[2023-06-19 06:19:20,528] [INFO] DFAST_QC pipeline started.
[2023-06-19 06:19:20,531] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 06:19:20,531] [INFO] DQC Reference Directory: /var/lib/cwl/stg3b668a0f-2151-4949-9b50-438786cc7910/dqc_reference
[2023-06-19 06:19:22,871] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 06:19:22,872] [INFO] Task started: Prodigal
[2023-06-19 06:19:22,872] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b8495c2-d785-4d14-948f-445c661ca41b/GCA_013203245.1_ASM1320324v1_genomic.fna.gz | prodigal -d GCA_013203245.1_ASM1320324v1_genomic.fna/cds.fna -a GCA_013203245.1_ASM1320324v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 06:19:25,450] [INFO] Task succeeded: Prodigal
[2023-06-19 06:19:25,451] [INFO] Task started: HMMsearch
[2023-06-19 06:19:25,451] [INFO] Running command: hmmsearch --tblout GCA_013203245.1_ASM1320324v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3b668a0f-2151-4949-9b50-438786cc7910/dqc_reference/reference_markers.hmm GCA_013203245.1_ASM1320324v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 06:19:25,636] [INFO] Task succeeded: HMMsearch
[2023-06-19 06:19:25,637] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg3b8495c2-d785-4d14-948f-445c661ca41b/GCA_013203245.1_ASM1320324v1_genomic.fna.gz]
[2023-06-19 06:19:25,661] [INFO] Query marker FASTA was written to GCA_013203245.1_ASM1320324v1_genomic.fna/markers.fasta
[2023-06-19 06:19:25,662] [INFO] Task started: Blastn
[2023-06-19 06:19:25,662] [INFO] Running command: blastn -query GCA_013203245.1_ASM1320324v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b668a0f-2151-4949-9b50-438786cc7910/dqc_reference/reference_markers.fasta -out GCA_013203245.1_ASM1320324v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 06:19:27,579] [INFO] Task succeeded: Blastn
[2023-06-19 06:19:27,586] [INFO] Selected 4 target genomes.
[2023-06-19 06:19:27,587] [INFO] Target genome list was writen to GCA_013203245.1_ASM1320324v1_genomic.fna/target_genomes.txt
[2023-06-19 06:19:27,589] [INFO] Task started: fastANI
[2023-06-19 06:19:27,589] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b8495c2-d785-4d14-948f-445c661ca41b/GCA_013203245.1_ASM1320324v1_genomic.fna.gz --refList GCA_013203245.1_ASM1320324v1_genomic.fna/target_genomes.txt --output GCA_013203245.1_ASM1320324v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 06:19:29,182] [INFO] Task succeeded: fastANI
[2023-06-19 06:19:29,182] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3b668a0f-2151-4949-9b50-438786cc7910/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 06:19:29,182] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3b668a0f-2151-4949-9b50-438786cc7910/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 06:19:29,188] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 06:19:29,188] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 06:19:29,188] [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	85.8168	313	408	95	below_threshold
Nitrosopumilus cobalaminigenes	strain=HCA1	GCA_013407145.1	1470066	1470066	type	True	84.3521	308	408	95	below_threshold
Nitrosopumilus adriaticus	strain=NF5	GCA_000956175.1	1580092	1580092	type	True	81.4065	271	408	95	below_threshold
Nitrosopumilus ureiphilus	strain=PS0	GCA_013407185.1	1470067	1470067	type	True	81.3573	282	408	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 06:19:29,191] [INFO] DFAST Taxonomy check result was written to GCA_013203245.1_ASM1320324v1_genomic.fna/tc_result.tsv
[2023-06-19 06:19:29,192] [INFO] ===== Taxonomy check completed =====
[2023-06-19 06:19:29,192] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 06:19:29,192] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3b668a0f-2151-4949-9b50-438786cc7910/dqc_reference/checkm_data
[2023-06-19 06:19:29,194] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 06:19:29,217] [INFO] Task started: CheckM
[2023-06-19 06:19:29,218] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013203245.1_ASM1320324v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013203245.1_ASM1320324v1_genomic.fna/checkm_input GCA_013203245.1_ASM1320324v1_genomic.fna/checkm_result
[2023-06-19 06:19:47,553] [INFO] Task succeeded: CheckM
[2023-06-19 06:19:47,554] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.53%
Contamintation: 5.07%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-19 06:19:47,605] [INFO] ===== Completeness check finished =====
[2023-06-19 06:19:47,606] [INFO] ===== Start GTDB Search =====
[2023-06-19 06:19:47,607] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013203245.1_ASM1320324v1_genomic.fna/markers.fasta)
[2023-06-19 06:19:47,608] [INFO] Task started: Blastn
[2023-06-19 06:19:47,608] [INFO] Running command: blastn -query GCA_013203245.1_ASM1320324v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b668a0f-2151-4949-9b50-438786cc7910/dqc_reference/reference_markers_gtdb.fasta -out GCA_013203245.1_ASM1320324v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 06:19:48,051] [INFO] Task succeeded: Blastn
[2023-06-19 06:19:48,056] [INFO] Selected 5 target genomes.
[2023-06-19 06:19:48,056] [INFO] Target genome list was writen to GCA_013203245.1_ASM1320324v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 06:19:48,060] [INFO] Task started: fastANI
[2023-06-19 06:19:48,061] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b8495c2-d785-4d14-948f-445c661ca41b/GCA_013203245.1_ASM1320324v1_genomic.fna.gz --refList GCA_013203245.1_ASM1320324v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013203245.1_ASM1320324v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 06:19:49,876] [INFO] Task succeeded: fastANI
[2023-06-19 06:19:49,885] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 06:19:49,885] [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_013203245.1	s__Nitrosopumilus sp013203245	100.0	400	408	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905479565.1	s__Nitrosopumilus sp905479565	84.3799	271	408	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013407145.1	s__Nitrosopumilus cobalaminigenes	84.3521	308	408	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000956175.1	s__Nitrosopumilus adriaticus	81.3814	272	408	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014078525.1	s__Nitrosopumilus sp014078525	81.1669	270	408	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 06:19:49,887] [INFO] GTDB search result was written to GCA_013203245.1_ASM1320324v1_genomic.fna/result_gtdb.tsv
[2023-06-19 06:19:49,888] [INFO] ===== GTDB Search completed =====
[2023-06-19 06:19:49,892] [INFO] DFAST_QC result json was written to GCA_013203245.1_ASM1320324v1_genomic.fna/dqc_result.json
[2023-06-19 06:19:49,892] [INFO] DFAST_QC completed!
[2023-06-19 06:19:49,892] [INFO] Total running time: 0h0m29s