[2023-06-13 10:49:46,742] [INFO] DFAST_QC pipeline started.
[2023-06-13 10:49:46,744] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 10:49:46,745] [INFO] DQC Reference Directory: /var/lib/cwl/stg31a4f8b7-0d02-4ce9-9b49-0836a719f254/dqc_reference
[2023-06-13 10:49:48,068] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 10:49:48,069] [INFO] Task started: Prodigal
[2023-06-13 10:49:48,069] [INFO] Running command: gunzip -c /var/lib/cwl/stg74c7c2a6-7c65-421e-b13e-b6a719a07662/GCA_938049585.1_MaE-04nov19-358_genomic.fna.gz | prodigal -d GCA_938049585.1_MaE-04nov19-358_genomic.fna/cds.fna -a GCA_938049585.1_MaE-04nov19-358_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 10:49:49,898] [INFO] Task succeeded: Prodigal
[2023-06-13 10:49:49,898] [INFO] Task started: HMMsearch
[2023-06-13 10:49:49,898] [INFO] Running command: hmmsearch --tblout GCA_938049585.1_MaE-04nov19-358_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31a4f8b7-0d02-4ce9-9b49-0836a719f254/dqc_reference/reference_markers.hmm GCA_938049585.1_MaE-04nov19-358_genomic.fna/protein.faa > /dev/null
[2023-06-13 10:49:50,168] [INFO] Task succeeded: HMMsearch
[2023-06-13 10:49:50,171] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg74c7c2a6-7c65-421e-b13e-b6a719a07662/GCA_938049585.1_MaE-04nov19-358_genomic.fna.gz]
[2023-06-13 10:49:50,199] [INFO] Query marker FASTA was written to GCA_938049585.1_MaE-04nov19-358_genomic.fna/markers.fasta
[2023-06-13 10:49:50,200] [INFO] Task started: Blastn
[2023-06-13 10:49:50,200] [INFO] Running command: blastn -query GCA_938049585.1_MaE-04nov19-358_genomic.fna/markers.fasta -db /var/lib/cwl/stg31a4f8b7-0d02-4ce9-9b49-0836a719f254/dqc_reference/reference_markers.fasta -out GCA_938049585.1_MaE-04nov19-358_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:49:52,535] [INFO] Task succeeded: Blastn
[2023-06-13 10:49:52,539] [INFO] Selected 4 target genomes.
[2023-06-13 10:49:52,540] [INFO] Target genome list was writen to GCA_938049585.1_MaE-04nov19-358_genomic.fna/target_genomes.txt
[2023-06-13 10:49:52,540] [INFO] Task started: fastANI
[2023-06-13 10:49:52,540] [INFO] Running command: fastANI --query /var/lib/cwl/stg74c7c2a6-7c65-421e-b13e-b6a719a07662/GCA_938049585.1_MaE-04nov19-358_genomic.fna.gz --refList GCA_938049585.1_MaE-04nov19-358_genomic.fna/target_genomes.txt --output GCA_938049585.1_MaE-04nov19-358_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 10:49:53,989] [INFO] Task succeeded: fastANI
[2023-06-13 10:49:53,989] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31a4f8b7-0d02-4ce9-9b49-0836a719f254/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 10:49:53,990] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31a4f8b7-0d02-4ce9-9b49-0836a719f254/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 10:49:53,995] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 10:49:53,995] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 10:49:53,996] [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 cobalaminigenes	strain=HCA1	GCA_013407145.1	1470066	1470066	type	True	80.8787	242	319	95	below_threshold
Nitrosopumilus oxyclinae	strain=HCE1	GCA_013407165.1	1959104	1959104	type	True	80.6312	240	319	95	below_threshold
Nitrosopumilus adriaticus	strain=NF5	GCA_000956175.1	1580092	1580092	type	True	80.1856	232	319	95	below_threshold
Nitrosopumilus ureiphilus	strain=PS0	GCA_013407185.1	1470067	1470067	type	True	79.892	226	319	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 10:49:53,998] [INFO] DFAST Taxonomy check result was written to GCA_938049585.1_MaE-04nov19-358_genomic.fna/tc_result.tsv
[2023-06-13 10:49:53,998] [INFO] ===== Taxonomy check completed =====
[2023-06-13 10:49:53,998] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 10:49:53,999] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31a4f8b7-0d02-4ce9-9b49-0836a719f254/dqc_reference/checkm_data
[2023-06-13 10:49:54,000] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 10:49:54,015] [INFO] Task started: CheckM
[2023-06-13 10:49:54,016] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938049585.1_MaE-04nov19-358_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938049585.1_MaE-04nov19-358_genomic.fna/checkm_input GCA_938049585.1_MaE-04nov19-358_genomic.fna/checkm_result
[2023-06-13 10:50:09,880] [INFO] Task succeeded: CheckM
[2023-06-13 10:50:09,881] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 10:50:09,911] [INFO] ===== Completeness check finished =====
[2023-06-13 10:50:09,912] [INFO] ===== Start GTDB Search =====
[2023-06-13 10:50:09,912] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938049585.1_MaE-04nov19-358_genomic.fna/markers.fasta)
[2023-06-13 10:50:09,914] [INFO] Task started: Blastn
[2023-06-13 10:50:09,914] [INFO] Running command: blastn -query GCA_938049585.1_MaE-04nov19-358_genomic.fna/markers.fasta -db /var/lib/cwl/stg31a4f8b7-0d02-4ce9-9b49-0836a719f254/dqc_reference/reference_markers_gtdb.fasta -out GCA_938049585.1_MaE-04nov19-358_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:50:10,422] [INFO] Task succeeded: Blastn
[2023-06-13 10:50:10,426] [INFO] Selected 5 target genomes.
[2023-06-13 10:50:10,426] [INFO] Target genome list was writen to GCA_938049585.1_MaE-04nov19-358_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 10:50:10,428] [INFO] Task started: fastANI
[2023-06-13 10:50:10,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg74c7c2a6-7c65-421e-b13e-b6a719a07662/GCA_938049585.1_MaE-04nov19-358_genomic.fna.gz --refList GCA_938049585.1_MaE-04nov19-358_genomic.fna/target_genomes_gtdb.txt --output GCA_938049585.1_MaE-04nov19-358_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 10:50:11,669] [INFO] Task succeeded: fastANI
[2023-06-13 10:50:11,723] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 10:50:11,723] [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_002737455.1	s__Nitrosopumilus sp002737455	98.8195	303	319	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	98.95	98.72	0.92	0.87	8	conclusive
GCA_905616385.1	s__Nitrosopumilus sp905616385	87.8728	160	319	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	97.32	96.75	0.55	0.53	3	-
GCA_902514095.1	s__Nitrosopumilus sp902514095	87.0674	185	319	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905612295.1	s__Nitrosopumilus sp905612295	85.75	194	319	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018674605.1	s__Nitrosopumilus sp018674605	84.649	134	319	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	98.83	98.50	0.79	0.69	12	-
--------------------------------------------------------------------------------
[2023-06-13 10:50:11,726] [INFO] GTDB search result was written to GCA_938049585.1_MaE-04nov19-358_genomic.fna/result_gtdb.tsv
[2023-06-13 10:50:11,727] [INFO] ===== GTDB Search completed =====
[2023-06-13 10:50:11,732] [INFO] DFAST_QC result json was written to GCA_938049585.1_MaE-04nov19-358_genomic.fna/dqc_result.json
[2023-06-13 10:50:11,732] [INFO] DFAST_QC completed!
[2023-06-13 10:50:11,732] [INFO] Total running time: 0h0m25s