[2024-01-24 13:57:16,520] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:16,523] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:16,524] [INFO] DQC Reference Directory: /var/lib/cwl/stg627ba086-7a13-467a-8e4d-b4baedfb7df3/dqc_reference
[2024-01-24 13:57:17,832] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:17,833] [INFO] Task started: Prodigal
[2024-01-24 13:57:17,833] [INFO] Running command: gunzip -c /var/lib/cwl/stg77c51a90-4152-4109-afef-973fbd405c40/GCF_003752135.1_ASM375213v1_genomic.fna.gz | prodigal -d GCF_003752135.1_ASM375213v1_genomic.fna/cds.fna -a GCF_003752135.1_ASM375213v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:21,356] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:21,356] [INFO] Task started: HMMsearch
[2024-01-24 13:57:21,356] [INFO] Running command: hmmsearch --tblout GCF_003752135.1_ASM375213v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg627ba086-7a13-467a-8e4d-b4baedfb7df3/dqc_reference/reference_markers.hmm GCF_003752135.1_ASM375213v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:21,604] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:21,606] [INFO] Found 6/6 markers.
[2024-01-24 13:57:21,629] [INFO] Query marker FASTA was written to GCF_003752135.1_ASM375213v1_genomic.fna/markers.fasta
[2024-01-24 13:57:21,629] [INFO] Task started: Blastn
[2024-01-24 13:57:21,629] [INFO] Running command: blastn -query GCF_003752135.1_ASM375213v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg627ba086-7a13-467a-8e4d-b4baedfb7df3/dqc_reference/reference_markers.fasta -out GCF_003752135.1_ASM375213v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:22,216] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:22,220] [INFO] Selected 11 target genomes.
[2024-01-24 13:57:22,220] [INFO] Target genome list was writen to GCF_003752135.1_ASM375213v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:22,226] [INFO] Task started: fastANI
[2024-01-24 13:57:22,226] [INFO] Running command: fastANI --query /var/lib/cwl/stg77c51a90-4152-4109-afef-973fbd405c40/GCF_003752135.1_ASM375213v1_genomic.fna.gz --refList GCF_003752135.1_ASM375213v1_genomic.fna/target_genomes.txt --output GCF_003752135.1_ASM375213v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:25,631] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:25,632] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg627ba086-7a13-467a-8e4d-b4baedfb7df3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:25,632] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg627ba086-7a13-467a-8e4d-b4baedfb7df3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:25,639] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:57:25,639] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:25,639] [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=DSM 27783	GCA_003752135.1	1424653	1424653	type	True	100.0	616	616	95	conclusive
Caminibacter pacificus	strain=TB6	GCA_005083985.2	1424653	1424653	type	True	99.9784	613	616	95	conclusive
Caminibacter mediatlanticus	strain=TB-2	GCA_005843985.1	291048	291048	type	True	78.135	205	616	95	below_threshold
Caminibacter mediatlanticus	strain=TB-2	GCA_000170735.1	291048	291048	type	True	78.0598	199	616	95	below_threshold
Lebetimonas natsushimae	strain=HS1857	GCA_002335445.1	1936991	1936991	type	True	77.7448	180	616	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:25,641] [INFO] DFAST Taxonomy check result was written to GCF_003752135.1_ASM375213v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:25,641] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:25,641] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:25,641] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg627ba086-7a13-467a-8e4d-b4baedfb7df3/dqc_reference/checkm_data
[2024-01-24 13:57:25,643] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:25,664] [INFO] Task started: CheckM
[2024-01-24 13:57:25,665] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003752135.1_ASM375213v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003752135.1_ASM375213v1_genomic.fna/checkm_input GCF_003752135.1_ASM375213v1_genomic.fna/checkm_result
[2024-01-24 13:57:44,694] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:44,696] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:44,712] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:44,712] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:44,713] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003752135.1_ASM375213v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:44,713] [INFO] Task started: Blastn
[2024-01-24 13:57:44,713] [INFO] Running command: blastn -query GCF_003752135.1_ASM375213v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg627ba086-7a13-467a-8e4d-b4baedfb7df3/dqc_reference/reference_markers_gtdb.fasta -out GCF_003752135.1_ASM375213v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:45,554] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:45,557] [INFO] Selected 13 target genomes.
[2024-01-24 13:57:45,557] [INFO] Target genome list was writen to GCF_003752135.1_ASM375213v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:45,569] [INFO] Task started: fastANI
[2024-01-24 13:57:45,569] [INFO] Running command: fastANI --query /var/lib/cwl/stg77c51a90-4152-4109-afef-973fbd405c40/GCF_003752135.1_ASM375213v1_genomic.fna.gz --refList GCF_003752135.1_ASM375213v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003752135.1_ASM375213v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:50,203] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:50,214] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:50,214] [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	100.0	616	616	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	79.2464	235	616	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	78.6	235	616	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	78.1176	206	616	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	77.7634	179	616	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 13:57:50,216] [INFO] GTDB search result was written to GCF_003752135.1_ASM375213v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:50,216] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:50,219] [INFO] DFAST_QC result json was written to GCF_003752135.1_ASM375213v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:50,219] [INFO] DFAST_QC completed!
[2024-01-24 13:57:50,219] [INFO] Total running time: 0h0m34s