[2023-03-14 11:17:27,735] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:17:27,735] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:17:27,735] [INFO] DQC Reference Directory: /var/lib/cwl/stg711c1d5a-1df7-4039-8efd-0f83a8d07ac8/dqc_reference
[2023-03-14 11:17:28,854] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:17:28,855] [INFO] Task started: Prodigal
[2023-03-14 11:17:28,855] [INFO] Running command: cat /var/lib/cwl/stg0d6cad44-d631-46c6-80ac-4e10e3838206/OceanDNA-a434.fa | prodigal -d OceanDNA-a434/cds.fna -a OceanDNA-a434/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:17:32,810] [INFO] Task succeeded: Prodigal
[2023-03-14 11:17:32,810] [INFO] Task started: HMMsearch
[2023-03-14 11:17:32,810] [INFO] Running command: hmmsearch --tblout OceanDNA-a434/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg711c1d5a-1df7-4039-8efd-0f83a8d07ac8/dqc_reference/reference_markers.hmm OceanDNA-a434/protein.faa > /dev/null
[2023-03-14 11:17:32,931] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:17:32,931] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg0d6cad44-d631-46c6-80ac-4e10e3838206/OceanDNA-a434.fa]
[2023-03-14 11:17:32,941] [INFO] Query marker FASTA was written to OceanDNA-a434/markers.fasta
[2023-03-14 11:17:32,943] [INFO] Task started: Blastn
[2023-03-14 11:17:32,943] [INFO] Running command: blastn -query OceanDNA-a434/markers.fasta -db /var/lib/cwl/stg711c1d5a-1df7-4039-8efd-0f83a8d07ac8/dqc_reference/reference_markers.fasta -out OceanDNA-a434/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:17:33,400] [INFO] Task succeeded: Blastn
[2023-03-14 11:17:33,401] [INFO] Selected 2 target genomes.
[2023-03-14 11:17:33,402] [INFO] Target genome list was writen to OceanDNA-a434/target_genomes.txt
[2023-03-14 11:17:33,403] [INFO] Task started: fastANI
[2023-03-14 11:17:33,403] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d6cad44-d631-46c6-80ac-4e10e3838206/OceanDNA-a434.fa --refList OceanDNA-a434/target_genomes.txt --output OceanDNA-a434/fastani_result.tsv --threads 1
[2023-03-14 11:17:34,002] [INFO] Task succeeded: fastANI
[2023-03-14 11:17:34,003] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg711c1d5a-1df7-4039-8efd-0f83a8d07ac8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:17:34,003] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg711c1d5a-1df7-4039-8efd-0f83a8d07ac8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:17:34,007] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:17:34,007] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:17:34,007] [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	77.1696	69	220	95	below_threshold
Nitrosopumilus ureiphilus	strain=PS0	GCA_013407185.1	1470067	1470067	type	True	77.0576	59	220	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:17:34,007] [INFO] DFAST Taxonomy check result was written to OceanDNA-a434/tc_result.tsv
[2023-03-14 11:17:34,007] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:17:34,007] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:17:34,007] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg711c1d5a-1df7-4039-8efd-0f83a8d07ac8/dqc_reference/checkm_data
[2023-03-14 11:17:34,008] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:17:34,011] [INFO] Task started: CheckM
[2023-03-14 11:17:34,011] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a434/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a434/checkm_input OceanDNA-a434/checkm_result
[2023-03-14 11:17:50,706] [INFO] Task succeeded: CheckM
[2023-03-14 11:17:50,706] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.95%
Contamintation: 4.63%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:17:50,710] [INFO] ===== Completeness check finished =====
[2023-03-14 11:17:50,710] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:17:50,710] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a434/markers.fasta)
[2023-03-14 11:17:50,712] [INFO] Task started: Blastn
[2023-03-14 11:17:50,712] [INFO] Running command: blastn -query OceanDNA-a434/markers.fasta -db /var/lib/cwl/stg711c1d5a-1df7-4039-8efd-0f83a8d07ac8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a434/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:17:51,224] [INFO] Task succeeded: Blastn
[2023-03-14 11:17:51,225] [INFO] Selected 5 target genomes.
[2023-03-14 11:17:51,225] [INFO] Target genome list was writen to OceanDNA-a434/target_genomes_gtdb.txt
[2023-03-14 11:17:51,234] [INFO] Task started: fastANI
[2023-03-14 11:17:51,234] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d6cad44-d631-46c6-80ac-4e10e3838206/OceanDNA-a434.fa --refList OceanDNA-a434/target_genomes_gtdb.txt --output OceanDNA-a434/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:17:52,130] [INFO] Task succeeded: fastANI
[2023-03-14 11:17:52,134] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:17:52,134] [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
GCF_000812185.1	s__Nitrosopelagicus brevis	97.3605	217	220	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	97.23	96.14	0.93	0.87	7	conclusive
GCA_902511735.1	s__Nitrosopelagicus sp902511735	87.9266	124	220	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	87.251	192	220	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	99.40	99.17	0.85	0.83	12	-
GCA_001510295.1	s__Nitrosopelagicus sp001510295	86.4085	138	220	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	85.1878	102	220	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:17:52,134] [INFO] GTDB search result was written to OceanDNA-a434/result_gtdb.tsv
[2023-03-14 11:17:52,134] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:17:52,135] [INFO] DFAST_QC result json was written to OceanDNA-a434/dqc_result.json
[2023-03-14 11:17:52,135] [INFO] DFAST_QC completed!
[2023-03-14 11:17:52,135] [INFO] Total running time: 0h0m24s