[2023-03-16 10:48:50,441] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:48:50,441] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:48:50,441] [INFO] DQC Reference Directory: /var/lib/cwl/stgacbb7a0d-3e6d-40e8-bf63-d2cc9fe4558f/dqc_reference
[2023-03-16 10:48:52,942] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:48:52,952] [INFO] Task started: Prodigal
[2023-03-16 10:48:52,952] [INFO] Running command: cat /var/lib/cwl/stg013e604a-c27a-4292-a695-6539ab1781a2/OceanDNA-a3689.fa | prodigal -d OceanDNA-a3689/cds.fna -a OceanDNA-a3689/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:49:03,673] [INFO] Task succeeded: Prodigal
[2023-03-16 10:49:03,674] [INFO] Task started: HMMsearch
[2023-03-16 10:49:03,674] [INFO] Running command: hmmsearch --tblout OceanDNA-a3689/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgacbb7a0d-3e6d-40e8-bf63-d2cc9fe4558f/dqc_reference/reference_markers.hmm OceanDNA-a3689/protein.faa > /dev/null
[2023-03-16 10:49:04,016] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:49:04,016] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg013e604a-c27a-4292-a695-6539ab1781a2/OceanDNA-a3689.fa]
[2023-03-16 10:49:04,046] [INFO] Query marker FASTA was written to OceanDNA-a3689/markers.fasta
[2023-03-16 10:49:04,048] [INFO] Task started: Blastn
[2023-03-16 10:49:04,048] [INFO] Running command: blastn -query OceanDNA-a3689/markers.fasta -db /var/lib/cwl/stgacbb7a0d-3e6d-40e8-bf63-d2cc9fe4558f/dqc_reference/reference_markers.fasta -out OceanDNA-a3689/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:49:04,577] [INFO] Task succeeded: Blastn
[2023-03-16 10:49:04,578] [INFO] Selected 5 target genomes.
[2023-03-16 10:49:04,578] [INFO] Target genome list was writen to OceanDNA-a3689/target_genomes.txt
[2023-03-16 10:49:04,585] [INFO] Task started: fastANI
[2023-03-16 10:49:04,586] [INFO] Running command: fastANI --query /var/lib/cwl/stg013e604a-c27a-4292-a695-6539ab1781a2/OceanDNA-a3689.fa --refList OceanDNA-a3689/target_genomes.txt --output OceanDNA-a3689/fastani_result.tsv --threads 1
[2023-03-16 10:49:07,756] [INFO] Task succeeded: fastANI
[2023-03-16 10:49:07,756] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgacbb7a0d-3e6d-40e8-bf63-d2cc9fe4558f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:49:07,757] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgacbb7a0d-3e6d-40e8-bf63-d2cc9fe4558f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:49:07,757] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:49:07,757] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 10:49:07,757] [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
--------------------------------------------------------------------------------
[2023-03-16 10:49:07,758] [INFO] DFAST Taxonomy check result was written to OceanDNA-a3689/tc_result.tsv
[2023-03-16 10:49:07,758] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:49:07,758] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:49:07,758] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgacbb7a0d-3e6d-40e8-bf63-d2cc9fe4558f/dqc_reference/checkm_data
[2023-03-16 10:49:07,761] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:49:07,764] [INFO] Task started: CheckM
[2023-03-16 10:49:07,764] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3689/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3689/checkm_input OceanDNA-a3689/checkm_result
[2023-03-16 10:49:31,544] [INFO] Task succeeded: CheckM
[2023-03-16 10:49:31,545] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.61%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:49:31,547] [INFO] ===== Completeness check finished =====
[2023-03-16 10:49:31,547] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:49:31,547] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3689/markers.fasta)
[2023-03-16 10:49:31,572] [INFO] Task started: Blastn
[2023-03-16 10:49:31,572] [INFO] Running command: blastn -query OceanDNA-a3689/markers.fasta -db /var/lib/cwl/stgacbb7a0d-3e6d-40e8-bf63-d2cc9fe4558f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3689/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:49:32,127] [INFO] Task succeeded: Blastn
[2023-03-16 10:49:32,129] [INFO] Selected 9 target genomes.
[2023-03-16 10:49:32,129] [INFO] Target genome list was writen to OceanDNA-a3689/target_genomes_gtdb.txt
[2023-03-16 10:49:32,157] [INFO] Task started: fastANI
[2023-03-16 10:49:32,157] [INFO] Running command: fastANI --query /var/lib/cwl/stg013e604a-c27a-4292-a695-6539ab1781a2/OceanDNA-a3689.fa --refList OceanDNA-a3689/target_genomes_gtdb.txt --output OceanDNA-a3689/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:49:34,505] [INFO] Task succeeded: fastANI
[2023-03-16 10:49:34,510] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 10:49:34,510] [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_002685415.1	s__MGIIb-O1 sp002685415	97.2367	326	409	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	96.63	96.41	0.81	0.77	3	conclusive
GCA_002502175.1	s__MGIIb-O1 sp002502175	86.7588	320	409	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	98.79	95.28	0.87	0.80	11	-
GCA_002496905.1	s__MGIIb-O1 sp002496905	85.9773	289	409	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	99.08	98.67	0.77	0.73	3	-
GCA_902560445.1	s__MGIIb-O1 sp902560445	82.2658	221	409	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002457555.1	s__MGIIb-O1 sp002457555	82.1349	290	409	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	99.79	99.79	0.86	0.86	2	-
GCA_002502365.1	s__MGIIb-O1 sp002502365	81.3428	160	409	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	96.24	96.24	0.82	0.82	2	-
GCA_002708385.1	s__MGIIb-O1 sp002708385	81.0239	174	409	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:49:34,511] [INFO] GTDB search result was written to OceanDNA-a3689/result_gtdb.tsv
[2023-03-16 10:49:34,511] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:49:34,513] [INFO] DFAST_QC result json was written to OceanDNA-a3689/dqc_result.json
[2023-03-16 10:49:34,513] [INFO] DFAST_QC completed!
[2023-03-16 10:49:34,513] [INFO] Total running time: 0h0m44s