[2024-01-24 11:44:23,928] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:23,930] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:23,931] [INFO] DQC Reference Directory: /var/lib/cwl/stgcfd81171-8a16-4e62-af8d-b3e98eec8d8d/dqc_reference
[2024-01-24 11:44:26,339] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:26,340] [INFO] Task started: Prodigal
[2024-01-24 11:44:26,340] [INFO] Running command: gunzip -c /var/lib/cwl/stg24861623-9df4-4359-a6e7-1503e5a96f7f/GCF_002335445.1_ASM233544v1_genomic.fna.gz | prodigal -d GCF_002335445.1_ASM233544v1_genomic.fna/cds.fna -a GCF_002335445.1_ASM233544v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:29,347] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:29,348] [INFO] Task started: HMMsearch
[2024-01-24 11:44:29,348] [INFO] Running command: hmmsearch --tblout GCF_002335445.1_ASM233544v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcfd81171-8a16-4e62-af8d-b3e98eec8d8d/dqc_reference/reference_markers.hmm GCF_002335445.1_ASM233544v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:29,557] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:29,559] [INFO] Found 6/6 markers.
[2024-01-24 11:44:29,580] [INFO] Query marker FASTA was written to GCF_002335445.1_ASM233544v1_genomic.fna/markers.fasta
[2024-01-24 11:44:29,580] [INFO] Task started: Blastn
[2024-01-24 11:44:29,580] [INFO] Running command: blastn -query GCF_002335445.1_ASM233544v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfd81171-8a16-4e62-af8d-b3e98eec8d8d/dqc_reference/reference_markers.fasta -out GCF_002335445.1_ASM233544v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:31,441] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:31,445] [INFO] Selected 13 target genomes.
[2024-01-24 11:44:31,446] [INFO] Target genome list was writen to GCF_002335445.1_ASM233544v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:31,893] [INFO] Task started: fastANI
[2024-01-24 11:44:31,894] [INFO] Running command: fastANI --query /var/lib/cwl/stg24861623-9df4-4359-a6e7-1503e5a96f7f/GCF_002335445.1_ASM233544v1_genomic.fna.gz --refList GCF_002335445.1_ASM233544v1_genomic.fna/target_genomes.txt --output GCF_002335445.1_ASM233544v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:36,147] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:36,148] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcfd81171-8a16-4e62-af8d-b3e98eec8d8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:36,149] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcfd81171-8a16-4e62-af8d-b3e98eec8d8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:36,162] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:36,163] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:36,163] [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	100.0	542	542	95	conclusive
Caminibacter mediatlanticus	strain=TB-2	GCA_000170735.1	291048	291048	type	True	78.4173	261	542	95	below_threshold
Caminibacter pacificus	strain=TB6	GCA_005083985.2	1424653	1424653	type	True	78.2764	176	542	95	below_threshold
Caminibacter mediatlanticus	strain=TB-2	GCA_005843985.1	291048	291048	type	True	78.1625	272	542	95	below_threshold
Caminibacter pacificus	strain=DSM 27783	GCA_003752135.1	1424653	1424653	type	True	78.0439	178	542	95	below_threshold
Malaciobacter canalis	strain=LMG 29148	GCA_008000835.1	1912871	1912871	type	True	75.9005	62	542	95	below_threshold
Malaciobacter canalis	strain=F138-33	GCA_002723485.1	1912871	1912871	type	True	75.5618	59	542	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:36,165] [INFO] DFAST Taxonomy check result was written to GCF_002335445.1_ASM233544v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:36,165] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:36,165] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:36,166] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcfd81171-8a16-4e62-af8d-b3e98eec8d8d/dqc_reference/checkm_data
[2024-01-24 11:44:36,167] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:36,195] [INFO] Task started: CheckM
[2024-01-24 11:44:36,195] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002335445.1_ASM233544v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002335445.1_ASM233544v1_genomic.fna/checkm_input GCF_002335445.1_ASM233544v1_genomic.fna/checkm_result
[2024-01-24 11:44:52,732] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:52,734] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:52,755] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:52,756] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:52,756] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002335445.1_ASM233544v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:52,757] [INFO] Task started: Blastn
[2024-01-24 11:44:52,757] [INFO] Running command: blastn -query GCF_002335445.1_ASM233544v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfd81171-8a16-4e62-af8d-b3e98eec8d8d/dqc_reference/reference_markers_gtdb.fasta -out GCF_002335445.1_ASM233544v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:53,563] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:53,567] [INFO] Selected 12 target genomes.
[2024-01-24 11:44:53,568] [INFO] Target genome list was writen to GCF_002335445.1_ASM233544v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:53,580] [INFO] Task started: fastANI
[2024-01-24 11:44:53,580] [INFO] Running command: fastANI --query /var/lib/cwl/stg24861623-9df4-4359-a6e7-1503e5a96f7f/GCF_002335445.1_ASM233544v1_genomic.fna.gz --refList GCF_002335445.1_ASM233544v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002335445.1_ASM233544v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:57,838] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:57,845] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:57,845] [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_002335445.1	s__Lebetimonas natsushimae	100.0	542	542	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Nautiliales;f__Nautiliaceae;g__Lebetimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000523275.1	s__Lebetimonas sp000523275	81.5052	412	542	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Nautiliales;f__Nautiliaceae;g__Lebetimonas	95.0	96.86	96.81	0.99	0.99	6	-
GCF_004006315.1	s__Nautilia profundicola_A	78.3719	207	542	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	78.1784	272	542	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Nautiliales;f__Nautiliaceae;g__Caminibacter	95.0	98.80	98.80	0.94	0.94	2	-
GCF_003752135.1	s__Cetia pacifica	78.0506	180	542	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Nautiliales;f__Nautiliaceae;g__Cetia	95.0	99.26	98.54	0.96	0.92	3	-
GCF_000021725.1	s__Nautilia profundicola	77.9038	221	542	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Nautiliales;f__Nautiliaceae;g__Nautilia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:57,847] [INFO] GTDB search result was written to GCF_002335445.1_ASM233544v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:57,847] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:57,850] [INFO] DFAST_QC result json was written to GCF_002335445.1_ASM233544v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:57,850] [INFO] DFAST_QC completed!
[2024-01-24 11:44:57,850] [INFO] Total running time: 0h0m34s