[2023-03-15 07:29:11,755] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:29:11,755] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:29:11,755] [INFO] DQC Reference Directory: /var/lib/cwl/stgf73a27a0-5971-43a1-8a54-3b19035f84db/dqc_reference
[2023-03-15 07:29:13,589] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:29:13,590] [INFO] Task started: Prodigal
[2023-03-15 07:29:13,590] [INFO] Running command: cat /var/lib/cwl/stge8eeeadb-2f32-415f-b0d5-dac35de63889/OceanDNA-a4786.fa | prodigal -d OceanDNA-a4786/cds.fna -a OceanDNA-a4786/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:29:25,266] [INFO] Task succeeded: Prodigal
[2023-03-15 07:29:25,266] [INFO] Task started: HMMsearch
[2023-03-15 07:29:25,267] [INFO] Running command: hmmsearch --tblout OceanDNA-a4786/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf73a27a0-5971-43a1-8a54-3b19035f84db/dqc_reference/reference_markers.hmm OceanDNA-a4786/protein.faa > /dev/null
[2023-03-15 07:29:25,422] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:29:25,423] [WARNING] Found 3/6 markers. [/var/lib/cwl/stge8eeeadb-2f32-415f-b0d5-dac35de63889/OceanDNA-a4786.fa]
[2023-03-15 07:29:25,436] [INFO] Query marker FASTA was written to OceanDNA-a4786/markers.fasta
[2023-03-15 07:29:25,437] [INFO] Task started: Blastn
[2023-03-15 07:29:25,437] [INFO] Running command: blastn -query OceanDNA-a4786/markers.fasta -db /var/lib/cwl/stgf73a27a0-5971-43a1-8a54-3b19035f84db/dqc_reference/reference_markers.fasta -out OceanDNA-a4786/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:29:25,872] [INFO] Task succeeded: Blastn
[2023-03-15 07:29:25,873] [INFO] Selected 3 target genomes.
[2023-03-15 07:29:25,873] [INFO] Target genome list was writen to OceanDNA-a4786/target_genomes.txt
[2023-03-15 07:29:25,875] [INFO] Task started: fastANI
[2023-03-15 07:29:25,875] [INFO] Running command: fastANI --query /var/lib/cwl/stge8eeeadb-2f32-415f-b0d5-dac35de63889/OceanDNA-a4786.fa --refList OceanDNA-a4786/target_genomes.txt --output OceanDNA-a4786/fastani_result.tsv --threads 1
[2023-03-15 07:29:27,374] [INFO] Task succeeded: fastANI
[2023-03-15 07:29:27,375] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf73a27a0-5971-43a1-8a54-3b19035f84db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:29:27,375] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf73a27a0-5971-43a1-8a54-3b19035f84db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:29:27,375] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:29:27,375] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 07:29:27,375] [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 07:29:27,375] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4786/tc_result.tsv
[2023-03-15 07:29:27,375] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:29:27,376] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:29:27,376] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf73a27a0-5971-43a1-8a54-3b19035f84db/dqc_reference/checkm_data
[2023-03-15 07:29:27,379] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:29:27,382] [INFO] Task started: CheckM
[2023-03-15 07:29:27,382] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4786/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4786/checkm_input OceanDNA-a4786/checkm_result
[2023-03-15 07:30:03,238] [INFO] Task succeeded: CheckM
[2023-03-15 07:30:03,239] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.73%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:30:03,241] [INFO] ===== Completeness check finished =====
[2023-03-15 07:30:03,241] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:30:03,241] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4786/markers.fasta)
[2023-03-15 07:30:03,242] [INFO] Task started: Blastn
[2023-03-15 07:30:03,242] [INFO] Running command: blastn -query OceanDNA-a4786/markers.fasta -db /var/lib/cwl/stgf73a27a0-5971-43a1-8a54-3b19035f84db/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4786/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:30:03,696] [INFO] Task succeeded: Blastn
[2023-03-15 07:30:03,697] [INFO] Selected 9 target genomes.
[2023-03-15 07:30:03,697] [INFO] Target genome list was writen to OceanDNA-a4786/target_genomes_gtdb.txt
[2023-03-15 07:30:03,702] [INFO] Task started: fastANI
[2023-03-15 07:30:03,703] [INFO] Running command: fastANI --query /var/lib/cwl/stge8eeeadb-2f32-415f-b0d5-dac35de63889/OceanDNA-a4786.fa --refList OceanDNA-a4786/target_genomes_gtdb.txt --output OceanDNA-a4786/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:30:06,707] [INFO] Task succeeded: fastANI
[2023-03-15 07:30:06,711] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 07:30:06,711] [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_002498455.1	s__MGIIb-P sp002498455	99.8169	507	597	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-P	95.0	98.13	97.46	0.87	0.81	6	conclusive
GCA_002724815.1	s__MGIIb-P sp002724815	90.3984	470	597	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-P	95.0	96.66	96.66	0.89	0.89	2	-
GCA_002701965.1	s__MGIIb-P sp002701965	81.0979	279	597	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-P	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002505685.1	s__MGIIb-P sp002505685	78.6409	244	597	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-P	95.0	99.68	99.68	0.73	0.73	2	-
GCA_002457195.1	s__MGIIb-P sp002457195	77.5313	129	597	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-P	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:30:06,711] [INFO] GTDB search result was written to OceanDNA-a4786/result_gtdb.tsv
[2023-03-15 07:30:06,711] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:30:06,712] [INFO] DFAST_QC result json was written to OceanDNA-a4786/dqc_result.json
[2023-03-15 07:30:06,712] [INFO] DFAST_QC completed!
[2023-03-15 07:30:06,712] [INFO] Total running time: 0h0m55s