[2024-01-25 17:37:05,793] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:37:05,796] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:37:05,796] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd5df2a3-fbde-448c-97d7-1837ef1c44f9/dqc_reference
[2024-01-25 17:37:06,960] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:37:06,960] [INFO] Task started: Prodigal
[2024-01-25 17:37:06,961] [INFO] Running command: gunzip -c /var/lib/cwl/stg5882e05d-8176-4a1d-a451-9e164ba5a6e6/GCF_013407185.1_ASM1340718v1_genomic.fna.gz | prodigal -d GCF_013407185.1_ASM1340718v1_genomic.fna/cds.fna -a GCF_013407185.1_ASM1340718v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:37:11,071] [INFO] Task succeeded: Prodigal
[2024-01-25 17:37:11,072] [INFO] Task started: HMMsearch
[2024-01-25 17:37:11,072] [INFO] Running command: hmmsearch --tblout GCF_013407185.1_ASM1340718v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd5df2a3-fbde-448c-97d7-1837ef1c44f9/dqc_reference/reference_markers.hmm GCF_013407185.1_ASM1340718v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:37:11,217] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:37:11,218] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg5882e05d-8176-4a1d-a451-9e164ba5a6e6/GCF_013407185.1_ASM1340718v1_genomic.fna.gz]
[2024-01-25 17:37:11,239] [INFO] Query marker FASTA was written to GCF_013407185.1_ASM1340718v1_genomic.fna/markers.fasta
[2024-01-25 17:37:11,239] [INFO] Task started: Blastn
[2024-01-25 17:37:11,239] [INFO] Running command: blastn -query GCF_013407185.1_ASM1340718v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd5df2a3-fbde-448c-97d7-1837ef1c44f9/dqc_reference/reference_markers.fasta -out GCF_013407185.1_ASM1340718v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:37:11,712] [INFO] Task succeeded: Blastn
[2024-01-25 17:37:11,715] [INFO] Selected 5 target genomes.
[2024-01-25 17:37:11,715] [INFO] Target genome list was writen to GCF_013407185.1_ASM1340718v1_genomic.fna/target_genomes.txt
[2024-01-25 17:37:11,718] [INFO] Task started: fastANI
[2024-01-25 17:37:11,718] [INFO] Running command: fastANI --query /var/lib/cwl/stg5882e05d-8176-4a1d-a451-9e164ba5a6e6/GCF_013407185.1_ASM1340718v1_genomic.fna.gz --refList GCF_013407185.1_ASM1340718v1_genomic.fna/target_genomes.txt --output GCF_013407185.1_ASM1340718v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:37:14,204] [INFO] Task succeeded: fastANI
[2024-01-25 17:37:14,204] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd5df2a3-fbde-448c-97d7-1837ef1c44f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:37:14,204] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd5df2a3-fbde-448c-97d7-1837ef1c44f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:37:14,209] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:37:14,210] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:37:14,210] [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 ureiphilus	strain=PS0	GCA_013407185.1	1470067	1470067	type	True	100.0	723	723	95	conclusive
Nitrosopumilus adriaticus	strain=NF5	GCA_000956175.1	1580092	1580092	type	True	86.3128	451	723	95	below_threshold
Nitrosopumilus zosterae	strain=NM25	GCA_003175215.1	718286	718286	type	True	85.4978	425	723	95	below_threshold
Nitrosopumilus oxyclinae	strain=HCE1	GCA_013407165.1	1959104	1959104	type	True	81.7878	351	723	95	below_threshold
Nitrosopumilus maritimus	strain=SCM1	GCA_000018465.1	338192	338192	type	True	81.1111	336	723	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:37:14,211] [INFO] DFAST Taxonomy check result was written to GCF_013407185.1_ASM1340718v1_genomic.fna/tc_result.tsv
[2024-01-25 17:37:14,212] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:37:14,212] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:37:14,212] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd5df2a3-fbde-448c-97d7-1837ef1c44f9/dqc_reference/checkm_data
[2024-01-25 17:37:14,213] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:37:14,237] [INFO] Task started: CheckM
[2024-01-25 17:37:14,237] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013407185.1_ASM1340718v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013407185.1_ASM1340718v1_genomic.fna/checkm_input GCF_013407185.1_ASM1340718v1_genomic.fna/checkm_result
[2024-01-25 17:37:32,445] [INFO] Task succeeded: CheckM
[2024-01-25 17:37:32,446] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:37:32,465] [INFO] ===== Completeness check finished =====
[2024-01-25 17:37:32,465] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:37:32,465] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013407185.1_ASM1340718v1_genomic.fna/markers.fasta)
[2024-01-25 17:37:32,465] [INFO] Task started: Blastn
[2024-01-25 17:37:32,465] [INFO] Running command: blastn -query GCF_013407185.1_ASM1340718v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd5df2a3-fbde-448c-97d7-1837ef1c44f9/dqc_reference/reference_markers_gtdb.fasta -out GCF_013407185.1_ASM1340718v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:37:32,940] [INFO] Task succeeded: Blastn
[2024-01-25 17:37:32,943] [INFO] Selected 8 target genomes.
[2024-01-25 17:37:32,943] [INFO] Target genome list was writen to GCF_013407185.1_ASM1340718v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:37:32,965] [INFO] Task started: fastANI
[2024-01-25 17:37:32,966] [INFO] Running command: fastANI --query /var/lib/cwl/stg5882e05d-8176-4a1d-a451-9e164ba5a6e6/GCF_013407185.1_ASM1340718v1_genomic.fna.gz --refList GCF_013407185.1_ASM1340718v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013407185.1_ASM1340718v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:37:36,662] [INFO] Task succeeded: fastANI
[2024-01-25 17:37:36,670] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:37:36,670] [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
GCF_013407185.1	s__Nitrosopumilus ureiphilus	100.0	723	723	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_000956175.1	s__Nitrosopumilus adriaticus	86.3514	449	723	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	86.3155	454	723	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003175215.1	s__Nitrosopumilus sp003175215	85.4781	426	723	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	82.8484	335	723	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	82.1231	362	723	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	81.7945	361	723	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018668425.1	s__Nitrosopumilus sp018668425	81.0023	287	723	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	99.76	99.71	0.87	0.86	3	-
--------------------------------------------------------------------------------
[2024-01-25 17:37:36,677] [INFO] GTDB search result was written to GCF_013407185.1_ASM1340718v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:37:36,678] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:37:36,682] [INFO] DFAST_QC result json was written to GCF_013407185.1_ASM1340718v1_genomic.fna/dqc_result.json
[2024-01-25 17:37:36,682] [INFO] DFAST_QC completed!
[2024-01-25 17:37:36,682] [INFO] Total running time: 0h0m31s