[2023-03-15 03:56:21,754] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:56:21,754] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:56:21,754] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0521165-cf77-47d4-9101-8a14e682d819/dqc_reference
[2023-03-15 03:56:23,406] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:56:23,406] [INFO] Task started: Prodigal
[2023-03-15 03:56:23,407] [INFO] Running command: cat /var/lib/cwl/stg1532d3a8-7eb6-4d54-a4be-dd2e092b0f73/OceanDNA-a3297.fa | prodigal -d OceanDNA-a3297/cds.fna -a OceanDNA-a3297/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:56:30,900] [INFO] Task succeeded: Prodigal
[2023-03-15 03:56:30,901] [INFO] Task started: HMMsearch
[2023-03-15 03:56:30,901] [INFO] Running command: hmmsearch --tblout OceanDNA-a3297/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0521165-cf77-47d4-9101-8a14e682d819/dqc_reference/reference_markers.hmm OceanDNA-a3297/protein.faa > /dev/null
[2023-03-15 03:56:31,109] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:56:31,110] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg1532d3a8-7eb6-4d54-a4be-dd2e092b0f73/OceanDNA-a3297.fa]
[2023-03-15 03:56:31,119] [INFO] Query marker FASTA was written to OceanDNA-a3297/markers.fasta
[2023-03-15 03:56:31,119] [INFO] Task started: Blastn
[2023-03-15 03:56:31,119] [INFO] Running command: blastn -query OceanDNA-a3297/markers.fasta -db /var/lib/cwl/stgc0521165-cf77-47d4-9101-8a14e682d819/dqc_reference/reference_markers.fasta -out OceanDNA-a3297/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:56:31,557] [INFO] Task succeeded: Blastn
[2023-03-15 03:56:31,557] [INFO] Selected 5 target genomes.
[2023-03-15 03:56:31,558] [INFO] Target genome list was writen to OceanDNA-a3297/target_genomes.txt
[2023-03-15 03:56:31,570] [INFO] Task started: fastANI
[2023-03-15 03:56:31,570] [INFO] Running command: fastANI --query /var/lib/cwl/stg1532d3a8-7eb6-4d54-a4be-dd2e092b0f73/OceanDNA-a3297.fa --refList OceanDNA-a3297/target_genomes.txt --output OceanDNA-a3297/fastani_result.tsv --threads 1
[2023-03-15 03:56:34,324] [INFO] Task succeeded: fastANI
[2023-03-15 03:56:34,324] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0521165-cf77-47d4-9101-8a14e682d819/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:56:34,325] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0521165-cf77-47d4-9101-8a14e682d819/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:56:34,325] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:56:34,325] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 03:56:34,325] [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 03:56:34,325] [INFO] DFAST Taxonomy check result was written to OceanDNA-a3297/tc_result.tsv
[2023-03-15 03:56:34,325] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:56:34,325] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:56:34,326] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0521165-cf77-47d4-9101-8a14e682d819/dqc_reference/checkm_data
[2023-03-15 03:56:34,328] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:56:34,331] [INFO] Task started: CheckM
[2023-03-15 03:56:34,331] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3297/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3297/checkm_input OceanDNA-a3297/checkm_result
[2023-03-15 03:56:58,990] [INFO] Task succeeded: CheckM
[2023-03-15 03:56:58,990] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.88%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:56:58,992] [INFO] ===== Completeness check finished =====
[2023-03-15 03:56:58,992] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:56:58,992] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3297/markers.fasta)
[2023-03-15 03:56:58,992] [INFO] Task started: Blastn
[2023-03-15 03:56:58,992] [INFO] Running command: blastn -query OceanDNA-a3297/markers.fasta -db /var/lib/cwl/stgc0521165-cf77-47d4-9101-8a14e682d819/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3297/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:56:59,424] [INFO] Task succeeded: Blastn
[2023-03-15 03:56:59,425] [INFO] Selected 6 target genomes.
[2023-03-15 03:56:59,425] [INFO] Target genome list was writen to OceanDNA-a3297/target_genomes_gtdb.txt
[2023-03-15 03:56:59,433] [INFO] Task started: fastANI
[2023-03-15 03:56:59,433] [INFO] Running command: fastANI --query /var/lib/cwl/stg1532d3a8-7eb6-4d54-a4be-dd2e092b0f73/OceanDNA-a3297.fa --refList OceanDNA-a3297/target_genomes_gtdb.txt --output OceanDNA-a3297/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:57:01,485] [INFO] Task succeeded: fastANI
[2023-03-15 03:57:01,490] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 03:57:01,490] [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_002504845.1	s__MGIIb-N1 sp002504845	97.49	317	408	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N1	95.0	98.34	97.20	0.81	0.69	5	conclusive
GCA_002712645.1	s__MGIIb-N1 sp002712645	90.861	353	408	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002497295.1	s__MGIIb-N1 sp002497295	90.4225	357	408	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002170775.2	s__MGIIb-N1 sp002170775	88.923	366	408	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002505455.1	s__MGIIb-N1 sp002505455	86.161	349	408	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N1	95.0	98.69	95.53	0.89	0.80	5	-
GCA_002717835.1	s__MGIIb-N1 sp002717835	85.7631	283	408	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 03:57:01,490] [INFO] GTDB search result was written to OceanDNA-a3297/result_gtdb.tsv
[2023-03-15 03:57:01,490] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:57:01,491] [INFO] DFAST_QC result json was written to OceanDNA-a3297/dqc_result.json
[2023-03-15 03:57:01,491] [INFO] DFAST_QC completed!
[2023-03-15 03:57:01,491] [INFO] Total running time: 0h0m40s