[2024-01-24 13:49:32,552] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:32,554] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:32,555] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e85beb5-9ea4-4144-b874-9d7cc0736450/dqc_reference
[2024-01-24 13:49:33,954] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:33,955] [INFO] Task started: Prodigal
[2024-01-24 13:49:33,955] [INFO] Running command: gunzip -c /var/lib/cwl/stg7afd2893-3240-4878-965f-8e998090d7f8/GCF_004798665.1_ASM479866v1_genomic.fna.gz | prodigal -d GCF_004798665.1_ASM479866v1_genomic.fna/cds.fna -a GCF_004798665.1_ASM479866v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:45,475] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:45,475] [INFO] Task started: HMMsearch
[2024-01-24 13:49:45,475] [INFO] Running command: hmmsearch --tblout GCF_004798665.1_ASM479866v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e85beb5-9ea4-4144-b874-9d7cc0736450/dqc_reference/reference_markers.hmm GCF_004798665.1_ASM479866v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:45,725] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:45,726] [INFO] Found 6/6 markers.
[2024-01-24 13:49:45,757] [INFO] Query marker FASTA was written to GCF_004798665.1_ASM479866v1_genomic.fna/markers.fasta
[2024-01-24 13:49:45,758] [INFO] Task started: Blastn
[2024-01-24 13:49:45,758] [INFO] Running command: blastn -query GCF_004798665.1_ASM479866v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e85beb5-9ea4-4144-b874-9d7cc0736450/dqc_reference/reference_markers.fasta -out GCF_004798665.1_ASM479866v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:46,993] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:46,997] [INFO] Selected 13 target genomes.
[2024-01-24 13:49:46,998] [INFO] Target genome list was writen to GCF_004798665.1_ASM479866v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:47,003] [INFO] Task started: fastANI
[2024-01-24 13:49:47,003] [INFO] Running command: fastANI --query /var/lib/cwl/stg7afd2893-3240-4878-965f-8e998090d7f8/GCF_004798665.1_ASM479866v1_genomic.fna.gz --refList GCF_004798665.1_ASM479866v1_genomic.fna/target_genomes.txt --output GCF_004798665.1_ASM479866v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:58,695] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:58,695] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e85beb5-9ea4-4144-b874-9d7cc0736450/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:58,695] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e85beb5-9ea4-4144-b874-9d7cc0736450/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:58,707] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:58,707] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:58,708] [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
Actinomyces procaprae	strain=dk561	GCA_004798665.1	2560010	2560010	type	True	100.0	1200	1200	95	conclusive
Actinomyces succiniciruminis	strain=AM4	GCA_900002405.2	1522002	1522002	type	True	89.1677	848	1200	95	below_threshold
Actinomyces ruminicola	strain=DSM 27982	GCA_900103885.1	332524	332524	type	True	87.8616	863	1200	95	below_threshold
Actinomyces qiguomingii	strain=410	GCA_004102025.1	2057800	2057800	type	True	85.0172	891	1200	95	below_threshold
Actinomyces israelii	strain=DSM 43320	GCA_000711965.1	1659	1659	type	True	80.7965	599	1200	95	below_threshold
Actinomyces denticolens	strain=DSM 20671	GCA_002072185.1	52767	52767	type	True	80.6335	437	1200	95	below_threshold
Actinomyces marmotae	strain=zg-325	GCA_009829655.1	2737173	2737173	type	True	80.4923	394	1200	95	below_threshold
Actinomyces viscosus	strain=CCUG 14476	GCA_004525795.1	1656	1656	type	True	80.4841	510	1200	95	below_threshold
Actinomyces radicidentis	strain=CCUG 36733	GCA_001553565.1	111015	111015	type	True	80.4792	522	1200	95	below_threshold
Actinomyces lilanjuaniae	strain=2129	GCA_003606385.1	2321394	2321394	type	True	79.499	398	1200	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.6418	190	1200	95	below_threshold
Ruania zhangjianzhongii	strain=HY168	GCA_008000995.1	2603206	2603206	type	True	76.5875	183	1200	95	below_threshold
Kineosporia corallincola	strain=J2-2	GCA_018499875.1	2835133	2835133	type	True	76.1807	218	1200	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:58,709] [INFO] DFAST Taxonomy check result was written to GCF_004798665.1_ASM479866v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:58,710] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:58,710] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:58,710] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e85beb5-9ea4-4144-b874-9d7cc0736450/dqc_reference/checkm_data
[2024-01-24 13:49:58,712] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:58,749] [INFO] Task started: CheckM
[2024-01-24 13:49:58,749] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004798665.1_ASM479866v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004798665.1_ASM479866v1_genomic.fna/checkm_input GCF_004798665.1_ASM479866v1_genomic.fna/checkm_result
[2024-01-24 13:50:37,194] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:37,195] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:37,223] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:37,223] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:37,224] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004798665.1_ASM479866v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:37,224] [INFO] Task started: Blastn
[2024-01-24 13:50:37,224] [INFO] Running command: blastn -query GCF_004798665.1_ASM479866v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e85beb5-9ea4-4144-b874-9d7cc0736450/dqc_reference/reference_markers_gtdb.fasta -out GCF_004798665.1_ASM479866v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:39,213] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:39,217] [INFO] Selected 5 target genomes.
[2024-01-24 13:50:39,218] [INFO] Target genome list was writen to GCF_004798665.1_ASM479866v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:39,223] [INFO] Task started: fastANI
[2024-01-24 13:50:39,223] [INFO] Running command: fastANI --query /var/lib/cwl/stg7afd2893-3240-4878-965f-8e998090d7f8/GCF_004798665.1_ASM479866v1_genomic.fna.gz --refList GCF_004798665.1_ASM479866v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004798665.1_ASM479866v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:45,189] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:45,200] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:45,200] [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_004798665.1	s__Actinomyces procaprae	100.0	1200	1200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.28	98.28	0.91	0.91	2	conclusive
GCF_900098745.1	s__Actinomyces glycerinitolerans	89.1914	900	1200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	96.3414	98.41	98.38	0.91	0.91	4	-
GCF_900002405.1	s__Actinomyces succiniciruminis	89.1628	848	1200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	96.3414	98.30	98.26	0.87	0.86	3	-
GCF_900103885.1	s__Actinomyces ruminicola	87.8616	863	1200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	96.80	96.66	0.89	0.87	3	-
GCF_009930875.1	s__Actinomyces sp009930875	86.6238	884	1200	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.69	98.69	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:45,203] [INFO] GTDB search result was written to GCF_004798665.1_ASM479866v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:45,204] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:45,208] [INFO] DFAST_QC result json was written to GCF_004798665.1_ASM479866v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:45,208] [INFO] DFAST_QC completed!
[2024-01-24 13:50:45,208] [INFO] Total running time: 0h1m13s