[2023-03-17 05:34:58,137] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:34:58,137] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:34:58,137] [INFO] DQC Reference Directory: /var/lib/cwl/stg1fef402e-6e13-4c53-a11c-c3deed2cbf99/dqc_reference
[2023-03-17 05:34:59,268] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:34:59,269] [INFO] Task started: Prodigal
[2023-03-17 05:34:59,269] [INFO] Running command: cat /var/lib/cwl/stga4773cc7-dea8-4860-afbf-e7e4cff9655c/OceanDNA-a506.fa | prodigal -d OceanDNA-a506/cds.fna -a OceanDNA-a506/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:35:03,015] [INFO] Task succeeded: Prodigal
[2023-03-17 05:35:03,016] [INFO] Task started: HMMsearch
[2023-03-17 05:35:03,016] [INFO] Running command: hmmsearch --tblout OceanDNA-a506/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1fef402e-6e13-4c53-a11c-c3deed2cbf99/dqc_reference/reference_markers.hmm OceanDNA-a506/protein.faa > /dev/null
[2023-03-17 05:35:03,123] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:35:03,123] [WARNING] Found 1/6 markers. [/var/lib/cwl/stga4773cc7-dea8-4860-afbf-e7e4cff9655c/OceanDNA-a506.fa]
[2023-03-17 05:35:03,141] [INFO] Query marker FASTA was written to OceanDNA-a506/markers.fasta
[2023-03-17 05:35:03,141] [INFO] Task started: Blastn
[2023-03-17 05:35:03,141] [INFO] Running command: blastn -query OceanDNA-a506/markers.fasta -db /var/lib/cwl/stg1fef402e-6e13-4c53-a11c-c3deed2cbf99/dqc_reference/reference_markers.fasta -out OceanDNA-a506/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:35:03,548] [INFO] Task succeeded: Blastn
[2023-03-17 05:35:03,550] [INFO] Selected 4 target genomes.
[2023-03-17 05:35:03,551] [INFO] Target genome list was writen to OceanDNA-a506/target_genomes.txt
[2023-03-17 05:35:03,553] [INFO] Task started: fastANI
[2023-03-17 05:35:03,553] [INFO] Running command: fastANI --query /var/lib/cwl/stga4773cc7-dea8-4860-afbf-e7e4cff9655c/OceanDNA-a506.fa --refList OceanDNA-a506/target_genomes.txt --output OceanDNA-a506/fastani_result.tsv --threads 1
[2023-03-17 05:35:04,725] [INFO] Task succeeded: fastANI
[2023-03-17 05:35:04,725] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1fef402e-6e13-4c53-a11c-c3deed2cbf99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:35:04,725] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1fef402e-6e13-4c53-a11c-c3deed2cbf99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:35:04,737] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:35:04,737] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 05:35:04,737] [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 cobalaminigenes	strain=HCA1	GCA_013407145.1	1470066	1470066	type	True	81.3832	184	215	95	below_threshold
Nitrosopumilus oxyclinae	strain=HCE1	GCA_013407165.1	1959104	1959104	type	True	81.3001	178	215	95	below_threshold
Nitrosopumilus adriaticus	strain=NF5	GCA_000956175.1	1580092	1580092	type	True	80.5024	172	215	95	below_threshold
Nitrosopumilus ureiphilus	strain=PS0	GCA_013407185.1	1470067	1470067	type	True	80.1122	176	215	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:35:04,738] [INFO] DFAST Taxonomy check result was written to OceanDNA-a506/tc_result.tsv
[2023-03-17 05:35:04,740] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:35:04,740] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:35:04,740] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1fef402e-6e13-4c53-a11c-c3deed2cbf99/dqc_reference/checkm_data
[2023-03-17 05:35:04,741] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:35:04,746] [INFO] Task started: CheckM
[2023-03-17 05:35:04,746] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a506/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a506/checkm_input OceanDNA-a506/checkm_result
[2023-03-17 05:35:22,075] [INFO] Task succeeded: CheckM
[2023-03-17 05:35:22,075] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:35:22,161] [INFO] ===== Completeness check finished =====
[2023-03-17 05:35:22,161] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:35:22,161] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a506/markers.fasta)
[2023-03-17 05:35:22,162] [INFO] Task started: Blastn
[2023-03-17 05:35:22,163] [INFO] Running command: blastn -query OceanDNA-a506/markers.fasta -db /var/lib/cwl/stg1fef402e-6e13-4c53-a11c-c3deed2cbf99/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a506/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:35:22,773] [INFO] Task succeeded: Blastn
[2023-03-17 05:35:22,776] [INFO] Selected 5 target genomes.
[2023-03-17 05:35:22,776] [INFO] Target genome list was writen to OceanDNA-a506/target_genomes_gtdb.txt
[2023-03-17 05:35:22,812] [INFO] Task started: fastANI
[2023-03-17 05:35:22,812] [INFO] Running command: fastANI --query /var/lib/cwl/stga4773cc7-dea8-4860-afbf-e7e4cff9655c/OceanDNA-a506.fa --refList OceanDNA-a506/target_genomes_gtdb.txt --output OceanDNA-a506/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:35:24,103] [INFO] Task succeeded: fastANI
[2023-03-17 05:35:24,107] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:35:24,107] [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_003702465.1	s__Nitrosopumilus sp003702465	98.1485	192	215	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001541925.1	s__Nitrosopumilus sp001541925	91.0952	208	215	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003331425.1	s__Nitrosopumilus sp002690535	89.4439	211	215	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	99.22	99.22	0.96	0.96	2	-
GCF_002156965.1	s__Nitrosopumilus catalinensis	89.2069	212	215	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	96.25	96.25	1.00	1.00	2	-
GCA_013867245.1	s__Nitrosopumilus sp013867245	88.2039	131	215	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:35:24,109] [INFO] GTDB search result was written to OceanDNA-a506/result_gtdb.tsv
[2023-03-17 05:35:24,111] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:35:24,113] [INFO] DFAST_QC result json was written to OceanDNA-a506/dqc_result.json
[2023-03-17 05:35:24,113] [INFO] DFAST_QC completed!
[2023-03-17 05:35:24,113] [INFO] Total running time: 0h0m26s