigal -d OceanDNA-b4249/cds.fna -a OceanDNA-b4249/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:31:57,662] [INFO] Task succeeded: Prodigal
[2023-03-17 02:31:57,663] [INFO] Task started: HMMsearch
[2023-03-17 02:31:57,663] [INFO] Running command: hmmsearch --tblout OceanDNA-b4249/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee1df070-ae72-4e62-bd0c-4923ca2cc55e/dqc_reference/reference_markers.hmm OceanDNA-b4249/protein.faa > /dev/null
[2023-03-17 02:31:57,904] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:31:57,905] [INFO] Found 6/6 markers.
[2023-03-17 02:31:57,936] [INFO] Query marker FASTA was written to OceanDNA-b4249/markers.fasta
[2023-03-17 02:31:57,937] [INFO] Task started: Blastn
[2023-03-17 02:31:57,937] [INFO] Running command: blastn -query OceanDNA-b4249/markers.fasta -db /var/lib/cwl/stgee1df070-ae72-4e62-bd0c-4923ca2cc55e/dqc_reference/reference_markers.fasta -out OceanDNA-b4249/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:31:58,477] [INFO] Task succeeded: Blastn
[2023-03-17 02:31:58,478] [INFO] Selected 34 target genomes.
[2023-03-17 02:31:58,478] [INFO] Target genome list was writen to OceanDNA-b4249/target_genomes.txt
[2023-03-17 02:31:58,496] [INFO] Task started: fastANI
[2023-03-17 02:31:58,496] [INFO] Running command: fastANI --query /var/lib/cwl/stg11e221ed-7598-45e4-9bc4-0a6133befd53/OceanDNA-b4249.fa --refList OceanDNA-b4249/target_genomes.txt --output OceanDNA-b4249/fastani_result.tsv --threads 1
[2023-03-17 02:32:24,523] [INFO] Task succeeded: fastANI
[2023-03-17 02:32:24,524] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee1df070-ae72-4e62-bd0c-4923ca2cc55e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:32:24,524] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee1df070-ae72-4e62-bd0c-4923ca2cc55e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:32:24,528] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:32:24,528] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 02:32:24,528] [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
Marinoscillum furvescens	strain=DSM 4134	GCA_003386095.1	1026	1026	type	True	76.4647	66	1948	95	below_threshold
Marinoscillum pacificum	strain=MRN461	GCA_024714495.1	392723	392723	type	True	75.6137	57	1948	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 02:32:24,528] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4249/tc_result.tsv
[2023-03-17 02:32:24,528] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:32:24,528] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:32:24,528] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee1df070-ae72-4e62-bd0c-4923ca2cc55e/dqc_reference/checkm_data
[2023-03-17 02:32:24,529] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:32:24,536] [INFO] Task started: CheckM
[2023-03-17 02:32:24,536] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4249/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4249/checkm_input OceanDNA-b4249/checkm_result
[2023-03-17 02:34:11,750] [INFO] Task succeeded: CheckM
[2023-03-17 02:34:11,751] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:34:11,754] [INFO] ===== Completeness check finished =====
[2023-03-17 02:34:11,754] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:34:11,754] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4249/markers.fasta)
[2023-03-17 02:34:11,756] [INFO] Task started: Blastn
[2023-03-17 02:34:11,756] [INFO] Running command: blastn -query OceanDNA-b4249/markers.fasta -db /var/lib/cwl/stgee1df070-ae72-4e62-bd0c-4923ca2cc55e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4249/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:34:12,482] [INFO] Task succeeded: Blastn
[2023-03-17 02:34:12,483] [INFO] Selected 23 target genomes.
[2023-03-17 02:34:12,483] [INFO] Target genome list was writen to OceanDNA-b4249/target_genomes_gtdb.txt
[2023-03-17 02:34:13,259] [INFO] Task started: fastANI
[2023-03-17 02:34:13,259] [INFO] Running command: fastANI --query /var/lib/cwl/stg11e221ed-7598-45e4-9bc4-0a6133befd53/OceanDNA-b4249.fa --refList OceanDNA-b4249/target_genomes_gtdb.txt --output OceanDNA-b4249/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:34:31,210] [INFO] Task succeeded: fastANI
[2023-03-17 02:34:31,213] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 02:34:31,214] [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_002471275.1	s__UBA7330 sp002471275	99.9903	1865	1948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA7330	95.0	99.98	99.97	0.98	0.96	3	conclusive
GCA_019192515.1	s__UBA7330 sp019192515	83.5354	1122	1948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA7330	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729235.1	s__Marinoscillum sp002729235	77.2286	51	1948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Marinoscillum	95.0	98.41	98.38	0.86	0.84	4	-
GCF_902506655.1	s__Marinoscillum sp902506655	75.6009	76	1948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Marinoscillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:34:31,214] [INFO] GTDB search result was written to OceanDNA-b4249/result_gtdb.tsv
[2023-03-17 02:34:31,214] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:34:31,214] [INFO] DFAST_QC result json was written to OceanDNA-b4249/dqc_result.json
[2023-03-17 02:34:31,215] [INFO] DFAST_QC completed!
[2023-03-17 02:34:31,215] [INFO] Total running time: 0h3m19s