[2024-01-25 18:10:05,556] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:10:05,558] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:10:05,558] [INFO] DQC Reference Directory: /var/lib/cwl/stg3068d97c-9d0e-4d80-ab89-67ad45b54cb8/dqc_reference
[2024-01-25 18:10:06,772] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:10:06,772] [INFO] Task started: Prodigal
[2024-01-25 18:10:06,773] [INFO] Running command: gunzip -c /var/lib/cwl/stgb87f59e0-0e5c-436a-a7fe-5b5837c8e32a/GCF_013407165.1_ASM1340716v1_genomic.fna.gz | prodigal -d GCF_013407165.1_ASM1340716v1_genomic.fna/cds.fna -a GCF_013407165.1_ASM1340716v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:10:11,659] [INFO] Task succeeded: Prodigal
[2024-01-25 18:10:11,660] [INFO] Task started: HMMsearch
[2024-01-25 18:10:11,660] [INFO] Running command: hmmsearch --tblout GCF_013407165.1_ASM1340716v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3068d97c-9d0e-4d80-ab89-67ad45b54cb8/dqc_reference/reference_markers.hmm GCF_013407165.1_ASM1340716v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:10:11,791] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:10:11,792] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgb87f59e0-0e5c-436a-a7fe-5b5837c8e32a/GCF_013407165.1_ASM1340716v1_genomic.fna.gz]
[2024-01-25 18:10:11,811] [INFO] Query marker FASTA was written to GCF_013407165.1_ASM1340716v1_genomic.fna/markers.fasta
[2024-01-25 18:10:11,811] [INFO] Task started: Blastn
[2024-01-25 18:10:11,811] [INFO] Running command: blastn -query GCF_013407165.1_ASM1340716v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3068d97c-9d0e-4d80-ab89-67ad45b54cb8/dqc_reference/reference_markers.fasta -out GCF_013407165.1_ASM1340716v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:12,252] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:12,254] [INFO] Selected 5 target genomes.
[2024-01-25 18:10:12,255] [INFO] Target genome list was writen to GCF_013407165.1_ASM1340716v1_genomic.fna/target_genomes.txt
[2024-01-25 18:10:12,276] [INFO] Task started: fastANI
[2024-01-25 18:10:12,276] [INFO] Running command: fastANI --query /var/lib/cwl/stgb87f59e0-0e5c-436a-a7fe-5b5837c8e32a/GCF_013407165.1_ASM1340716v1_genomic.fna.gz --refList GCF_013407165.1_ASM1340716v1_genomic.fna/target_genomes.txt --output GCF_013407165.1_ASM1340716v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:10:14,427] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:14,427] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3068d97c-9d0e-4d80-ab89-67ad45b54cb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:10:14,427] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3068d97c-9d0e-4d80-ab89-67ad45b54cb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:10:14,433] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:10:14,433] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:10:14,433] [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	100.0	528	528	95	conclusive
Nitrosopumilus cobalaminigenes	strain=HCA1	GCA_013407145.1	1470066	1470066	type	True	85.2883	423	528	95	below_threshold
Nitrosopumilus ureiphilus	strain=PS0	GCA_013407185.1	1470067	1470067	type	True	81.8969	368	528	95	below_threshold
Nitrosopumilus adriaticus	strain=NF5	GCA_000956175.1	1580092	1580092	type	True	81.7765	360	528	95	below_threshold
Nitrosopumilus zosterae	strain=NM25	GCA_003175215.1	718286	718286	type	True	81.0688	360	528	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:10:14,434] [INFO] DFAST Taxonomy check result was written to GCF_013407165.1_ASM1340716v1_genomic.fna/tc_result.tsv
[2024-01-25 18:10:14,435] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:10:14,435] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:10:14,435] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3068d97c-9d0e-4d80-ab89-67ad45b54cb8/dqc_reference/checkm_data
[2024-01-25 18:10:14,436] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:10:14,454] [INFO] Task started: CheckM
[2024-01-25 18:10:14,454] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013407165.1_ASM1340716v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013407165.1_ASM1340716v1_genomic.fna/checkm_input GCF_013407165.1_ASM1340716v1_genomic.fna/checkm_result
[2024-01-25 18:10:31,582] [INFO] Task succeeded: CheckM
[2024-01-25 18:10:31,584] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:10:31,600] [INFO] ===== Completeness check finished =====
[2024-01-25 18:10:31,600] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:10:31,601] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013407165.1_ASM1340716v1_genomic.fna/markers.fasta)
[2024-01-25 18:10:31,601] [INFO] Task started: Blastn
[2024-01-25 18:10:31,601] [INFO] Running command: blastn -query GCF_013407165.1_ASM1340716v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3068d97c-9d0e-4d80-ab89-67ad45b54cb8/dqc_reference/reference_markers_gtdb.fasta -out GCF_013407165.1_ASM1340716v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:32,049] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:32,052] [INFO] Selected 9 target genomes.
[2024-01-25 18:10:32,052] [INFO] Target genome list was writen to GCF_013407165.1_ASM1340716v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:10:32,063] [INFO] Task started: fastANI
[2024-01-25 18:10:32,063] [INFO] Running command: fastANI --query /var/lib/cwl/stgb87f59e0-0e5c-436a-a7fe-5b5837c8e32a/GCF_013407165.1_ASM1340716v1_genomic.fna.gz --refList GCF_013407165.1_ASM1340716v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013407165.1_ASM1340716v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:10:35,362] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:35,371] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:10:35,371] [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_013407165.1	s__Nitrosopumilus oxyclinae	100.0	528	528	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	87.1452	363	528	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013203245.1	s__Nitrosopumilus sp013203245	85.8224	313	528	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000299395.1	s__Nitrosopumilus sediminis	83.9199	418	528	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	81.7967	359	528	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	81.7081	354	528	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	81.6991	335	528	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	81.6762	290	528	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	99.76	99.71	0.87	0.86	3	-
GCF_003175215.1	s__Nitrosopumilus sp003175215	81.0688	360	528	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:10:35,373] [INFO] GTDB search result was written to GCF_013407165.1_ASM1340716v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:10:35,373] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:10:35,376] [INFO] DFAST_QC result json was written to GCF_013407165.1_ASM1340716v1_genomic.fna/dqc_result.json
[2024-01-25 18:10:35,376] [INFO] DFAST_QC completed!
[2024-01-25 18:10:35,376] [INFO] Total running time: 0h0m30s