[2023-06-17 04:19:58,979] [INFO] DFAST_QC pipeline started.
[2023-06-17 04:19:58,984] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 04:19:58,984] [INFO] DQC Reference Directory: /var/lib/cwl/stg6884062a-3595-4029-9f36-1f9ca04088e1/dqc_reference
[2023-06-17 04:20:01,791] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 04:20:01,792] [INFO] Task started: Prodigal
[2023-06-17 04:20:01,792] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a70cdae-af47-4f0d-90dd-8632944e7202/GCA_013140415.1_ASM1314041v1_genomic.fna.gz | prodigal -d GCA_013140415.1_ASM1314041v1_genomic.fna/cds.fna -a GCA_013140415.1_ASM1314041v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 04:20:03,874] [INFO] Task succeeded: Prodigal
[2023-06-17 04:20:03,874] [INFO] Task started: HMMsearch
[2023-06-17 04:20:03,875] [INFO] Running command: hmmsearch --tblout GCA_013140415.1_ASM1314041v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6884062a-3595-4029-9f36-1f9ca04088e1/dqc_reference/reference_markers.hmm GCA_013140415.1_ASM1314041v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 04:20:04,053] [INFO] Task succeeded: HMMsearch
[2023-06-17 04:20:04,055] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg9a70cdae-af47-4f0d-90dd-8632944e7202/GCA_013140415.1_ASM1314041v1_genomic.fna.gz]
[2023-06-17 04:20:04,076] [INFO] Query marker FASTA was written to GCA_013140415.1_ASM1314041v1_genomic.fna/markers.fasta
[2023-06-17 04:20:04,077] [INFO] Task started: Blastn
[2023-06-17 04:20:04,077] [INFO] Running command: blastn -query GCA_013140415.1_ASM1314041v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6884062a-3595-4029-9f36-1f9ca04088e1/dqc_reference/reference_markers.fasta -out GCA_013140415.1_ASM1314041v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 04:20:05,380] [INFO] Task succeeded: Blastn
[2023-06-17 04:20:05,384] [INFO] Selected 5 target genomes.
[2023-06-17 04:20:05,384] [INFO] Target genome list was writen to GCA_013140415.1_ASM1314041v1_genomic.fna/target_genomes.txt
[2023-06-17 04:20:05,388] [INFO] Task started: fastANI
[2023-06-17 04:20:05,389] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a70cdae-af47-4f0d-90dd-8632944e7202/GCA_013140415.1_ASM1314041v1_genomic.fna.gz --refList GCA_013140415.1_ASM1314041v1_genomic.fna/target_genomes.txt --output GCA_013140415.1_ASM1314041v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 04:20:07,369] [INFO] Task succeeded: fastANI
[2023-06-17 04:20:07,370] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6884062a-3595-4029-9f36-1f9ca04088e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 04:20:07,370] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6884062a-3595-4029-9f36-1f9ca04088e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 04:20:07,377] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 04:20:07,377] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 04:20:07,377] [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	79.4507	179	298	95	below_threshold
Nitrosopumilus maritimus	strain=SCM1	GCA_000018465.1	338192	338192	type	True	79.3606	169	298	95	below_threshold
Nitrosopumilus cobalaminigenes	strain=HCA1	GCA_013407145.1	1470066	1470066	type	True	79.2989	198	298	95	below_threshold
Nitrosopumilus oxyclinae	strain=HCE1	GCA_013407165.1	1959104	1959104	type	True	79.2316	185	298	95	below_threshold
Nitrosopumilus piranensis	strain=D3C	GCA_000875775.1	1582439	1582439	type	True	78.8689	167	298	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 04:20:07,381] [INFO] DFAST Taxonomy check result was written to GCA_013140415.1_ASM1314041v1_genomic.fna/tc_result.tsv
[2023-06-17 04:20:07,382] [INFO] ===== Taxonomy check completed =====
[2023-06-17 04:20:07,382] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 04:20:07,382] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6884062a-3595-4029-9f36-1f9ca04088e1/dqc_reference/checkm_data
[2023-06-17 04:20:07,383] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 04:20:07,403] [INFO] Task started: CheckM
[2023-06-17 04:20:07,404] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013140415.1_ASM1314041v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013140415.1_ASM1314041v1_genomic.fna/checkm_input GCA_013140415.1_ASM1314041v1_genomic.fna/checkm_result
[2023-06-17 04:20:25,302] [INFO] Task succeeded: CheckM
[2023-06-17 04:20:25,303] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.62%
Contamintation: 4.92%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-17 04:20:25,338] [INFO] ===== Completeness check finished =====
[2023-06-17 04:20:25,338] [INFO] ===== Start GTDB Search =====
[2023-06-17 04:20:25,339] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013140415.1_ASM1314041v1_genomic.fna/markers.fasta)
[2023-06-17 04:20:25,339] [INFO] Task started: Blastn
[2023-06-17 04:20:25,339] [INFO] Running command: blastn -query GCA_013140415.1_ASM1314041v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6884062a-3595-4029-9f36-1f9ca04088e1/dqc_reference/reference_markers_gtdb.fasta -out GCA_013140415.1_ASM1314041v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 04:20:25,919] [INFO] Task succeeded: Blastn
[2023-06-17 04:20:25,923] [INFO] Selected 5 target genomes.
[2023-06-17 04:20:25,923] [INFO] Target genome list was writen to GCA_013140415.1_ASM1314041v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 04:20:25,946] [INFO] Task started: fastANI
[2023-06-17 04:20:25,946] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a70cdae-af47-4f0d-90dd-8632944e7202/GCA_013140415.1_ASM1314041v1_genomic.fna.gz --refList GCA_013140415.1_ASM1314041v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013140415.1_ASM1314041v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 04:20:27,539] [INFO] Task succeeded: fastANI
[2023-06-17 04:20:27,549] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 04:20:27,550] [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_013140415.1	s__Nitrosarchaeum sp013140415	100.0	297	298	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosarchaeum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009697485.1	s__Nitrosarchaeum sp009697485	94.1233	145	298	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297665.1	s__Nitrosarchaeum sp004297665	92.3415	181	298	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosarchaeum	95.0	96.40	95.66	0.66	0.65	5	-
GCA_003569705.1	s__Nitrosarchaeum sp003569705	89.7571	264	298	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosarchaeum	95.0	99.59	99.59	0.99	0.99	2	-
GCA_005798405.1	s__Nitrosarchaeum sp005798405	87.8381	234	298	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosarchaeum	95.0	99.84	99.81	0.94	0.93	4	-
--------------------------------------------------------------------------------
[2023-06-17 04:20:27,552] [INFO] GTDB search result was written to GCA_013140415.1_ASM1314041v1_genomic.fna/result_gtdb.tsv
[2023-06-17 04:20:27,552] [INFO] ===== GTDB Search completed =====
[2023-06-17 04:20:27,556] [INFO] DFAST_QC result json was written to GCA_013140415.1_ASM1314041v1_genomic.fna/dqc_result.json
[2023-06-17 04:20:27,556] [INFO] DFAST_QC completed!
[2023-06-17 04:20:27,556] [INFO] Total running time: 0h0m29s