[2024-01-24 13:12:54,774] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:54,778] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:54,778] [INFO] DQC Reference Directory: /var/lib/cwl/stgfbb7bbbc-e21a-4ee7-9618-74a65f4c9afc/dqc_reference
[2024-01-24 13:12:56,145] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:56,146] [INFO] Task started: Prodigal
[2024-01-24 13:12:56,147] [INFO] Running command: gunzip -c /var/lib/cwl/stgf955d5fd-9eb4-4122-901c-7ccce5466277/GCF_000956175.1_ASM95617v1_genomic.fna.gz | prodigal -d GCF_000956175.1_ASM95617v1_genomic.fna/cds.fna -a GCF_000956175.1_ASM95617v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:00,032] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:00,033] [INFO] Task started: HMMsearch
[2024-01-24 13:13:00,033] [INFO] Running command: hmmsearch --tblout GCF_000956175.1_ASM95617v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfbb7bbbc-e21a-4ee7-9618-74a65f4c9afc/dqc_reference/reference_markers.hmm GCF_000956175.1_ASM95617v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:00,219] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:00,220] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgf955d5fd-9eb4-4122-901c-7ccce5466277/GCF_000956175.1_ASM95617v1_genomic.fna.gz]
[2024-01-24 13:13:00,244] [INFO] Query marker FASTA was written to GCF_000956175.1_ASM95617v1_genomic.fna/markers.fasta
[2024-01-24 13:13:00,244] [INFO] Task started: Blastn
[2024-01-24 13:13:00,245] [INFO] Running command: blastn -query GCF_000956175.1_ASM95617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbb7bbbc-e21a-4ee7-9618-74a65f4c9afc/dqc_reference/reference_markers.fasta -out GCF_000956175.1_ASM95617v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:00,734] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:00,737] [INFO] Selected 5 target genomes.
[2024-01-24 13:13:00,737] [INFO] Target genome list was writen to GCF_000956175.1_ASM95617v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:00,756] [INFO] Task started: fastANI
[2024-01-24 13:13:00,757] [INFO] Running command: fastANI --query /var/lib/cwl/stgf955d5fd-9eb4-4122-901c-7ccce5466277/GCF_000956175.1_ASM95617v1_genomic.fna.gz --refList GCF_000956175.1_ASM95617v1_genomic.fna/target_genomes.txt --output GCF_000956175.1_ASM95617v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:02,921] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:02,921] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfbb7bbbc-e21a-4ee7-9618-74a65f4c9afc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:02,922] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfbb7bbbc-e21a-4ee7-9618-74a65f4c9afc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:02,932] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:02,933] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:02,933] [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 adriaticus	strain=NF5	GCA_000956175.1	1580092	1580092	type	True	100.0	601	601	95	conclusive
Nitrosopumilus ureiphilus	strain=PS0	GCA_013407185.1	1470067	1470067	type	True	86.2523	457	601	95	below_threshold
Nitrosopumilus cobalaminigenes	strain=HCA1	GCA_013407145.1	1470066	1470066	type	True	81.9521	368	601	95	below_threshold
Nitrosopumilus oxyclinae	strain=HCE1	GCA_013407165.1	1959104	1959104	type	True	81.7863	368	601	95	below_threshold
Nitrosopumilus piranensis	strain=D3C	GCA_000875775.1	1582439	1582439	type	True	81.1854	354	601	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:02,938] [INFO] DFAST Taxonomy check result was written to GCF_000956175.1_ASM95617v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:02,939] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:02,939] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:02,939] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfbb7bbbc-e21a-4ee7-9618-74a65f4c9afc/dqc_reference/checkm_data
[2024-01-24 13:13:02,940] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:02,962] [INFO] Task started: CheckM
[2024-01-24 13:13:02,962] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000956175.1_ASM95617v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000956175.1_ASM95617v1_genomic.fna/checkm_input GCF_000956175.1_ASM95617v1_genomic.fna/checkm_result
[2024-01-24 13:13:22,386] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:22,388] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:22,404] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:22,404] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:22,405] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000956175.1_ASM95617v1_genomic.fna/markers.fasta)
[2024-01-24 13:13:22,405] [INFO] Task started: Blastn
[2024-01-24 13:13:22,406] [INFO] Running command: blastn -query GCF_000956175.1_ASM95617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbb7bbbc-e21a-4ee7-9618-74a65f4c9afc/dqc_reference/reference_markers_gtdb.fasta -out GCF_000956175.1_ASM95617v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:22,932] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:22,935] [INFO] Selected 8 target genomes.
[2024-01-24 13:13:22,935] [INFO] Target genome list was writen to GCF_000956175.1_ASM95617v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:22,954] [INFO] Task started: fastANI
[2024-01-24 13:13:22,954] [INFO] Running command: fastANI --query /var/lib/cwl/stgf955d5fd-9eb4-4122-901c-7ccce5466277/GCF_000956175.1_ASM95617v1_genomic.fna.gz --refList GCF_000956175.1_ASM95617v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000956175.1_ASM95617v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:13:26,448] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:26,456] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:13:26,456] [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_000956175.1	s__Nitrosopumilus adriaticus	100.0	601	601	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_014078525.1	s__Nitrosopumilus sp014078525	90.0642	502	601	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013407185.1	s__Nitrosopumilus ureiphilus	86.2391	458	601	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	81.9315	369	601	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	81.7863	368	601	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013043295.1	s__Nitrosopumilus sp013043295	81.7125	250	601	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	100.00	100.00	0.98	0.98	2	-
GCA_013203245.1	s__Nitrosopumilus sp013203245	81.3092	286	601	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	80.9106	285	601	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	99.76	99.71	0.87	0.86	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:13:26,479] [INFO] GTDB search result was written to GCF_000956175.1_ASM95617v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:13:26,480] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:13:26,484] [INFO] DFAST_QC result json was written to GCF_000956175.1_ASM95617v1_genomic.fna/dqc_result.json
[2024-01-24 13:13:26,485] [INFO] DFAST_QC completed!
[2024-01-24 13:13:26,485] [INFO] Total running time: 0h0m32s