[2023-03-15 11:10:12,311] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:10:12,311] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:10:12,312] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb8a4d84-1327-43f8-befe-76dcd05da23c/dqc_reference
[2023-03-15 11:10:13,461] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:10:13,462] [INFO] Task started: Prodigal
[2023-03-15 11:10:13,462] [INFO] Running command: cat /var/lib/cwl/stg6e0ad634-f20b-4d41-a6c3-dbeb885beb35/OceanDNA-a720.fa | prodigal -d OceanDNA-a720/cds.fna -a OceanDNA-a720/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:10:17,938] [INFO] Task succeeded: Prodigal
[2023-03-15 11:10:17,938] [INFO] Task started: HMMsearch
[2023-03-15 11:10:17,938] [INFO] Running command: hmmsearch --tblout OceanDNA-a720/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb8a4d84-1327-43f8-befe-76dcd05da23c/dqc_reference/reference_markers.hmm OceanDNA-a720/protein.faa > /dev/null
[2023-03-15 11:10:18,048] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:10:18,048] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg6e0ad634-f20b-4d41-a6c3-dbeb885beb35/OceanDNA-a720.fa]
[2023-03-15 11:10:18,085] [INFO] Query marker FASTA was written to OceanDNA-a720/markers.fasta
[2023-03-15 11:10:18,087] [INFO] Task started: Blastn
[2023-03-15 11:10:18,087] [INFO] Running command: blastn -query OceanDNA-a720/markers.fasta -db /var/lib/cwl/stgbb8a4d84-1327-43f8-befe-76dcd05da23c/dqc_reference/reference_markers.fasta -out OceanDNA-a720/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:10:18,561] [INFO] Task succeeded: Blastn
[2023-03-15 11:10:18,567] [INFO] Selected 5 target genomes.
[2023-03-15 11:10:18,568] [INFO] Target genome list was writen to OceanDNA-a720/target_genomes.txt
[2023-03-15 11:10:18,572] [INFO] Task started: fastANI
[2023-03-15 11:10:18,572] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e0ad634-f20b-4d41-a6c3-dbeb885beb35/OceanDNA-a720.fa --refList OceanDNA-a720/target_genomes.txt --output OceanDNA-a720/fastani_result.tsv --threads 1
[2023-03-15 11:10:20,145] [INFO] Task succeeded: fastANI
[2023-03-15 11:10:20,146] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb8a4d84-1327-43f8-befe-76dcd05da23c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:10:20,146] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb8a4d84-1327-43f8-befe-76dcd05da23c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:10:20,159] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:10:20,159] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:10:20,159] [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	82.0831	207	266	95	below_threshold
Nitrosopumilus cobalaminigenes	strain=HCA1	GCA_013407145.1	1470066	1470066	type	True	81.9168	205	266	95	below_threshold
Nitrosopumilus ureiphilus	strain=PS0	GCA_013407185.1	1470067	1470067	type	True	81.2508	202	266	95	below_threshold
Nitrosopumilus adriaticus	strain=NF5	GCA_000956175.1	1580092	1580092	type	True	81.0343	202	266	95	below_threshold
Nitrosopumilus maritimus	strain=SCM1	GCA_000018465.1	338192	338192	type	True	80.8444	205	266	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:10:20,162] [INFO] DFAST Taxonomy check result was written to OceanDNA-a720/tc_result.tsv
[2023-03-15 11:10:20,165] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:10:20,165] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:10:20,165] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb8a4d84-1327-43f8-befe-76dcd05da23c/dqc_reference/checkm_data
[2023-03-15 11:10:20,166] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:10:20,171] [INFO] Task started: CheckM
[2023-03-15 11:10:20,171] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a720/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a720/checkm_input OceanDNA-a720/checkm_result
[2023-03-15 11:10:38,878] [INFO] Task succeeded: CheckM
[2023-03-15 11:10:38,879] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.52%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 11:10:38,947] [INFO] ===== Completeness check finished =====
[2023-03-15 11:10:38,947] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:10:38,947] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a720/markers.fasta)
[2023-03-15 11:10:38,949] [INFO] Task started: Blastn
[2023-03-15 11:10:38,949] [INFO] Running command: blastn -query OceanDNA-a720/markers.fasta -db /var/lib/cwl/stgbb8a4d84-1327-43f8-befe-76dcd05da23c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a720/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:10:39,517] [INFO] Task succeeded: Blastn
[2023-03-15 11:10:39,523] [INFO] Selected 5 target genomes.
[2023-03-15 11:10:39,523] [INFO] Target genome list was writen to OceanDNA-a720/target_genomes_gtdb.txt
[2023-03-15 11:10:39,529] [INFO] Task started: fastANI
[2023-03-15 11:10:39,530] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e0ad634-f20b-4d41-a6c3-dbeb885beb35/OceanDNA-a720.fa --refList OceanDNA-a720/target_genomes_gtdb.txt --output OceanDNA-a720/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:10:41,208] [INFO] Task succeeded: fastANI
[2023-03-15 11:10:41,212] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:10:41,212] [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_002317795.1	s__Nitrosopumilus sp002317795	88.8447	239	266	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215285.1	s__Nitrosopumilus sp013215285	82.718	215	266	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	82.5368	174	266	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	82.4288	201	266	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911135.1	s__Nitrosopumilus sp013911135	82.3822	196	266	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:10:41,215] [INFO] GTDB search result was written to OceanDNA-a720/result_gtdb.tsv
[2023-03-15 11:10:41,219] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:10:41,223] [INFO] DFAST_QC result json was written to OceanDNA-a720/dqc_result.json
[2023-03-15 11:10:41,223] [INFO] DFAST_QC completed!
[2023-03-15 11:10:41,223] [INFO] Total running time: 0h0m29s