[2024-01-25 18:50:50,473] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:50:50,475] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:50:50,475] [INFO] DQC Reference Directory: /var/lib/cwl/stgaaef627a-25f0-4d65-9d1c-f2a091b2c4bb/dqc_reference
[2024-01-25 18:50:51,749] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:50:51,750] [INFO] Task started: Prodigal
[2024-01-25 18:50:51,751] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd476221-3261-43ba-8c0c-d5057e90c67d/GCF_014230145.1_ASM1423014v1_genomic.fna.gz | prodigal -d GCF_014230145.1_ASM1423014v1_genomic.fna/cds.fna -a GCF_014230145.1_ASM1423014v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:51:12,893] [INFO] Task succeeded: Prodigal
[2024-01-25 18:51:12,893] [INFO] Task started: HMMsearch
[2024-01-25 18:51:12,893] [INFO] Running command: hmmsearch --tblout GCF_014230145.1_ASM1423014v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaaef627a-25f0-4d65-9d1c-f2a091b2c4bb/dqc_reference/reference_markers.hmm GCF_014230145.1_ASM1423014v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:51:13,170] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:51:13,172] [INFO] Found 6/6 markers.
[2024-01-25 18:51:13,209] [INFO] Query marker FASTA was written to GCF_014230145.1_ASM1423014v1_genomic.fna/markers.fasta
[2024-01-25 18:51:13,210] [INFO] Task started: Blastn
[2024-01-25 18:51:13,210] [INFO] Running command: blastn -query GCF_014230145.1_ASM1423014v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaaef627a-25f0-4d65-9d1c-f2a091b2c4bb/dqc_reference/reference_markers.fasta -out GCF_014230145.1_ASM1423014v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:13,803] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:13,807] [INFO] Selected 17 target genomes.
[2024-01-25 18:51:13,808] [INFO] Target genome list was writen to GCF_014230145.1_ASM1423014v1_genomic.fna/target_genomes.txt
[2024-01-25 18:51:13,825] [INFO] Task started: fastANI
[2024-01-25 18:51:13,825] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd476221-3261-43ba-8c0c-d5057e90c67d/GCF_014230145.1_ASM1423014v1_genomic.fna.gz --refList GCF_014230145.1_ASM1423014v1_genomic.fna/target_genomes.txt --output GCF_014230145.1_ASM1423014v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:51:26,794] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:26,794] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaaef627a-25f0-4d65-9d1c-f2a091b2c4bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:51:26,794] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaaef627a-25f0-4d65-9d1c-f2a091b2c4bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:51:26,799] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:51:26,799] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:51:26,799] [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
Pelagicoccus albus	strain=JCM23202	GCA_014230145.1	415222	415222	type	True	100.0	1581	1585	95	conclusive
Pelagicoccus enzymogenes	strain=NFK12	GCA_014803405.1	2773457	2773457	type	True	78.8204	389	1585	95	below_threshold
Pelagicoccus mobilis	strain=KCTC 13126	GCA_016595505.1	415221	415221	type	True	78.4793	329	1585	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:51:26,801] [INFO] DFAST Taxonomy check result was written to GCF_014230145.1_ASM1423014v1_genomic.fna/tc_result.tsv
[2024-01-25 18:51:26,801] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:51:26,802] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:51:26,802] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaaef627a-25f0-4d65-9d1c-f2a091b2c4bb/dqc_reference/checkm_data
[2024-01-25 18:51:26,803] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:51:26,849] [INFO] Task started: CheckM
[2024-01-25 18:51:26,849] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014230145.1_ASM1423014v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014230145.1_ASM1423014v1_genomic.fna/checkm_input GCF_014230145.1_ASM1423014v1_genomic.fna/checkm_result
[2024-01-25 18:52:24,015] [INFO] Task succeeded: CheckM
[2024-01-25 18:52:24,016] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:52:24,033] [INFO] ===== Completeness check finished =====
[2024-01-25 18:52:24,033] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:52:24,035] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014230145.1_ASM1423014v1_genomic.fna/markers.fasta)
[2024-01-25 18:52:24,035] [INFO] Task started: Blastn
[2024-01-25 18:52:24,035] [INFO] Running command: blastn -query GCF_014230145.1_ASM1423014v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaaef627a-25f0-4d65-9d1c-f2a091b2c4bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_014230145.1_ASM1423014v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:25,014] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:25,017] [INFO] Selected 15 target genomes.
[2024-01-25 18:52:25,017] [INFO] Target genome list was writen to GCF_014230145.1_ASM1423014v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:52:25,028] [INFO] Task started: fastANI
[2024-01-25 18:52:25,029] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd476221-3261-43ba-8c0c-d5057e90c67d/GCF_014230145.1_ASM1423014v1_genomic.fna.gz --refList GCF_014230145.1_ASM1423014v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014230145.1_ASM1423014v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:52:36,932] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:36,936] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:52:36,937] [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_014230145.1	s__Pelagicoccus albus	100.0	1581	1585	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Pelagicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014803405.1	s__Pelagicoccus sp014803405	78.8393	386	1585	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Pelagicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595505.1	s__Pelagicoccus mobilis	78.4669	330	1585	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Pelagicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000155695.1	s__Pelagicoccus sp000155695	78.2867	356	1585	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Pelagicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:52:36,938] [INFO] GTDB search result was written to GCF_014230145.1_ASM1423014v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:52:36,938] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:52:36,940] [INFO] DFAST_QC result json was written to GCF_014230145.1_ASM1423014v1_genomic.fna/dqc_result.json
[2024-01-25 18:52:36,940] [INFO] DFAST_QC completed!
[2024-01-25 18:52:36,941] [INFO] Total running time: 0h1m46s