[2023-06-27 06:39:03,893] [INFO] DFAST_QC pipeline started.
[2023-06-27 06:39:03,895] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 06:39:03,896] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b8d8626-d87f-4d71-ae4c-ea8d886d5132/dqc_reference
[2023-06-27 06:39:05,090] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 06:39:05,091] [INFO] Task started: Prodigal
[2023-06-27 06:39:05,091] [INFO] Running command: gunzip -c /var/lib/cwl/stg51411fcf-1e20-4800-acde-8b486c51d674/GCA_027082715.1_ASM2708271v1_genomic.fna.gz | prodigal -d GCA_027082715.1_ASM2708271v1_genomic.fna/cds.fna -a GCA_027082715.1_ASM2708271v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 06:39:06,391] [INFO] Task succeeded: Prodigal
[2023-06-27 06:39:06,392] [INFO] Task started: HMMsearch
[2023-06-27 06:39:06,392] [INFO] Running command: hmmsearch --tblout GCA_027082715.1_ASM2708271v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b8d8626-d87f-4d71-ae4c-ea8d886d5132/dqc_reference/reference_markers.hmm GCA_027082715.1_ASM2708271v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 06:39:06,581] [INFO] Task succeeded: HMMsearch
[2023-06-27 06:39:06,583] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg51411fcf-1e20-4800-acde-8b486c51d674/GCA_027082715.1_ASM2708271v1_genomic.fna.gz]
[2023-06-27 06:39:06,598] [INFO] Query marker FASTA was written to GCA_027082715.1_ASM2708271v1_genomic.fna/markers.fasta
[2023-06-27 06:39:06,599] [INFO] Task started: Blastn
[2023-06-27 06:39:06,599] [INFO] Running command: blastn -query GCA_027082715.1_ASM2708271v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b8d8626-d87f-4d71-ae4c-ea8d886d5132/dqc_reference/reference_markers.fasta -out GCA_027082715.1_ASM2708271v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:39:07,152] [INFO] Task succeeded: Blastn
[2023-06-27 06:39:07,161] [INFO] Selected 18 target genomes.
[2023-06-27 06:39:07,161] [INFO] Target genome list was writen to GCA_027082715.1_ASM2708271v1_genomic.fna/target_genomes.txt
[2023-06-27 06:39:07,169] [INFO] Task started: fastANI
[2023-06-27 06:39:07,169] [INFO] Running command: fastANI --query /var/lib/cwl/stg51411fcf-1e20-4800-acde-8b486c51d674/GCA_027082715.1_ASM2708271v1_genomic.fna.gz --refList GCA_027082715.1_ASM2708271v1_genomic.fna/target_genomes.txt --output GCA_027082715.1_ASM2708271v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 06:39:13,261] [INFO] Task succeeded: fastANI
[2023-06-27 06:39:13,262] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b8d8626-d87f-4d71-ae4c-ea8d886d5132/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 06:39:13,262] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b8d8626-d87f-4d71-ae4c-ea8d886d5132/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 06:39:13,273] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 06:39:13,274] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 06:39:13,274] [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
Lebetimonas natsushimae	strain=HS1857	GCA_002335445.1	1936991	1936991	type	True	79.1354	65	102	95	below_threshold
Caminibacter mediatlanticus	strain=TB-2	GCA_005843985.1	291048	291048	type	True	78.8451	63	102	95	below_threshold
Caminibacter mediatlanticus	strain=TB-2	GCA_000170735.1	291048	291048	type	True	78.7948	62	102	95	below_threshold
Caminibacter pacificus	strain=TB6	GCA_005083985.2	1424653	1424653	type	True	78.4771	54	102	95	below_threshold
Caminibacter pacificus	strain=DSM 27783	GCA_003752135.1	1424653	1424653	type	True	78.4022	55	102	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 06:39:13,276] [INFO] DFAST Taxonomy check result was written to GCA_027082715.1_ASM2708271v1_genomic.fna/tc_result.tsv
[2023-06-27 06:39:13,277] [INFO] ===== Taxonomy check completed =====
[2023-06-27 06:39:13,277] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 06:39:13,277] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b8d8626-d87f-4d71-ae4c-ea8d886d5132/dqc_reference/checkm_data
[2023-06-27 06:39:13,279] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 06:39:13,309] [INFO] Task started: CheckM
[2023-06-27 06:39:13,309] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027082715.1_ASM2708271v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027082715.1_ASM2708271v1_genomic.fna/checkm_input GCA_027082715.1_ASM2708271v1_genomic.fna/checkm_result
[2023-06-27 06:39:26,290] [INFO] Task succeeded: CheckM
[2023-06-27 06:39:26,291] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-27 06:39:26,326] [INFO] ===== Completeness check finished =====
[2023-06-27 06:39:26,326] [INFO] ===== Start GTDB Search =====
[2023-06-27 06:39:26,326] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027082715.1_ASM2708271v1_genomic.fna/markers.fasta)
[2023-06-27 06:39:26,327] [INFO] Task started: Blastn
[2023-06-27 06:39:26,327] [INFO] Running command: blastn -query GCA_027082715.1_ASM2708271v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b8d8626-d87f-4d71-ae4c-ea8d886d5132/dqc_reference/reference_markers_gtdb.fasta -out GCA_027082715.1_ASM2708271v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:39:27,072] [INFO] Task succeeded: Blastn
[2023-06-27 06:39:27,076] [INFO] Selected 22 target genomes.
[2023-06-27 06:39:27,076] [INFO] Target genome list was writen to GCA_027082715.1_ASM2708271v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 06:39:27,127] [INFO] Task started: fastANI
[2023-06-27 06:39:27,127] [INFO] Running command: fastANI --query /var/lib/cwl/stg51411fcf-1e20-4800-acde-8b486c51d674/GCA_027082715.1_ASM2708271v1_genomic.fna.gz --refList GCA_027082715.1_ASM2708271v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027082715.1_ASM2708271v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 06:39:36,566] [INFO] Task succeeded: fastANI
[2023-06-27 06:39:36,578] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 06:39:36,578] [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_000523275.1	s__Lebetimonas sp000523275	79.1518	58	102	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Nautiliales;f__Nautiliaceae;g__Lebetimonas	95.0	96.86	96.81	0.99	0.99	6	-
GCF_002335445.1	s__Lebetimonas natsushimae	79.1354	65	102	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Nautiliales;f__Nautiliaceae;g__Lebetimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005843985.1	s__Caminibacter mediatlanticus	78.9166	62	102	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Nautiliales;f__Nautiliaceae;g__Caminibacter	95.0	98.80	98.80	0.94	0.94	2	-
GCF_000021725.1	s__Nautilia profundicola	78.4043	55	102	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Nautiliales;f__Nautiliaceae;g__Nautilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752135.1	s__Cetia pacifica	78.4022	55	102	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Nautiliales;f__Nautiliaceae;g__Cetia	95.0	99.26	98.54	0.96	0.92	3	-
--------------------------------------------------------------------------------
[2023-06-27 06:39:36,582] [INFO] GTDB search result was written to GCA_027082715.1_ASM2708271v1_genomic.fna/result_gtdb.tsv
[2023-06-27 06:39:36,583] [INFO] ===== GTDB Search completed =====
[2023-06-27 06:39:36,594] [INFO] DFAST_QC result json was written to GCA_027082715.1_ASM2708271v1_genomic.fna/dqc_result.json
[2023-06-27 06:39:36,594] [INFO] DFAST_QC completed!
[2023-06-27 06:39:36,594] [INFO] Total running time: 0h0m33s