[2023-03-19 00:18:46,061] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:18:46,061] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:18:46,061] [INFO] DQC Reference Directory: /var/lib/cwl/stg5484e26a-6650-4d5b-9b9e-97de4f43d72a/dqc_reference
[2023-03-19 00:18:47,195] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:18:47,195] [INFO] Task started: Prodigal
[2023-03-19 00:18:47,195] [INFO] Running command: cat /var/lib/cwl/stgbfbca27b-4d74-4a05-9763-da5a4b89c359/OceanDNA-a1986.fa | prodigal -d OceanDNA-a1986/cds.fna -a OceanDNA-a1986/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:18:56,049] [INFO] Task succeeded: Prodigal
[2023-03-19 00:18:56,049] [INFO] Task started: HMMsearch
[2023-03-19 00:18:56,049] [INFO] Running command: hmmsearch --tblout OceanDNA-a1986/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5484e26a-6650-4d5b-9b9e-97de4f43d72a/dqc_reference/reference_markers.hmm OceanDNA-a1986/protein.faa > /dev/null
[2023-03-19 00:18:56,203] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:18:56,203] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgbfbca27b-4d74-4a05-9763-da5a4b89c359/OceanDNA-a1986.fa]
[2023-03-19 00:18:56,215] [INFO] Query marker FASTA was written to OceanDNA-a1986/markers.fasta
[2023-03-19 00:18:56,217] [INFO] Task started: Blastn
[2023-03-19 00:18:56,217] [INFO] Running command: blastn -query OceanDNA-a1986/markers.fasta -db /var/lib/cwl/stg5484e26a-6650-4d5b-9b9e-97de4f43d72a/dqc_reference/reference_markers.fasta -out OceanDNA-a1986/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:18:56,687] [INFO] Task succeeded: Blastn
[2023-03-19 00:18:56,688] [INFO] Selected 5 target genomes.
[2023-03-19 00:18:56,688] [INFO] Target genome list was writen to OceanDNA-a1986/target_genomes.txt
[2023-03-19 00:18:56,691] [INFO] Task started: fastANI
[2023-03-19 00:18:56,691] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfbca27b-4d74-4a05-9763-da5a4b89c359/OceanDNA-a1986.fa --refList OceanDNA-a1986/target_genomes.txt --output OceanDNA-a1986/fastani_result.tsv --threads 1
[2023-03-19 00:18:58,930] [INFO] Task succeeded: fastANI
[2023-03-19 00:18:58,931] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5484e26a-6650-4d5b-9b9e-97de4f43d72a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:18:58,931] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5484e26a-6650-4d5b-9b9e-97de4f43d72a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:18:58,931] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:18:58,931] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:18:58,931] [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
--------------------------------------------------------------------------------
[2023-03-19 00:18:59,144] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1986/tc_result.tsv
[2023-03-19 00:18:59,144] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:18:59,144] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:18:59,144] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5484e26a-6650-4d5b-9b9e-97de4f43d72a/dqc_reference/checkm_data
[2023-03-19 00:18:59,147] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:18:59,183] [INFO] Task started: CheckM
[2023-03-19 00:18:59,183] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1986/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1986/checkm_input OceanDNA-a1986/checkm_result
[2023-03-19 00:19:26,513] [INFO] Task succeeded: CheckM
[2023-03-19 00:19:26,513] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:19:26,515] [INFO] ===== Completeness check finished =====
[2023-03-19 00:19:26,515] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:19:26,516] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1986/markers.fasta)
[2023-03-19 00:19:26,517] [INFO] Task started: Blastn
[2023-03-19 00:19:26,517] [INFO] Running command: blastn -query OceanDNA-a1986/markers.fasta -db /var/lib/cwl/stg5484e26a-6650-4d5b-9b9e-97de4f43d72a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1986/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:19:27,777] [INFO] Task succeeded: Blastn
[2023-03-19 00:19:27,777] [INFO] Selected 8 target genomes.
[2023-03-19 00:19:27,778] [INFO] Target genome list was writen to OceanDNA-a1986/target_genomes_gtdb.txt
[2023-03-19 00:19:27,788] [INFO] Task started: fastANI
[2023-03-19 00:19:27,788] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfbca27b-4d74-4a05-9763-da5a4b89c359/OceanDNA-a1986.fa --refList OceanDNA-a1986/target_genomes_gtdb.txt --output OceanDNA-a1986/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:19:30,208] [INFO] Task succeeded: fastANI
[2023-03-19 00:19:30,213] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:19:30,213] [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_002706615.1	s__MGIIa-K1 sp002706615	98.2499	464	529	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	98.10	98.10	0.84	0.84	2	conclusive
GCA_009936765.1	s__MGIIa-K1 sp009936765	77.4908	67	529	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	98.29	98.25	0.77	0.75	3	-
GCA_003602415.1	s__MGIIa-K1 sp003602415	77.0773	83	529	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	97.94	97.94	0.93	0.93	2	-
GCA_902605365.1	s__MGIIa-K1 sp902605365	77.0296	71	529	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709705.1	s__MGIIa-K1 sp002709705	76.7847	69	529	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002727695.1	s__MGIIa-K1 sp002727695	76.0032	60	529	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:19:30,213] [INFO] GTDB search result was written to OceanDNA-a1986/result_gtdb.tsv
[2023-03-19 00:19:30,213] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:19:30,214] [INFO] DFAST_QC result json was written to OceanDNA-a1986/dqc_result.json
[2023-03-19 00:19:30,214] [INFO] DFAST_QC completed!
[2023-03-19 00:19:30,214] [INFO] Total running time: 0h0m44s