[2023-03-19 00:15:41,734] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:15:41,734] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:15:41,734] [INFO] DQC Reference Directory: /var/lib/cwl/stg1dac81e8-a73c-4b5f-b3d6-fcdd11b29bab/dqc_reference
[2023-03-19 00:15:43,440] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:15:43,441] [INFO] Task started: Prodigal
[2023-03-19 00:15:43,441] [INFO] Running command: cat /var/lib/cwl/stgc81eedfb-896b-41ea-825f-b1ab72a2b027/OceanDNA-a749.fa | prodigal -d OceanDNA-a749/cds.fna -a OceanDNA-a749/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:15:47,773] [INFO] Task succeeded: Prodigal
[2023-03-19 00:15:47,773] [INFO] Task started: HMMsearch
[2023-03-19 00:15:47,774] [INFO] Running command: hmmsearch --tblout OceanDNA-a749/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1dac81e8-a73c-4b5f-b3d6-fcdd11b29bab/dqc_reference/reference_markers.hmm OceanDNA-a749/protein.faa > /dev/null
[2023-03-19 00:15:47,889] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:15:47,890] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgc81eedfb-896b-41ea-825f-b1ab72a2b027/OceanDNA-a749.fa]
[2023-03-19 00:15:47,899] [INFO] Query marker FASTA was written to OceanDNA-a749/markers.fasta
[2023-03-19 00:15:47,900] [INFO] Task started: Blastn
[2023-03-19 00:15:47,900] [INFO] Running command: blastn -query OceanDNA-a749/markers.fasta -db /var/lib/cwl/stg1dac81e8-a73c-4b5f-b3d6-fcdd11b29bab/dqc_reference/reference_markers.fasta -out OceanDNA-a749/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:15:48,322] [INFO] Task succeeded: Blastn
[2023-03-19 00:15:48,323] [INFO] Selected 5 target genomes.
[2023-03-19 00:15:48,323] [INFO] Target genome list was writen to OceanDNA-a749/target_genomes.txt
[2023-03-19 00:15:48,329] [INFO] Task started: fastANI
[2023-03-19 00:15:48,329] [INFO] Running command: fastANI --query /var/lib/cwl/stgc81eedfb-896b-41ea-825f-b1ab72a2b027/OceanDNA-a749.fa --refList OceanDNA-a749/target_genomes.txt --output OceanDNA-a749/fastani_result.tsv --threads 1
[2023-03-19 00:15:50,040] [INFO] Task succeeded: fastANI
[2023-03-19 00:15:50,041] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1dac81e8-a73c-4b5f-b3d6-fcdd11b29bab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:15:50,041] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1dac81e8-a73c-4b5f-b3d6-fcdd11b29bab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:15:50,048] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:15:50,048] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:15:50,049] [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 ureiphilus	strain=PS0	GCA_013407185.1	1470067	1470067	type	True	81.8363	226	263	95	below_threshold
Nitrosopumilus cobalaminigenes	strain=HCA1	GCA_013407145.1	1470066	1470066	type	True	81.1989	221	263	95	below_threshold
Nitrosopumilus adriaticus	strain=NF5	GCA_000956175.1	1580092	1580092	type	True	81.1267	218	263	95	below_threshold
Nitrosopumilus oxyclinae	strain=HCE1	GCA_013407165.1	1959104	1959104	type	True	81.0882	216	263	95	below_threshold
Nitrosopumilus piranensis	strain=D3C	GCA_000875775.1	1582439	1582439	type	True	80.8638	202	263	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:15:50,049] [INFO] DFAST Taxonomy check result was written to OceanDNA-a749/tc_result.tsv
[2023-03-19 00:15:50,049] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:15:50,049] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:15:50,050] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1dac81e8-a73c-4b5f-b3d6-fcdd11b29bab/dqc_reference/checkm_data
[2023-03-19 00:15:50,051] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:15:50,060] [INFO] Task started: CheckM
[2023-03-19 00:15:50,060] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a749/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a749/checkm_input OceanDNA-a749/checkm_result
[2023-03-19 00:16:08,184] [INFO] Task succeeded: CheckM
[2023-03-19 00:16:08,184] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.05%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 00:16:08,186] [INFO] ===== Completeness check finished =====
[2023-03-19 00:16:08,186] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:16:08,186] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a749/markers.fasta)
[2023-03-19 00:16:08,187] [INFO] Task started: Blastn
[2023-03-19 00:16:08,187] [INFO] Running command: blastn -query OceanDNA-a749/markers.fasta -db /var/lib/cwl/stg1dac81e8-a73c-4b5f-b3d6-fcdd11b29bab/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a749/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:16:08,580] [INFO] Task succeeded: Blastn
[2023-03-19 00:16:08,581] [INFO] Selected 5 target genomes.
[2023-03-19 00:16:08,581] [INFO] Target genome list was writen to OceanDNA-a749/target_genomes_gtdb.txt
[2023-03-19 00:16:08,612] [INFO] Task started: fastANI
[2023-03-19 00:16:08,612] [INFO] Running command: fastANI --query /var/lib/cwl/stgc81eedfb-896b-41ea-825f-b1ab72a2b027/OceanDNA-a749.fa --refList OceanDNA-a749/target_genomes_gtdb.txt --output OceanDNA-a749/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:16:09,989] [INFO] Task succeeded: fastANI
[2023-03-19 00:16:09,993] [INFO] Found 5 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-19 00:16:09,993] [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_013390905.1	s__Nitrosopumilus sp013390905	99.7573	254	263	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0649	99.67	99.07	0.94	0.85	10	inconclusive
GCA_000484975.1	s__Nitrosopumilus sp000484975	95.0956	200	263	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0649	N/A	N/A	N/A	N/A	1	inconclusive
GCA_013911135.1	s__Nitrosopumilus sp013911135	87.8697	241	263	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001510275.1	s__Nitrosopumilus sp001510275	87.1922	242	263	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002730325.1	s__Nitrosopumilus sp002730325	80.9225	193	263	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:16:09,993] [INFO] GTDB search result was written to OceanDNA-a749/result_gtdb.tsv
[2023-03-19 00:16:09,994] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:16:09,994] [INFO] DFAST_QC result json was written to OceanDNA-a749/dqc_result.json
[2023-03-19 00:16:09,995] [INFO] DFAST_QC completed!
[2023-03-19 00:16:09,995] [INFO] Total running time: 0h0m28s