[2023-03-18 23:27:53,735] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:27:53,735] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:27:53,735] [INFO] DQC Reference Directory: /var/lib/cwl/stg04cb1418-acf8-4a2f-b0ba-e23a5a9c4194/dqc_reference
[2023-03-18 23:27:55,545] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:27:55,545] [INFO] Task started: Prodigal
[2023-03-18 23:27:55,545] [INFO] Running command: cat /var/lib/cwl/stg0936665f-e5ac-4589-838a-90da12d6eafa/OceanDNA-a752.fa | prodigal -d OceanDNA-a752/cds.fna -a OceanDNA-a752/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:28:01,045] [INFO] Task succeeded: Prodigal
[2023-03-18 23:28:01,045] [INFO] Task started: HMMsearch
[2023-03-18 23:28:01,045] [INFO] Running command: hmmsearch --tblout OceanDNA-a752/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04cb1418-acf8-4a2f-b0ba-e23a5a9c4194/dqc_reference/reference_markers.hmm OceanDNA-a752/protein.faa > /dev/null
[2023-03-18 23:28:01,214] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:28:01,215] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg0936665f-e5ac-4589-838a-90da12d6eafa/OceanDNA-a752.fa]
[2023-03-18 23:28:01,225] [INFO] Query marker FASTA was written to OceanDNA-a752/markers.fasta
[2023-03-18 23:28:01,226] [INFO] Task started: Blastn
[2023-03-18 23:28:01,226] [INFO] Running command: blastn -query OceanDNA-a752/markers.fasta -db /var/lib/cwl/stg04cb1418-acf8-4a2f-b0ba-e23a5a9c4194/dqc_reference/reference_markers.fasta -out OceanDNA-a752/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:28:01,673] [INFO] Task succeeded: Blastn
[2023-03-18 23:28:01,674] [INFO] Selected 4 target genomes.
[2023-03-18 23:28:01,674] [INFO] Target genome list was writen to OceanDNA-a752/target_genomes.txt
[2023-03-18 23:28:01,678] [INFO] Task started: fastANI
[2023-03-18 23:28:01,678] [INFO] Running command: fastANI --query /var/lib/cwl/stg0936665f-e5ac-4589-838a-90da12d6eafa/OceanDNA-a752.fa --refList OceanDNA-a752/target_genomes.txt --output OceanDNA-a752/fastani_result.tsv --threads 1
[2023-03-18 23:28:03,221] [INFO] Task succeeded: fastANI
[2023-03-18 23:28:03,222] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04cb1418-acf8-4a2f-b0ba-e23a5a9c4194/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:28:03,222] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04cb1418-acf8-4a2f-b0ba-e23a5a9c4194/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:28:03,279] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:28:03,279] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:28:03,279] [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	80.9277	265	352	95	below_threshold
Nitrosopumilus oxyclinae	strain=HCE1	GCA_013407165.1	1959104	1959104	type	True	80.821	272	352	95	below_threshold
Nitrosopumilus adriaticus	strain=NF5	GCA_000956175.1	1580092	1580092	type	True	80.3569	251	352	95	below_threshold
Nitrosopumilus ureiphilus	strain=PS0	GCA_013407185.1	1470067	1470067	type	True	80.1565	265	352	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:28:03,279] [INFO] DFAST Taxonomy check result was written to OceanDNA-a752/tc_result.tsv
[2023-03-18 23:28:03,279] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:28:03,279] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:28:03,280] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04cb1418-acf8-4a2f-b0ba-e23a5a9c4194/dqc_reference/checkm_data
[2023-03-18 23:28:03,280] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:28:03,339] [INFO] Task started: CheckM
[2023-03-18 23:28:03,339] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a752/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a752/checkm_input OceanDNA-a752/checkm_result
[2023-03-18 23:28:24,320] [INFO] Task succeeded: CheckM
[2023-03-18 23:28:24,321] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:28:24,322] [INFO] ===== Completeness check finished =====
[2023-03-18 23:28:24,322] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:28:24,323] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a752/markers.fasta)
[2023-03-18 23:28:24,324] [INFO] Task started: Blastn
[2023-03-18 23:28:24,324] [INFO] Running command: blastn -query OceanDNA-a752/markers.fasta -db /var/lib/cwl/stg04cb1418-acf8-4a2f-b0ba-e23a5a9c4194/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a752/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:28:24,849] [INFO] Task succeeded: Blastn
[2023-03-18 23:28:24,850] [INFO] Selected 5 target genomes.
[2023-03-18 23:28:24,850] [INFO] Target genome list was writen to OceanDNA-a752/target_genomes_gtdb.txt
[2023-03-18 23:28:24,857] [INFO] Task started: fastANI
[2023-03-18 23:28:24,858] [INFO] Running command: fastANI --query /var/lib/cwl/stg0936665f-e5ac-4589-838a-90da12d6eafa/OceanDNA-a752.fa --refList OceanDNA-a752/target_genomes_gtdb.txt --output OceanDNA-a752/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:28:26,092] [INFO] Task succeeded: fastANI
[2023-03-18 23:28:26,096] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:28:26,096] [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_001437625.1	s__Nitrosopumilus sp001437625	99.4913	298	352	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	98.62	95.42	0.85	0.75	5	conclusive
GCA_905612295.1	s__Nitrosopumilus sp905612295	93.197	224	352	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014384445.1	s__Nitrosopumilus sp014384445	90.9359	222	352	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018657375.1	s__Nitrosopumilus sp018657375	90.1676	191	352	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	98.79	98.40	0.79	0.75	5	-
GCA_018674605.1	s__Nitrosopumilus sp018674605	86.7504	150	352	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	98.83	98.50	0.79	0.69	12	-
--------------------------------------------------------------------------------
[2023-03-18 23:28:26,097] [INFO] GTDB search result was written to OceanDNA-a752/result_gtdb.tsv
[2023-03-18 23:28:26,097] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:28:26,098] [INFO] DFAST_QC result json was written to OceanDNA-a752/dqc_result.json
[2023-03-18 23:28:26,098] [INFO] DFAST_QC completed!
[2023-03-18 23:28:26,098] [INFO] Total running time: 0h0m32s