[2024-01-25 19:47:20,766] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:47:20,768] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:47:20,768] [INFO] DQC Reference Directory: /var/lib/cwl/stgb4682d08-ea90-4871-995f-04fdbd753a72/dqc_reference
[2024-01-25 19:47:21,978] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:47:21,979] [INFO] Task started: Prodigal
[2024-01-25 19:47:21,979] [INFO] Running command: gunzip -c /var/lib/cwl/stgf28d2572-3738-4940-9457-46761542e1d7/GCF_025998175.1_ASM2599817v1_genomic.fna.gz | prodigal -d GCF_025998175.1_ASM2599817v1_genomic.fna/cds.fna -a GCF_025998175.1_ASM2599817v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:47:25,754] [INFO] Task succeeded: Prodigal
[2024-01-25 19:47:25,754] [INFO] Task started: HMMsearch
[2024-01-25 19:47:25,754] [INFO] Running command: hmmsearch --tblout GCF_025998175.1_ASM2599817v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb4682d08-ea90-4871-995f-04fdbd753a72/dqc_reference/reference_markers.hmm GCF_025998175.1_ASM2599817v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:47:25,929] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:47:25,933] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgf28d2572-3738-4940-9457-46761542e1d7/GCF_025998175.1_ASM2599817v1_genomic.fna.gz]
[2024-01-25 19:47:25,964] [INFO] Query marker FASTA was written to GCF_025998175.1_ASM2599817v1_genomic.fna/markers.fasta
[2024-01-25 19:47:25,964] [INFO] Task started: Blastn
[2024-01-25 19:47:25,964] [INFO] Running command: blastn -query GCF_025998175.1_ASM2599817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4682d08-ea90-4871-995f-04fdbd753a72/dqc_reference/reference_markers.fasta -out GCF_025998175.1_ASM2599817v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:26,464] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:26,467] [INFO] Selected 4 target genomes.
[2024-01-25 19:47:26,467] [INFO] Target genome list was writen to GCF_025998175.1_ASM2599817v1_genomic.fna/target_genomes.txt
[2024-01-25 19:47:26,470] [INFO] Task started: fastANI
[2024-01-25 19:47:26,470] [INFO] Running command: fastANI --query /var/lib/cwl/stgf28d2572-3738-4940-9457-46761542e1d7/GCF_025998175.1_ASM2599817v1_genomic.fna.gz --refList GCF_025998175.1_ASM2599817v1_genomic.fna/target_genomes.txt --output GCF_025998175.1_ASM2599817v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:47:28,221] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:28,222] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb4682d08-ea90-4871-995f-04fdbd753a72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:47:28,222] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb4682d08-ea90-4871-995f-04fdbd753a72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:47:28,226] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:47:28,227] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:47:28,227] [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 zosterae	strain=NM25	GCA_003175215.1	718286	718286	type	True	99.988	577	591	95	conclusive
Nitrosopumilus ureiphilus	strain=PS0	GCA_013407185.1	1470067	1470067	type	True	85.2338	441	591	95	below_threshold
Nitrosopumilus oxyclinae	strain=HCE1	GCA_013407165.1	1959104	1959104	type	True	81.134	349	591	95	below_threshold
Nitrosopumilus piranensis	strain=D3C	GCA_000875775.1	1582439	1582439	type	True	80.7983	331	591	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:47:28,228] [INFO] DFAST Taxonomy check result was written to GCF_025998175.1_ASM2599817v1_genomic.fna/tc_result.tsv
[2024-01-25 19:47:28,230] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:47:28,230] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:47:28,231] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb4682d08-ea90-4871-995f-04fdbd753a72/dqc_reference/checkm_data
[2024-01-25 19:47:28,231] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:47:28,253] [INFO] Task started: CheckM
[2024-01-25 19:47:28,254] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025998175.1_ASM2599817v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025998175.1_ASM2599817v1_genomic.fna/checkm_input GCF_025998175.1_ASM2599817v1_genomic.fna/checkm_result
[2024-01-25 19:47:45,347] [INFO] Task succeeded: CheckM
[2024-01-25 19:47:45,348] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:47:45,367] [INFO] ===== Completeness check finished =====
[2024-01-25 19:47:45,367] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:47:45,368] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025998175.1_ASM2599817v1_genomic.fna/markers.fasta)
[2024-01-25 19:47:45,368] [INFO] Task started: Blastn
[2024-01-25 19:47:45,368] [INFO] Running command: blastn -query GCF_025998175.1_ASM2599817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4682d08-ea90-4871-995f-04fdbd753a72/dqc_reference/reference_markers_gtdb.fasta -out GCF_025998175.1_ASM2599817v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:45,844] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:45,848] [INFO] Selected 8 target genomes.
[2024-01-25 19:47:45,848] [INFO] Target genome list was writen to GCF_025998175.1_ASM2599817v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:47:45,857] [INFO] Task started: fastANI
[2024-01-25 19:47:45,858] [INFO] Running command: fastANI --query /var/lib/cwl/stgf28d2572-3738-4940-9457-46761542e1d7/GCF_025998175.1_ASM2599817v1_genomic.fna.gz --refList GCF_025998175.1_ASM2599817v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025998175.1_ASM2599817v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:47:48,767] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:48,773] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:47:48,773] [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_003175215.1	s__Nitrosopumilus sp003175215	99.988	577	591	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_013407185.1	s__Nitrosopumilus ureiphilus	85.2278	441	591	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013407165.1	s__Nitrosopumilus oxyclinae	81.1149	350	591	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125975.1	s__Nitrosopumilus sp016125975	80.7617	307	591	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002317795.1	s__Nitrosopumilus sp002317795	80.4794	328	591	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	80.463	277	591	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	99.76	99.71	0.87	0.86	3	-
GCF_018128925.1	s__Nitrosarchaeum_A sp018128925	79.2403	276	591	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosarchaeum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297665.1	s__Nitrosarchaeum sp004297665	78.7395	158	591	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosarchaeum	95.0	96.40	95.66	0.66	0.65	5	-
--------------------------------------------------------------------------------
[2024-01-25 19:47:48,775] [INFO] GTDB search result was written to GCF_025998175.1_ASM2599817v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:47:48,775] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:47:48,778] [INFO] DFAST_QC result json was written to GCF_025998175.1_ASM2599817v1_genomic.fna/dqc_result.json
[2024-01-25 19:47:48,778] [INFO] DFAST_QC completed!
[2024-01-25 19:47:48,778] [INFO] Total running time: 0h0m28s