[2024-01-24 14:46:56,564] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:56,568] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:56,568] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb8930e5-2441-4e1b-960c-32a033c8fa9a/dqc_reference
[2024-01-24 14:46:57,963] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:57,964] [INFO] Task started: Prodigal
[2024-01-24 14:46:57,964] [INFO] Running command: gunzip -c /var/lib/cwl/stgedb21d42-904e-4539-93c1-5e474add5d0d/GCF_005083985.2_ASM508398v2_genomic.fna.gz | prodigal -d GCF_005083985.2_ASM508398v2_genomic.fna/cds.fna -a GCF_005083985.2_ASM508398v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:01,570] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:01,570] [INFO] Task started: HMMsearch
[2024-01-24 14:47:01,570] [INFO] Running command: hmmsearch --tblout GCF_005083985.2_ASM508398v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb8930e5-2441-4e1b-960c-32a033c8fa9a/dqc_reference/reference_markers.hmm GCF_005083985.2_ASM508398v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:01,929] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:01,931] [INFO] Found 6/6 markers.
[2024-01-24 14:47:01,954] [INFO] Query marker FASTA was written to GCF_005083985.2_ASM508398v2_genomic.fna/markers.fasta
[2024-01-24 14:47:01,955] [INFO] Task started: Blastn
[2024-01-24 14:47:01,955] [INFO] Running command: blastn -query GCF_005083985.2_ASM508398v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb8930e5-2441-4e1b-960c-32a033c8fa9a/dqc_reference/reference_markers.fasta -out GCF_005083985.2_ASM508398v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:05,819] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:05,822] [INFO] Selected 11 target genomes.
[2024-01-24 14:47:05,823] [INFO] Target genome list was writen to GCF_005083985.2_ASM508398v2_genomic.fna/target_genomes.txt
[2024-01-24 14:47:05,874] [INFO] Task started: fastANI
[2024-01-24 14:47:05,874] [INFO] Running command: fastANI --query /var/lib/cwl/stgedb21d42-904e-4539-93c1-5e474add5d0d/GCF_005083985.2_ASM508398v2_genomic.fna.gz --refList GCF_005083985.2_ASM508398v2_genomic.fna/target_genomes.txt --output GCF_005083985.2_ASM508398v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:09,466] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:09,466] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb8930e5-2441-4e1b-960c-32a033c8fa9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:09,466] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb8930e5-2441-4e1b-960c-32a033c8fa9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:09,473] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:47:09,473] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:09,473] [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
Caminibacter pacificus	strain=TB6	GCA_005083985.2	1424653	1424653	type	True	100.0	622	623	95	conclusive
Caminibacter pacificus	strain=DSM 27783	GCA_003752135.1	1424653	1424653	type	True	99.9654	613	623	95	conclusive
Caminibacter mediatlanticus	strain=TB-2	GCA_000170735.1	291048	291048	type	True	78.5913	207	623	95	below_threshold
Caminibacter mediatlanticus	strain=TB-2	GCA_005843985.1	291048	291048	type	True	78.3716	218	623	95	below_threshold
Lebetimonas natsushimae	strain=HS1857	GCA_002335445.1	1936991	1936991	type	True	77.7344	188	623	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:09,475] [INFO] DFAST Taxonomy check result was written to GCF_005083985.2_ASM508398v2_genomic.fna/tc_result.tsv
[2024-01-24 14:47:09,475] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:09,475] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:09,476] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb8930e5-2441-4e1b-960c-32a033c8fa9a/dqc_reference/checkm_data
[2024-01-24 14:47:09,477] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:09,498] [INFO] Task started: CheckM
[2024-01-24 14:47:09,498] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005083985.2_ASM508398v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005083985.2_ASM508398v2_genomic.fna/checkm_input GCF_005083985.2_ASM508398v2_genomic.fna/checkm_result
[2024-01-24 14:47:34,008] [INFO] Task succeeded: CheckM
[2024-01-24 14:47:34,010] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:47:34,032] [INFO] ===== Completeness check finished =====
[2024-01-24 14:47:34,032] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:47:34,032] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005083985.2_ASM508398v2_genomic.fna/markers.fasta)
[2024-01-24 14:47:34,033] [INFO] Task started: Blastn
[2024-01-24 14:47:34,033] [INFO] Running command: blastn -query GCF_005083985.2_ASM508398v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb8930e5-2441-4e1b-960c-32a033c8fa9a/dqc_reference/reference_markers_gtdb.fasta -out GCF_005083985.2_ASM508398v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:34,964] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:34,969] [INFO] Selected 13 target genomes.
[2024-01-24 14:47:34,969] [INFO] Target genome list was writen to GCF_005083985.2_ASM508398v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:47:34,983] [INFO] Task started: fastANI
[2024-01-24 14:47:34,984] [INFO] Running command: fastANI --query /var/lib/cwl/stgedb21d42-904e-4539-93c1-5e474add5d0d/GCF_005083985.2_ASM508398v2_genomic.fna.gz --refList GCF_005083985.2_ASM508398v2_genomic.fna/target_genomes_gtdb.txt --output GCF_005083985.2_ASM508398v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:47:40,591] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:40,600] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:47:40,601] [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_003752135.1	s__Cetia pacifica	99.9654	613	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Nautiliales;f__Nautiliaceae;g__Cetia	95.0	99.26	98.54	0.96	0.92	3	conclusive
GCF_000021725.1	s__Nautilia profundicola	79.2611	255	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Nautiliales;f__Nautiliaceae;g__Nautilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004006315.1	s__Nautilia profundicola_A	78.824	242	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Nautiliales;f__Nautiliaceae;g__Nautilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005843985.1	s__Caminibacter mediatlanticus	78.3286	218	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Nautiliales;f__Nautiliaceae;g__Caminibacter	95.0	98.80	98.80	0.94	0.94	2	-
GCF_002335445.1	s__Lebetimonas natsushimae	77.7533	190	623	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Nautiliales;f__Nautiliaceae;g__Lebetimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:47:40,627] [INFO] GTDB search result was written to GCF_005083985.2_ASM508398v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:47:40,630] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:47:40,637] [INFO] DFAST_QC result json was written to GCF_005083985.2_ASM508398v2_genomic.fna/dqc_result.json
[2024-01-24 14:47:40,637] [INFO] DFAST_QC completed!
[2024-01-24 14:47:40,638] [INFO] Total running time: 0h0m44s