[2024-01-25 18:58:36,266] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:58:36,269] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:58:36,269] [INFO] DQC Reference Directory: /var/lib/cwl/stgb70bef2a-52d5-4138-a9df-ad8128b99a0c/dqc_reference
[2024-01-25 18:58:37,377] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:58:37,378] [INFO] Task started: Prodigal
[2024-01-25 18:58:37,378] [INFO] Running command: gunzip -c /var/lib/cwl/stg59e5aad9-7635-4e0c-9666-535c871683b5/GCF_011326735.1_ASM1132673v1_genomic.fna.gz | prodigal -d GCF_011326735.1_ASM1132673v1_genomic.fna/cds.fna -a GCF_011326735.1_ASM1132673v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:58:44,907] [INFO] Task succeeded: Prodigal
[2024-01-25 18:58:44,907] [INFO] Task started: HMMsearch
[2024-01-25 18:58:44,907] [INFO] Running command: hmmsearch --tblout GCF_011326735.1_ASM1132673v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb70bef2a-52d5-4138-a9df-ad8128b99a0c/dqc_reference/reference_markers.hmm GCF_011326735.1_ASM1132673v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:58:45,132] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:58:45,133] [INFO] Found 6/6 markers.
[2024-01-25 18:58:45,162] [INFO] Query marker FASTA was written to GCF_011326735.1_ASM1132673v1_genomic.fna/markers.fasta
[2024-01-25 18:58:45,162] [INFO] Task started: Blastn
[2024-01-25 18:58:45,162] [INFO] Running command: blastn -query GCF_011326735.1_ASM1132673v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb70bef2a-52d5-4138-a9df-ad8128b99a0c/dqc_reference/reference_markers.fasta -out GCF_011326735.1_ASM1132673v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:46,363] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:46,365] [INFO] Selected 12 target genomes.
[2024-01-25 18:58:46,366] [INFO] Target genome list was writen to GCF_011326735.1_ASM1132673v1_genomic.fna/target_genomes.txt
[2024-01-25 18:58:46,375] [INFO] Task started: fastANI
[2024-01-25 18:58:46,375] [INFO] Running command: fastANI --query /var/lib/cwl/stg59e5aad9-7635-4e0c-9666-535c871683b5/GCF_011326735.1_ASM1132673v1_genomic.fna.gz --refList GCF_011326735.1_ASM1132673v1_genomic.fna/target_genomes.txt --output GCF_011326735.1_ASM1132673v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:58:56,491] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:56,491] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb70bef2a-52d5-4138-a9df-ad8128b99a0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:58:56,492] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb70bef2a-52d5-4138-a9df-ad8128b99a0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:58:56,500] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:58:56,500] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:58:56,500] [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
Phycicoccus endophyticus	strain=IP6SC6	GCA_011326735.1	1690220	1690220	type	True	100.0	1047	1048	95	conclusive
Phycicoccus endophyticus	strain=CGMCC 4.7300	GCA_014646175.1	1690220	1690220	type	True	99.9921	1043	1048	95	conclusive
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	84.1019	763	1048	95	below_threshold
Phycicoccus mangrovi	strain=KQZ13P-1	GCA_018729305.1	2840470	2840470	type	True	84.0759	780	1048	95	below_threshold
Phycicoccus flavus	strain=CMS6Z-2	GCA_004025965.2	2502783	2502783	type	True	83.4981	752	1048	95	below_threshold
Phycicoccus duodecadis	strain=DSM 12806	GCA_002846495.1	173053	173053	type	True	82.887	709	1048	95	below_threshold
Knoellia remsis	strain=ATCC BAA-1496	GCA_003002895.1	407159	407159	type	True	80.3816	549	1048	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	79.9362	528	1048	95	below_threshold
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	79.7158	482	1048	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	78.5403	429	1048	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	78.5376	389	1048	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	78.4178	412	1048	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:58:56,502] [INFO] DFAST Taxonomy check result was written to GCF_011326735.1_ASM1132673v1_genomic.fna/tc_result.tsv
[2024-01-25 18:58:56,503] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:58:56,503] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:58:56,503] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb70bef2a-52d5-4138-a9df-ad8128b99a0c/dqc_reference/checkm_data
[2024-01-25 18:58:56,504] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:58:56,537] [INFO] Task started: CheckM
[2024-01-25 18:58:56,537] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011326735.1_ASM1132673v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011326735.1_ASM1132673v1_genomic.fna/checkm_input GCF_011326735.1_ASM1132673v1_genomic.fna/checkm_result
[2024-01-25 18:59:38,010] [INFO] Task succeeded: CheckM
[2024-01-25 18:59:38,011] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:59:38,025] [INFO] ===== Completeness check finished =====
[2024-01-25 18:59:38,025] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:59:38,026] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011326735.1_ASM1132673v1_genomic.fna/markers.fasta)
[2024-01-25 18:59:38,026] [INFO] Task started: Blastn
[2024-01-25 18:59:38,026] [INFO] Running command: blastn -query GCF_011326735.1_ASM1132673v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb70bef2a-52d5-4138-a9df-ad8128b99a0c/dqc_reference/reference_markers_gtdb.fasta -out GCF_011326735.1_ASM1132673v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:39,984] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:39,988] [INFO] Selected 10 target genomes.
[2024-01-25 18:59:39,988] [INFO] Target genome list was writen to GCF_011326735.1_ASM1132673v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:59:39,999] [INFO] Task started: fastANI
[2024-01-25 18:59:39,999] [INFO] Running command: fastANI --query /var/lib/cwl/stg59e5aad9-7635-4e0c-9666-535c871683b5/GCF_011326735.1_ASM1132673v1_genomic.fna.gz --refList GCF_011326735.1_ASM1132673v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011326735.1_ASM1132673v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:59:49,242] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:49,249] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:59:49,249] [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_011326735.1	s__Phycicoccus endophyticus	100.0	1047	1048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	99.99	99.99	1.00	1.00	3	conclusive
GCA_014763705.1	s__Phycicoccus sp014763705	84.1946	594	1048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016887965.1	s__Phycicoccus sp016887965	84.1797	785	1048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720925.1	s__Phycicoccus jejuensis	84.0935	764	1048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	96.36	95.39	0.88	0.87	4	-
GCF_013201035.1	s__Phycicoccus sp013201035	84.0609	785	1048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011383005.1	s__Phycicoccus sp011383005	84.0123	765	1048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004025965.2	s__Phycicoccus flavus	83.4925	753	1048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139485.1	s__Phycicoccus sp018139485	83.1141	696	1048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846495.1	s__Phycicoccus duodecadis	82.8611	712	1048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428065.1	s__Phycicoccus sp001428065	82.8101	694	1048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:59:49,251] [INFO] GTDB search result was written to GCF_011326735.1_ASM1132673v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:59:49,251] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:59:49,253] [INFO] DFAST_QC result json was written to GCF_011326735.1_ASM1132673v1_genomic.fna/dqc_result.json
[2024-01-25 18:59:49,254] [INFO] DFAST_QC completed!
[2024-01-25 18:59:49,254] [INFO] Total running time: 0h1m13s