[2023-03-18 02:27:54,722] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:27:54,722] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:27:54,722] [INFO] DQC Reference Directory: /var/lib/cwl/stg241a0e8a-dd34-41ef-8f4b-b65b647cce6f/dqc_reference
[2023-03-18 02:27:55,934] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:27:55,934] [INFO] Task started: Prodigal
[2023-03-18 02:27:55,934] [INFO] Running command: cat /var/lib/cwl/stg3e3cd99d-938b-44bf-bfc9-14587ec4eb38/OceanDNA-a158.fa | prodigal -d OceanDNA-a158/cds.fna -a OceanDNA-a158/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:28:01,328] [INFO] Task succeeded: Prodigal
[2023-03-18 02:28:01,328] [INFO] Task started: HMMsearch
[2023-03-18 02:28:01,328] [INFO] Running command: hmmsearch --tblout OceanDNA-a158/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg241a0e8a-dd34-41ef-8f4b-b65b647cce6f/dqc_reference/reference_markers.hmm OceanDNA-a158/protein.faa > /dev/null
[2023-03-18 02:28:01,511] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:28:01,512] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg3e3cd99d-938b-44bf-bfc9-14587ec4eb38/OceanDNA-a158.fa]
[2023-03-18 02:28:01,521] [INFO] Query marker FASTA was written to OceanDNA-a158/markers.fasta
[2023-03-18 02:28:01,521] [INFO] Task started: Blastn
[2023-03-18 02:28:01,521] [INFO] Running command: blastn -query OceanDNA-a158/markers.fasta -db /var/lib/cwl/stg241a0e8a-dd34-41ef-8f4b-b65b647cce6f/dqc_reference/reference_markers.fasta -out OceanDNA-a158/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:28:01,939] [INFO] Task succeeded: Blastn
[2023-03-18 02:28:01,940] [INFO] Selected 4 target genomes.
[2023-03-18 02:28:01,940] [INFO] Target genome list was writen to OceanDNA-a158/target_genomes.txt
[2023-03-18 02:28:01,942] [INFO] Task started: fastANI
[2023-03-18 02:28:01,942] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e3cd99d-938b-44bf-bfc9-14587ec4eb38/OceanDNA-a158.fa --refList OceanDNA-a158/target_genomes.txt --output OceanDNA-a158/fastani_result.tsv --threads 1
[2023-03-18 02:28:03,318] [INFO] Task succeeded: fastANI
[2023-03-18 02:28:03,319] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg241a0e8a-dd34-41ef-8f4b-b65b647cce6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:28:03,319] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg241a0e8a-dd34-41ef-8f4b-b65b647cce6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:28:03,323] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:28:03,323] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 02:28:03,323] [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 oxyclinae	strain=HCE1	GCA_013407165.1	1959104	1959104	type	True	77.1561	107	338	95	below_threshold
Nitrosopumilus adriaticus	strain=NF5	GCA_000956175.1	1580092	1580092	type	True	76.7016	97	338	95	below_threshold
Nitrosopumilus ureiphilus	strain=PS0	GCA_013407185.1	1470067	1470067	type	True	76.6895	85	338	95	below_threshold
Nitrosopumilus piranensis	strain=D3C	GCA_000875775.1	1582439	1582439	type	True	76.5298	97	338	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 02:28:03,323] [INFO] DFAST Taxonomy check result was written to OceanDNA-a158/tc_result.tsv
[2023-03-18 02:28:03,323] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:28:03,324] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:28:03,324] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg241a0e8a-dd34-41ef-8f4b-b65b647cce6f/dqc_reference/checkm_data
[2023-03-18 02:28:03,324] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:28:03,332] [INFO] Task started: CheckM
[2023-03-18 02:28:03,332] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a158/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a158/checkm_input OceanDNA-a158/checkm_result
[2023-03-18 02:28:22,890] [INFO] Task succeeded: CheckM
[2023-03-18 02:28:22,890] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.73%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:28:22,892] [INFO] ===== Completeness check finished =====
[2023-03-18 02:28:22,892] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:28:22,892] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a158/markers.fasta)
[2023-03-18 02:28:22,893] [INFO] Task started: Blastn
[2023-03-18 02:28:22,893] [INFO] Running command: blastn -query OceanDNA-a158/markers.fasta -db /var/lib/cwl/stg241a0e8a-dd34-41ef-8f4b-b65b647cce6f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a158/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:28:23,275] [INFO] Task succeeded: Blastn
[2023-03-18 02:28:23,275] [INFO] Selected 5 target genomes.
[2023-03-18 02:28:23,275] [INFO] Target genome list was writen to OceanDNA-a158/target_genomes_gtdb.txt
[2023-03-18 02:28:23,284] [INFO] Task started: fastANI
[2023-03-18 02:28:23,284] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e3cd99d-938b-44bf-bfc9-14587ec4eb38/OceanDNA-a158.fa --refList OceanDNA-a158/target_genomes_gtdb.txt --output OceanDNA-a158/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:28:24,376] [INFO] Task succeeded: fastANI
[2023-03-18 02:28:24,380] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 02:28:24,380] [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_018647405.1	s__Nitrosopelagicus sp018647405	99.4571	284	338	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	99.40	99.17	0.85	0.83	12	conclusive
GCA_001510295.1	s__Nitrosopelagicus sp001510295	90.1846	180	338	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	87.6911	141	338	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902511735.1	s__Nitrosopelagicus sp902511735	87.4639	171	338	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000812185.1	s__Nitrosopelagicus brevis	87.3102	314	338	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	97.23	96.14	0.93	0.87	7	-
--------------------------------------------------------------------------------
[2023-03-18 02:28:24,381] [INFO] GTDB search result was written to OceanDNA-a158/result_gtdb.tsv
[2023-03-18 02:28:24,381] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:28:24,382] [INFO] DFAST_QC result json was written to OceanDNA-a158/dqc_result.json
[2023-03-18 02:28:24,382] [INFO] DFAST_QC completed!
[2023-03-18 02:28:24,382] [INFO] Total running time: 0h0m30s