[2023-03-18 22:17:12,540] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:17:12,540] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:17:12,540] [INFO] DQC Reference Directory: /var/lib/cwl/stgc49497fc-4e96-4b6b-8a4c-12978b64176c/dqc_reference
[2023-03-18 22:17:13,667] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:17:13,668] [INFO] Task started: Prodigal
[2023-03-18 22:17:13,668] [INFO] Running command: cat /var/lib/cwl/stge4c48547-2753-45fa-9d27-db86212c5e1f/OceanDNA-a5075.fa | prodigal -d OceanDNA-a5075/cds.fna -a OceanDNA-a5075/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:17:21,098] [INFO] Task succeeded: Prodigal
[2023-03-18 22:17:21,098] [INFO] Task started: HMMsearch
[2023-03-18 22:17:21,099] [INFO] Running command: hmmsearch --tblout OceanDNA-a5075/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc49497fc-4e96-4b6b-8a4c-12978b64176c/dqc_reference/reference_markers.hmm OceanDNA-a5075/protein.faa > /dev/null
[2023-03-18 22:17:21,254] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:17:21,254] [WARNING] Found 3/6 markers. [/var/lib/cwl/stge4c48547-2753-45fa-9d27-db86212c5e1f/OceanDNA-a5075.fa]
[2023-03-18 22:17:21,263] [INFO] Query marker FASTA was written to OceanDNA-a5075/markers.fasta
[2023-03-18 22:17:21,265] [INFO] Task started: Blastn
[2023-03-18 22:17:21,265] [INFO] Running command: blastn -query OceanDNA-a5075/markers.fasta -db /var/lib/cwl/stgc49497fc-4e96-4b6b-8a4c-12978b64176c/dqc_reference/reference_markers.fasta -out OceanDNA-a5075/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:17:21,689] [INFO] Task succeeded: Blastn
[2023-03-18 22:17:21,693] [INFO] Selected 1 target genomes.
[2023-03-18 22:17:21,693] [INFO] Target genome list was writen to OceanDNA-a5075/target_genomes.txt
[2023-03-18 22:17:21,694] [INFO] Task started: fastANI
[2023-03-18 22:17:21,694] [INFO] Running command: fastANI --query /var/lib/cwl/stge4c48547-2753-45fa-9d27-db86212c5e1f/OceanDNA-a5075.fa --refList OceanDNA-a5075/target_genomes.txt --output OceanDNA-a5075/fastani_result.tsv --threads 1
[2023-03-18 22:17:22,332] [INFO] Task succeeded: fastANI
[2023-03-18 22:17:22,332] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc49497fc-4e96-4b6b-8a4c-12978b64176c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:17:22,332] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc49497fc-4e96-4b6b-8a4c-12978b64176c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:17:22,333] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:17:22,333] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:17:22,333] [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
--------------------------------------------------------------------------------
[2023-03-18 22:17:22,333] [INFO] DFAST Taxonomy check result was written to OceanDNA-a5075/tc_result.tsv
[2023-03-18 22:17:22,333] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:17:22,333] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:17:22,333] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc49497fc-4e96-4b6b-8a4c-12978b64176c/dqc_reference/checkm_data
[2023-03-18 22:17:22,336] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:17:22,339] [INFO] Task started: CheckM
[2023-03-18 22:17:22,339] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a5075/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a5075/checkm_input OceanDNA-a5075/checkm_result
[2023-03-18 22:17:46,289] [INFO] Task succeeded: CheckM
[2023-03-18 22:17:46,289] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:17:46,308] [INFO] ===== Completeness check finished =====
[2023-03-18 22:17:46,308] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:17:46,309] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a5075/markers.fasta)
[2023-03-18 22:17:46,310] [INFO] Task started: Blastn
[2023-03-18 22:17:46,310] [INFO] Running command: blastn -query OceanDNA-a5075/markers.fasta -db /var/lib/cwl/stgc49497fc-4e96-4b6b-8a4c-12978b64176c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a5075/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:17:46,750] [INFO] Task succeeded: Blastn
[2023-03-18 22:17:46,751] [INFO] Selected 7 target genomes.
[2023-03-18 22:17:46,751] [INFO] Target genome list was writen to OceanDNA-a5075/target_genomes_gtdb.txt
[2023-03-18 22:17:46,758] [INFO] Task started: fastANI
[2023-03-18 22:17:46,758] [INFO] Running command: fastANI --query /var/lib/cwl/stge4c48547-2753-45fa-9d27-db86212c5e1f/OceanDNA-a5075.fa --refList OceanDNA-a5075/target_genomes_gtdb.txt --output OceanDNA-a5075/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:17:48,540] [INFO] Task succeeded: fastANI
[2023-03-18 22:17:48,544] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 22:17:48,544] [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_002503055.1	s__Thalassarchaeum sp002503055	97.8295	360	420	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	99.71	99.22	0.93	0.84	5	conclusive
GCA_002501885.1	s__Thalassarchaeum sp002501885	89.2167	328	420	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	98.85	97.05	0.83	0.68	9	-
GCA_002727275.1	s__Thalassarchaeum sp002727275	80.4813	270	420	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698225.1	s__Thalassarchaeum sp002698225	78.6477	195	420	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	99.66	99.66	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-03-18 22:17:48,545] [INFO] GTDB search result was written to OceanDNA-a5075/result_gtdb.tsv
[2023-03-18 22:17:48,547] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:17:48,549] [INFO] DFAST_QC result json was written to OceanDNA-a5075/dqc_result.json
[2023-03-18 22:17:48,549] [INFO] DFAST_QC completed!
[2023-03-18 22:17:48,549] [INFO] Total running time: 0h0m36s