[2023-03-15 05:51:32,066] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:51:32,067] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:51:32,067] [INFO] DQC Reference Directory: /var/lib/cwl/stgd999ea88-60ae-4faa-9ed6-42cd003d0d21/dqc_reference
[2023-03-15 05:51:33,647] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:51:33,648] [INFO] Task started: Prodigal
[2023-03-15 05:51:33,648] [INFO] Running command: cat /var/lib/cwl/stgeec8899f-b4ed-4989-944a-d667dcf16164/OceanDNA-a213.fa | prodigal -d OceanDNA-a213/cds.fna -a OceanDNA-a213/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:51:38,478] [INFO] Task succeeded: Prodigal
[2023-03-15 05:51:38,478] [INFO] Task started: HMMsearch
[2023-03-15 05:51:38,478] [INFO] Running command: hmmsearch --tblout OceanDNA-a213/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd999ea88-60ae-4faa-9ed6-42cd003d0d21/dqc_reference/reference_markers.hmm OceanDNA-a213/protein.faa > /dev/null
[2023-03-15 05:51:38,648] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:51:38,648] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgeec8899f-b4ed-4989-944a-d667dcf16164/OceanDNA-a213.fa]
[2023-03-15 05:51:38,659] [INFO] Query marker FASTA was written to OceanDNA-a213/markers.fasta
[2023-03-15 05:51:38,660] [INFO] Task started: Blastn
[2023-03-15 05:51:38,661] [INFO] Running command: blastn -query OceanDNA-a213/markers.fasta -db /var/lib/cwl/stgd999ea88-60ae-4faa-9ed6-42cd003d0d21/dqc_reference/reference_markers.fasta -out OceanDNA-a213/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:51:41,936] [INFO] Task succeeded: Blastn
[2023-03-15 05:51:41,940] [INFO] Selected 1 target genomes.
[2023-03-15 05:51:41,941] [INFO] Target genome list was writen to OceanDNA-a213/target_genomes.txt
[2023-03-15 05:51:41,942] [INFO] Task started: fastANI
[2023-03-15 05:51:41,942] [INFO] Running command: fastANI --query /var/lib/cwl/stgeec8899f-b4ed-4989-944a-d667dcf16164/OceanDNA-a213.fa --refList OceanDNA-a213/target_genomes.txt --output OceanDNA-a213/fastani_result.tsv --threads 1
[2023-03-15 05:51:42,274] [INFO] Task succeeded: fastANI
[2023-03-15 05:51:42,274] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd999ea88-60ae-4faa-9ed6-42cd003d0d21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:51:42,275] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd999ea88-60ae-4faa-9ed6-42cd003d0d21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:51:42,285] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:51:42,285] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 05:51:42,285] [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
Nitrosopumilus adriaticus	strain=NF5	GCA_000956175.1	1580092	1580092	type	True	76.5672	91	295	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:51:42,287] [INFO] DFAST Taxonomy check result was written to OceanDNA-a213/tc_result.tsv
[2023-03-15 05:51:42,288] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:51:42,288] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:51:42,288] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd999ea88-60ae-4faa-9ed6-42cd003d0d21/dqc_reference/checkm_data
[2023-03-15 05:51:42,289] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:51:42,292] [INFO] Task started: CheckM
[2023-03-15 05:51:42,292] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a213/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a213/checkm_input OceanDNA-a213/checkm_result
[2023-03-15 05:52:03,045] [INFO] Task succeeded: CheckM
[2023-03-15 05:52:03,045] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:52:03,053] [INFO] ===== Completeness check finished =====
[2023-03-15 05:52:03,053] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:52:03,053] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a213/markers.fasta)
[2023-03-15 05:52:03,054] [INFO] Task started: Blastn
[2023-03-15 05:52:03,055] [INFO] Running command: blastn -query OceanDNA-a213/markers.fasta -db /var/lib/cwl/stgd999ea88-60ae-4faa-9ed6-42cd003d0d21/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a213/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:52:03,587] [INFO] Task succeeded: Blastn
[2023-03-15 05:52:03,590] [INFO] Selected 5 target genomes.
[2023-03-15 05:52:03,590] [INFO] Target genome list was writen to OceanDNA-a213/target_genomes_gtdb.txt
[2023-03-15 05:52:03,594] [INFO] Task started: fastANI
[2023-03-15 05:52:03,595] [INFO] Running command: fastANI --query /var/lib/cwl/stgeec8899f-b4ed-4989-944a-d667dcf16164/OceanDNA-a213.fa --refList OceanDNA-a213/target_genomes_gtdb.txt --output OceanDNA-a213/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:52:04,477] [INFO] Task succeeded: fastANI
[2023-03-15 05:52:04,481] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:52:04,481] [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_002698885.1	s__Nitrosopelagicus sp002698885	83.8818	145	295	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902512865.1	s__Nitrosopelagicus sp902512865	79.8064	82	295	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018647405.1	s__Nitrosopelagicus sp018647405	78.8805	153	295	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	99.40	99.17	0.85	0.83	12	-
GCA_902511735.1	s__Nitrosopelagicus sp902511735	78.8549	98	295	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001627235.1	s__Nitrosopelagicus sp001627235	77.9929	124	295	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	97.70	95.15	0.86	0.83	5	-
--------------------------------------------------------------------------------
[2023-03-15 05:52:04,482] [INFO] GTDB search result was written to OceanDNA-a213/result_gtdb.tsv
[2023-03-15 05:52:04,484] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:52:04,485] [INFO] DFAST_QC result json was written to OceanDNA-a213/dqc_result.json
[2023-03-15 05:52:04,485] [INFO] DFAST_QC completed!
[2023-03-15 05:52:04,485] [INFO] Total running time: 0h0m32s