[2023-06-13 13:00:43,477] [INFO] DFAST_QC pipeline started.
[2023-06-13 13:00:43,481] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 13:00:43,481] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a12717d-241f-4f57-b772-3ddae74f6c9c/dqc_reference
[2023-06-13 13:00:44,721] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 13:00:44,722] [INFO] Task started: Prodigal
[2023-06-13 13:00:44,722] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c8a7f84-d626-41ed-be31-edfdfd9a26a1/GCA_022564515.1_ASM2256451v1_genomic.fna.gz | prodigal -d GCA_022564515.1_ASM2256451v1_genomic.fna/cds.fna -a GCA_022564515.1_ASM2256451v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 13:00:50,303] [INFO] Task succeeded: Prodigal
[2023-06-13 13:00:50,303] [INFO] Task started: HMMsearch
[2023-06-13 13:00:50,303] [INFO] Running command: hmmsearch --tblout GCA_022564515.1_ASM2256451v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a12717d-241f-4f57-b772-3ddae74f6c9c/dqc_reference/reference_markers.hmm GCA_022564515.1_ASM2256451v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 13:00:50,510] [INFO] Task succeeded: HMMsearch
[2023-06-13 13:00:50,512] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg3c8a7f84-d626-41ed-be31-edfdfd9a26a1/GCA_022564515.1_ASM2256451v1_genomic.fna.gz]
[2023-06-13 13:00:50,554] [INFO] Query marker FASTA was written to GCA_022564515.1_ASM2256451v1_genomic.fna/markers.fasta
[2023-06-13 13:00:50,555] [INFO] Task started: Blastn
[2023-06-13 13:00:50,555] [INFO] Running command: blastn -query GCA_022564515.1_ASM2256451v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a12717d-241f-4f57-b772-3ddae74f6c9c/dqc_reference/reference_markers.fasta -out GCA_022564515.1_ASM2256451v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:00:51,071] [INFO] Task succeeded: Blastn
[2023-06-13 13:00:51,075] [INFO] Selected 2 target genomes.
[2023-06-13 13:00:51,076] [INFO] Target genome list was writen to GCA_022564515.1_ASM2256451v1_genomic.fna/target_genomes.txt
[2023-06-13 13:00:51,078] [INFO] Task started: fastANI
[2023-06-13 13:00:51,078] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c8a7f84-d626-41ed-be31-edfdfd9a26a1/GCA_022564515.1_ASM2256451v1_genomic.fna.gz --refList GCA_022564515.1_ASM2256451v1_genomic.fna/target_genomes.txt --output GCA_022564515.1_ASM2256451v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 13:00:51,871] [INFO] Task succeeded: fastANI
[2023-06-13 13:00:51,871] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a12717d-241f-4f57-b772-3ddae74f6c9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 13:00:51,872] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a12717d-241f-4f57-b772-3ddae74f6c9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 13:00:51,876] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 13:00:51,876] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 13:00:51,876] [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	76.5585	90	460	95	below_threshold
Nitrosopumilus adriaticus	strain=NF5	GCA_000956175.1	1580092	1580092	type	True	76.5404	85	460	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 13:00:51,881] [INFO] DFAST Taxonomy check result was written to GCA_022564515.1_ASM2256451v1_genomic.fna/tc_result.tsv
[2023-06-13 13:00:51,881] [INFO] ===== Taxonomy check completed =====
[2023-06-13 13:00:51,881] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 13:00:51,882] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a12717d-241f-4f57-b772-3ddae74f6c9c/dqc_reference/checkm_data
[2023-06-13 13:00:51,883] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 13:00:51,901] [INFO] Task started: CheckM
[2023-06-13 13:00:51,901] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022564515.1_ASM2256451v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022564515.1_ASM2256451v1_genomic.fna/checkm_input GCA_022564515.1_ASM2256451v1_genomic.fna/checkm_result
[2023-06-13 13:01:15,682] [INFO] Task succeeded: CheckM
[2023-06-13 13:01:15,683] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 13:01:15,705] [INFO] ===== Completeness check finished =====
[2023-06-13 13:01:15,705] [INFO] ===== Start GTDB Search =====
[2023-06-13 13:01:15,706] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022564515.1_ASM2256451v1_genomic.fna/markers.fasta)
[2023-06-13 13:01:15,706] [INFO] Task started: Blastn
[2023-06-13 13:01:15,707] [INFO] Running command: blastn -query GCA_022564515.1_ASM2256451v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a12717d-241f-4f57-b772-3ddae74f6c9c/dqc_reference/reference_markers_gtdb.fasta -out GCA_022564515.1_ASM2256451v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:01:16,239] [INFO] Task succeeded: Blastn
[2023-06-13 13:01:16,243] [INFO] Selected 8 target genomes.
[2023-06-13 13:01:16,244] [INFO] Target genome list was writen to GCA_022564515.1_ASM2256451v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 13:01:16,251] [INFO] Task started: fastANI
[2023-06-13 13:01:16,251] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c8a7f84-d626-41ed-be31-edfdfd9a26a1/GCA_022564515.1_ASM2256451v1_genomic.fna.gz --refList GCA_022564515.1_ASM2256451v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022564515.1_ASM2256451v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 13:01:18,397] [INFO] Task succeeded: fastANI
[2023-06-13 13:01:18,408] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 13:01:18,409] [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_011055585.1	s__DRGT01 sp011055585	79.4542	195	460	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__DRGT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016838845.1	s__DRGT01 sp016838845	79.2031	192	460	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__DRGT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016838795.1	s__DRGT01 sp016838795	78.9136	131	460	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__DRGT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016276965.1	s__CSP1-1 sp016276965	77.104	92	460	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__CSP1-1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000299365.1	s__Nitrosopumilus koreensis	76.6735	90	460	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	99.95	99.95	0.99	0.99	2	-
GCA_003352285.1	s__PXYB01 sp003352285	76.6383	92	460	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__PXYB01	95.0	99.99	99.99	0.99	0.99	4	-
GCF_014078545.1	s__PXYB01 sp014078545	76.5967	93	460	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__PXYB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005798405.1	s__Nitrosarchaeum sp005798405	76.3472	77	460	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosarchaeum	95.0	99.84	99.81	0.94	0.93	4	-
--------------------------------------------------------------------------------
[2023-06-13 13:01:18,411] [INFO] GTDB search result was written to GCA_022564515.1_ASM2256451v1_genomic.fna/result_gtdb.tsv
[2023-06-13 13:01:18,412] [INFO] ===== GTDB Search completed =====
[2023-06-13 13:01:18,415] [INFO] DFAST_QC result json was written to GCA_022564515.1_ASM2256451v1_genomic.fna/dqc_result.json
[2023-06-13 13:01:18,415] [INFO] DFAST_QC completed!
[2023-06-13 13:01:18,415] [INFO] Total running time: 0h0m35s