[2023-06-27 15:19:48,485] [INFO] DFAST_QC pipeline started.
[2023-06-27 15:19:48,487] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 15:19:48,487] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0032f0b-0acb-4400-8460-fdbbc46050c9/dqc_reference
[2023-06-27 15:19:49,714] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 15:19:49,715] [INFO] Task started: Prodigal
[2023-06-27 15:19:49,715] [INFO] Running command: gunzip -c /var/lib/cwl/stgf205cc17-9ee0-4f4f-b05f-cbe8a0b685d1/GCA_027082175.1_ASM2708217v1_genomic.fna.gz | prodigal -d GCA_027082175.1_ASM2708217v1_genomic.fna/cds.fna -a GCA_027082175.1_ASM2708217v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 15:19:52,614] [INFO] Task succeeded: Prodigal
[2023-06-27 15:19:52,614] [INFO] Task started: HMMsearch
[2023-06-27 15:19:52,614] [INFO] Running command: hmmsearch --tblout GCA_027082175.1_ASM2708217v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0032f0b-0acb-4400-8460-fdbbc46050c9/dqc_reference/reference_markers.hmm GCA_027082175.1_ASM2708217v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 15:19:52,785] [INFO] Task succeeded: HMMsearch
[2023-06-27 15:19:52,787] [INFO] Found 6/6 markers.
[2023-06-27 15:19:52,825] [INFO] Query marker FASTA was written to GCA_027082175.1_ASM2708217v1_genomic.fna/markers.fasta
[2023-06-27 15:19:52,826] [INFO] Task started: Blastn
[2023-06-27 15:19:52,826] [INFO] Running command: blastn -query GCA_027082175.1_ASM2708217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0032f0b-0acb-4400-8460-fdbbc46050c9/dqc_reference/reference_markers.fasta -out GCA_027082175.1_ASM2708217v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 15:19:53,375] [INFO] Task succeeded: Blastn
[2023-06-27 15:19:53,379] [INFO] Selected 18 target genomes.
[2023-06-27 15:19:53,379] [INFO] Target genome list was writen to GCA_027082175.1_ASM2708217v1_genomic.fna/target_genomes.txt
[2023-06-27 15:19:53,381] [INFO] Task started: fastANI
[2023-06-27 15:19:53,381] [INFO] Running command: fastANI --query /var/lib/cwl/stgf205cc17-9ee0-4f4f-b05f-cbe8a0b685d1/GCA_027082175.1_ASM2708217v1_genomic.fna.gz --refList GCA_027082175.1_ASM2708217v1_genomic.fna/target_genomes.txt --output GCA_027082175.1_ASM2708217v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 15:19:58,869] [INFO] Task succeeded: fastANI
[2023-06-27 15:19:58,869] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0032f0b-0acb-4400-8460-fdbbc46050c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 15:19:58,870] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0032f0b-0acb-4400-8460-fdbbc46050c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 15:19:58,875] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 15:19:58,875] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 15:19:58,875] [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
Nitrosophilus labii	strain=HRV44	GCA_014466985.1	2706014	2706014	type	True	91.307	486	549	95	below_threshold
Nitrosophilus alvini	strain=EPR55-1	GCA_015100395.1	2714855	2714855	type	True	77.1224	104	549	95	below_threshold
Nitratiruptor tergarcus	strain=DSM 16512	GCA_900176045.1	269259	269259	type	True	76.1771	71	549	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 15:19:58,879] [INFO] DFAST Taxonomy check result was written to GCA_027082175.1_ASM2708217v1_genomic.fna/tc_result.tsv
[2023-06-27 15:19:58,880] [INFO] ===== Taxonomy check completed =====
[2023-06-27 15:19:58,880] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 15:19:58,880] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0032f0b-0acb-4400-8460-fdbbc46050c9/dqc_reference/checkm_data
[2023-06-27 15:19:58,881] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 15:19:58,902] [INFO] Task started: CheckM
[2023-06-27 15:19:58,902] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027082175.1_ASM2708217v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027082175.1_ASM2708217v1_genomic.fna/checkm_input GCA_027082175.1_ASM2708217v1_genomic.fna/checkm_result
[2023-06-27 15:20:14,762] [INFO] Task succeeded: CheckM
[2023-06-27 15:20:14,763] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 15:20:14,786] [INFO] ===== Completeness check finished =====
[2023-06-27 15:20:14,786] [INFO] ===== Start GTDB Search =====
[2023-06-27 15:20:14,786] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027082175.1_ASM2708217v1_genomic.fna/markers.fasta)
[2023-06-27 15:20:14,787] [INFO] Task started: Blastn
[2023-06-27 15:20:14,787] [INFO] Running command: blastn -query GCA_027082175.1_ASM2708217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0032f0b-0acb-4400-8460-fdbbc46050c9/dqc_reference/reference_markers_gtdb.fasta -out GCA_027082175.1_ASM2708217v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 15:20:15,554] [INFO] Task succeeded: Blastn
[2023-06-27 15:20:15,558] [INFO] Selected 17 target genomes.
[2023-06-27 15:20:15,558] [INFO] Target genome list was writen to GCA_027082175.1_ASM2708217v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 15:20:15,574] [INFO] Task started: fastANI
[2023-06-27 15:20:15,575] [INFO] Running command: fastANI --query /var/lib/cwl/stgf205cc17-9ee0-4f4f-b05f-cbe8a0b685d1/GCA_027082175.1_ASM2708217v1_genomic.fna.gz --refList GCA_027082175.1_ASM2708217v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027082175.1_ASM2708217v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 15:20:20,851] [INFO] Task succeeded: fastANI
[2023-06-27 15:20:20,855] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 15:20:20,855] [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_014466985.1	s__Nitrosophilus_A labii	91.342	485	549	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Nitratiruptoraceae;g__Nitrosophilus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015100395.1	s__Nitrosophilus alvini	77.1224	104	549	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Nitratiruptoraceae;g__Nitrosophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176045.1	s__Nitratiruptor tergarcus	76.1771	71	549	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Nitratiruptoraceae;g__Nitratiruptor	95.0	95.63	95.63	0.89	0.89	3	-
--------------------------------------------------------------------------------
[2023-06-27 15:20:20,858] [INFO] GTDB search result was written to GCA_027082175.1_ASM2708217v1_genomic.fna/result_gtdb.tsv
[2023-06-27 15:20:20,859] [INFO] ===== GTDB Search completed =====
[2023-06-27 15:20:20,861] [INFO] DFAST_QC result json was written to GCA_027082175.1_ASM2708217v1_genomic.fna/dqc_result.json
[2023-06-27 15:20:20,862] [INFO] DFAST_QC completed!
[2023-06-27 15:20:20,862] [INFO] Total running time: 0h0m32s