[2023-03-15 09:25:29,163] [INFO] DFAST_QC pipeline started.
[2023-03-15 09:25:29,163] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 09:25:29,164] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0e14f30-ac07-4790-913a-85152c963b80/dqc_reference
[2023-03-15 09:25:30,383] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 09:25:30,383] [INFO] Task started: Prodigal
[2023-03-15 09:25:30,384] [INFO] Running command: cat /var/lib/cwl/stgc8b15ee4-5a27-465a-9814-30ea19c971d3/OceanDNA-a4748.fa | prodigal -d OceanDNA-a4748/cds.fna -a OceanDNA-a4748/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:25:40,091] [INFO] Task succeeded: Prodigal
[2023-03-15 09:25:40,091] [INFO] Task started: HMMsearch
[2023-03-15 09:25:40,091] [INFO] Running command: hmmsearch --tblout OceanDNA-a4748/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0e14f30-ac07-4790-913a-85152c963b80/dqc_reference/reference_markers.hmm OceanDNA-a4748/protein.faa > /dev/null
[2023-03-15 09:25:40,246] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:25:40,247] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc8b15ee4-5a27-465a-9814-30ea19c971d3/OceanDNA-a4748.fa]
[2023-03-15 09:25:40,256] [INFO] Query marker FASTA was written to OceanDNA-a4748/markers.fasta
[2023-03-15 09:25:40,256] [INFO] Task started: Blastn
[2023-03-15 09:25:40,256] [INFO] Running command: blastn -query OceanDNA-a4748/markers.fasta -db /var/lib/cwl/stgd0e14f30-ac07-4790-913a-85152c963b80/dqc_reference/reference_markers.fasta -out OceanDNA-a4748/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:25:40,678] [INFO] Task succeeded: Blastn
[2023-03-15 09:25:40,679] [INFO] Selected 1 target genomes.
[2023-03-15 09:25:40,679] [INFO] Target genome list was writen to OceanDNA-a4748/target_genomes.txt
[2023-03-15 09:25:40,680] [INFO] Task started: fastANI
[2023-03-15 09:25:40,680] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8b15ee4-5a27-465a-9814-30ea19c971d3/OceanDNA-a4748.fa --refList OceanDNA-a4748/target_genomes.txt --output OceanDNA-a4748/fastani_result.tsv --threads 1
[2023-03-15 09:25:41,263] [INFO] Task succeeded: fastANI
[2023-03-15 09:25:41,263] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0e14f30-ac07-4790-913a-85152c963b80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:25:41,264] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0e14f30-ac07-4790-913a-85152c963b80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:25:41,264] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:25:41,264] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 09:25:41,264] [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
--------------------------------------------------------------------------------
[2023-03-15 09:25:41,264] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4748/tc_result.tsv
[2023-03-15 09:25:41,264] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:25:41,264] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:25:41,264] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0e14f30-ac07-4790-913a-85152c963b80/dqc_reference/checkm_data
[2023-03-15 09:25:41,267] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:25:41,269] [INFO] Task started: CheckM
[2023-03-15 09:25:41,269] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4748/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4748/checkm_input OceanDNA-a4748/checkm_result
[2023-03-15 09:26:10,811] [INFO] Task succeeded: CheckM
[2023-03-15 09:26:10,812] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.97%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 09:26:10,813] [INFO] ===== Completeness check finished =====
[2023-03-15 09:26:10,813] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:26:10,813] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4748/markers.fasta)
[2023-03-15 09:26:10,814] [INFO] Task started: Blastn
[2023-03-15 09:26:10,814] [INFO] Running command: blastn -query OceanDNA-a4748/markers.fasta -db /var/lib/cwl/stgd0e14f30-ac07-4790-913a-85152c963b80/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4748/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:26:11,232] [INFO] Task succeeded: Blastn
[2023-03-15 09:26:11,232] [INFO] Selected 7 target genomes.
[2023-03-15 09:26:11,232] [INFO] Target genome list was writen to OceanDNA-a4748/target_genomes_gtdb.txt
[2023-03-15 09:26:11,314] [INFO] Task started: fastANI
[2023-03-15 09:26:11,314] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8b15ee4-5a27-465a-9814-30ea19c971d3/OceanDNA-a4748.fa --refList OceanDNA-a4748/target_genomes_gtdb.txt --output OceanDNA-a4748/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:26:12,982] [INFO] Task succeeded: fastANI
[2023-03-15 09:26:12,986] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 09:26:12,986] [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_002730095.1	s__MGIIb-O5 sp002730095	98.5822	339	401	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	98.71	97.66	0.85	0.80	5	conclusive
GCA_002505775.1	s__MGIIb-O5 sp002505775	79.6744	238	401	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	99.25	97.62	0.92	0.83	5	-
GCA_002501605.1	s__MGIIb-O5 sp002501605	79.3414	226	401	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	99.05	98.72	0.89	0.86	6	-
GCA_002501805.1	s__MGIIb-O5 sp002501805	78.0308	127	401	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	97.49	96.31	0.90	0.85	5	-
GCA_002506825.1	s__MGIIb-O5 sp002506825	77.9163	129	401	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	98.02	97.97	0.86	0.84	3	-
GCA_002496725.1	s__MGIIb-O5 sp002496725	76.8914	103	401	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	99.85	99.85	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-03-15 09:26:12,986] [INFO] GTDB search result was written to OceanDNA-a4748/result_gtdb.tsv
[2023-03-15 09:26:12,987] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:26:12,987] [INFO] DFAST_QC result json was written to OceanDNA-a4748/dqc_result.json
[2023-03-15 09:26:12,987] [INFO] DFAST_QC completed!
[2023-03-15 09:26:12,987] [INFO] Total running time: 0h0m44s