[2023-06-08 09:05:47,364] [INFO] DFAST_QC pipeline started.
[2023-06-08 09:05:47,366] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 09:05:47,366] [INFO] DQC Reference Directory: /var/lib/cwl/stg43f2cfec-febd-4257-8884-e91f260fbe20/dqc_reference
[2023-06-08 09:05:50,043] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 09:05:50,044] [INFO] Task started: Prodigal
[2023-06-08 09:05:50,045] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c71bde0-663e-4e18-8835-1012cdd328c2/GCA_902752385.1_P1994_129_bin89_mag_fasta_genomic.fna.gz | prodigal -d GCA_902752385.1_P1994_129_bin89_mag_fasta_genomic.fna/cds.fna -a GCA_902752385.1_P1994_129_bin89_mag_fasta_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 09:05:54,394] [INFO] Task succeeded: Prodigal
[2023-06-08 09:05:54,395] [INFO] Task started: HMMsearch
[2023-06-08 09:05:54,395] [INFO] Running command: hmmsearch --tblout GCA_902752385.1_P1994_129_bin89_mag_fasta_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43f2cfec-febd-4257-8884-e91f260fbe20/dqc_reference/reference_markers.hmm GCA_902752385.1_P1994_129_bin89_mag_fasta_genomic.fna/protein.faa > /dev/null
[2023-06-08 09:05:54,575] [INFO] Task succeeded: HMMsearch
[2023-06-08 09:05:54,577] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg5c71bde0-663e-4e18-8835-1012cdd328c2/GCA_902752385.1_P1994_129_bin89_mag_fasta_genomic.fna.gz]
[2023-06-08 09:05:54,595] [INFO] Query marker FASTA was written to GCA_902752385.1_P1994_129_bin89_mag_fasta_genomic.fna/markers.fasta
[2023-06-08 09:05:54,595] [INFO] Task started: Blastn
[2023-06-08 09:05:54,596] [INFO] Running command: blastn -query GCA_902752385.1_P1994_129_bin89_mag_fasta_genomic.fna/markers.fasta -db /var/lib/cwl/stg43f2cfec-febd-4257-8884-e91f260fbe20/dqc_reference/reference_markers.fasta -out GCA_902752385.1_P1994_129_bin89_mag_fasta_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:05:55,075] [INFO] Task succeeded: Blastn
[2023-06-08 09:05:55,080] [INFO] Selected 4 target genomes.
[2023-06-08 09:05:55,080] [INFO] Target genome list was writen to GCA_902752385.1_P1994_129_bin89_mag_fasta_genomic.fna/target_genomes.txt
[2023-06-08 09:05:55,082] [INFO] Task started: fastANI
[2023-06-08 09:05:55,083] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c71bde0-663e-4e18-8835-1012cdd328c2/GCA_902752385.1_P1994_129_bin89_mag_fasta_genomic.fna.gz --refList GCA_902752385.1_P1994_129_bin89_mag_fasta_genomic.fna/target_genomes.txt --output GCA_902752385.1_P1994_129_bin89_mag_fasta_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 09:05:56,590] [INFO] Task succeeded: fastANI
[2023-06-08 09:05:56,591] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43f2cfec-febd-4257-8884-e91f260fbe20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 09:05:56,591] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43f2cfec-febd-4257-8884-e91f260fbe20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 09:05:56,600] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 09:05:56,600] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 09:05:56,601] [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	80.9505	274	369	95	below_threshold
Nitrosopumilus oxyclinae	strain=HCE1	GCA_013407165.1	1959104	1959104	type	True	80.823	277	369	95	below_threshold
Nitrosopumilus adriaticus	strain=NF5	GCA_000956175.1	1580092	1580092	type	True	80.174	257	369	95	below_threshold
Nitrosopumilus ureiphilus	strain=PS0	GCA_013407185.1	1470067	1470067	type	True	80.1582	261	369	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 09:05:56,603] [INFO] DFAST Taxonomy check result was written to GCA_902752385.1_P1994_129_bin89_mag_fasta_genomic.fna/tc_result.tsv
[2023-06-08 09:05:56,603] [INFO] ===== Taxonomy check completed =====
[2023-06-08 09:05:56,603] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 09:05:56,604] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43f2cfec-febd-4257-8884-e91f260fbe20/dqc_reference/checkm_data
[2023-06-08 09:05:56,605] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 09:05:56,625] [INFO] Task started: CheckM
[2023-06-08 09:05:56,626] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902752385.1_P1994_129_bin89_mag_fasta_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902752385.1_P1994_129_bin89_mag_fasta_genomic.fna/checkm_input GCA_902752385.1_P1994_129_bin89_mag_fasta_genomic.fna/checkm_result
[2023-06-08 09:06:19,222] [INFO] Task succeeded: CheckM
[2023-06-08 09:06:19,223] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 09:06:19,244] [INFO] ===== Completeness check finished =====
[2023-06-08 09:06:19,244] [INFO] ===== Start GTDB Search =====
[2023-06-08 09:06:19,245] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902752385.1_P1994_129_bin89_mag_fasta_genomic.fna/markers.fasta)
[2023-06-08 09:06:19,245] [INFO] Task started: Blastn
[2023-06-08 09:06:19,245] [INFO] Running command: blastn -query GCA_902752385.1_P1994_129_bin89_mag_fasta_genomic.fna/markers.fasta -db /var/lib/cwl/stg43f2cfec-febd-4257-8884-e91f260fbe20/dqc_reference/reference_markers_gtdb.fasta -out GCA_902752385.1_P1994_129_bin89_mag_fasta_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:06:19,738] [INFO] Task succeeded: Blastn
[2023-06-08 09:06:19,743] [INFO] Selected 5 target genomes.
[2023-06-08 09:06:19,743] [INFO] Target genome list was writen to GCA_902752385.1_P1994_129_bin89_mag_fasta_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 09:06:19,749] [INFO] Task started: fastANI
[2023-06-08 09:06:19,750] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c71bde0-663e-4e18-8835-1012cdd328c2/GCA_902752385.1_P1994_129_bin89_mag_fasta_genomic.fna.gz --refList GCA_902752385.1_P1994_129_bin89_mag_fasta_genomic.fna/target_genomes_gtdb.txt --output GCA_902752385.1_P1994_129_bin89_mag_fasta_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 09:06:21,072] [INFO] Task succeeded: fastANI
[2023-06-08 09:06:21,079] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 09:06:21,079] [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_001437625.1	s__Nitrosopumilus sp001437625	99.6228	301	369	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	98.62	95.42	0.85	0.75	5	conclusive
GCA_905612295.1	s__Nitrosopumilus sp905612295	93.1744	225	369	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014384445.1	s__Nitrosopumilus sp014384445	91.2143	229	369	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018657375.1	s__Nitrosopumilus sp018657375	90.306	196	369	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	98.79	98.40	0.79	0.75	5	-
GCA_018674605.1	s__Nitrosopumilus sp018674605	86.3504	154	369	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	98.83	98.50	0.79	0.69	12	-
--------------------------------------------------------------------------------
[2023-06-08 09:06:21,081] [INFO] GTDB search result was written to GCA_902752385.1_P1994_129_bin89_mag_fasta_genomic.fna/result_gtdb.tsv
[2023-06-08 09:06:21,081] [INFO] ===== GTDB Search completed =====
[2023-06-08 09:06:21,095] [INFO] DFAST_QC result json was written to GCA_902752385.1_P1994_129_bin89_mag_fasta_genomic.fna/dqc_result.json
[2023-06-08 09:06:21,096] [INFO] DFAST_QC completed!
[2023-06-08 09:06:21,096] [INFO] Total running time: 0h0m34s