[2023-06-28 18:14:41,166] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:14:41,168] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:14:41,169] [INFO] DQC Reference Directory: /var/lib/cwl/stg2df6b573-139f-47b4-99aa-e4302ba715a5/dqc_reference
[2023-06-28 18:14:42,500] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:14:42,501] [INFO] Task started: Prodigal
[2023-06-28 18:14:42,501] [INFO] Running command: gunzip -c /var/lib/cwl/stg2c04d7b8-e93f-4ede-8f67-e585f62abdda/GCA_005883465.1_ASM588346v1_genomic.fna.gz | prodigal -d GCA_005883465.1_ASM588346v1_genomic.fna/cds.fna -a GCA_005883465.1_ASM588346v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:14:47,759] [INFO] Task succeeded: Prodigal
[2023-06-28 18:14:47,759] [INFO] Task started: HMMsearch
[2023-06-28 18:14:47,759] [INFO] Running command: hmmsearch --tblout GCA_005883465.1_ASM588346v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2df6b573-139f-47b4-99aa-e4302ba715a5/dqc_reference/reference_markers.hmm GCA_005883465.1_ASM588346v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:14:48,010] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:14:48,011] [INFO] Found 6/6 markers.
[2023-06-28 18:14:48,034] [INFO] Query marker FASTA was written to GCA_005883465.1_ASM588346v1_genomic.fna/markers.fasta
[2023-06-28 18:14:48,035] [INFO] Task started: Blastn
[2023-06-28 18:14:48,035] [INFO] Running command: blastn -query GCA_005883465.1_ASM588346v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2df6b573-139f-47b4-99aa-e4302ba715a5/dqc_reference/reference_markers.fasta -out GCA_005883465.1_ASM588346v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:14:48,840] [INFO] Task succeeded: Blastn
[2023-06-28 18:14:48,845] [INFO] Selected 30 target genomes.
[2023-06-28 18:14:48,845] [INFO] Target genome list was writen to GCA_005883465.1_ASM588346v1_genomic.fna/target_genomes.txt
[2023-06-28 18:14:48,849] [INFO] Task started: fastANI
[2023-06-28 18:14:48,850] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c04d7b8-e93f-4ede-8f67-e585f62abdda/GCA_005883465.1_ASM588346v1_genomic.fna.gz --refList GCA_005883465.1_ASM588346v1_genomic.fna/target_genomes.txt --output GCA_005883465.1_ASM588346v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:15:11,143] [INFO] Task succeeded: fastANI
[2023-06-28 18:15:11,143] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2df6b573-139f-47b4-99aa-e4302ba715a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:15:11,143] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2df6b573-139f-47b4-99aa-e4302ba715a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:15:11,151] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:15:11,151] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 18:15:11,151] [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
Thermopolyspora flexuosa	strain=DSM 43186	GCA_006716785.1	103836	103836	type	True	75.625	50	549	95	below_threshold
Phycicoccus mangrovi	strain=KQZ13P-1	GCA_018729305.1	2840470	2840470	type	True	75.4848	53	549	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	75.4493	76	549	95	below_threshold
Microbacterium immunditiarum	strain=DSM 24662	GCA_013409785.1	337480	337480	type	True	75.3557	54	549	95	below_threshold
Agrococcus pavilionensis	strain=RW1	GCA_000400485.1	1346502	1346502	type	True	75.3384	57	549	95	below_threshold
Agrococcus sediminis	strain=NS18	GCA_007923295.1	2599924	2599924	type	True	75.315	59	549	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	75.2232	51	549	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 18:15:11,153] [INFO] DFAST Taxonomy check result was written to GCA_005883465.1_ASM588346v1_genomic.fna/tc_result.tsv
[2023-06-28 18:15:11,154] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:15:11,154] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:15:11,154] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2df6b573-139f-47b4-99aa-e4302ba715a5/dqc_reference/checkm_data
[2023-06-28 18:15:11,155] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:15:11,184] [INFO] Task started: CheckM
[2023-06-28 18:15:11,184] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_005883465.1_ASM588346v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_005883465.1_ASM588346v1_genomic.fna/checkm_input GCA_005883465.1_ASM588346v1_genomic.fna/checkm_result
[2023-06-28 18:15:32,470] [INFO] Task succeeded: CheckM
[2023-06-28 18:15:32,472] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:15:32,498] [INFO] ===== Completeness check finished =====
[2023-06-28 18:15:32,498] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:15:32,499] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_005883465.1_ASM588346v1_genomic.fna/markers.fasta)
[2023-06-28 18:15:32,499] [INFO] Task started: Blastn
[2023-06-28 18:15:32,499] [INFO] Running command: blastn -query GCA_005883465.1_ASM588346v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2df6b573-139f-47b4-99aa-e4302ba715a5/dqc_reference/reference_markers_gtdb.fasta -out GCA_005883465.1_ASM588346v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:15:33,687] [INFO] Task succeeded: Blastn
[2023-06-28 18:15:33,692] [INFO] Selected 20 target genomes.
[2023-06-28 18:15:33,693] [INFO] Target genome list was writen to GCA_005883465.1_ASM588346v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:15:33,710] [INFO] Task started: fastANI
[2023-06-28 18:15:33,710] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c04d7b8-e93f-4ede-8f67-e585f62abdda/GCA_005883465.1_ASM588346v1_genomic.fna.gz --refList GCA_005883465.1_ASM588346v1_genomic.fna/target_genomes_gtdb.txt --output GCA_005883465.1_ASM588346v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:15:48,060] [INFO] Task succeeded: fastANI
[2023-06-28 18:15:48,075] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 18:15:48,075] [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
GCA_005883175.1	s__AC-67 sp005883175	95.2893	342	549	d__Bacteria;p__Actinobacteriota;c__UBA4738;o__AC-67;f__AC-67;g__AC-67	95.0	95.81	95.81	0.74	0.74	2	conclusive
GCA_005884515.1	s__AC-67 sp005884515	92.4512	428	549	d__Bacteria;p__Actinobacteriota;c__UBA4738;o__AC-67;f__AC-67;g__AC-67	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016208485.1	s__JACQXY01 sp016208485	76.706	84	549	d__Bacteria;p__Actinobacteriota;c__UBA4738;o__AC-67;f__AC-67;g__JACQXY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013201035.1	s__Phycicoccus sp013201035	75.668	59	549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716785.1	s__Thermopolyspora flexuosa	75.6246	52	549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermopolyspora	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016887965.1	s__Phycicoccus sp016887965	75.5408	62	549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650075.1	s__Streptomyces microflavus	75.3929	52	549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.25	97.27	0.91	0.85	13	-
GCF_006715055.1	s__Lapillicoccus jejuensis	75.3194	70	549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Lapillicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003999975.1	s__Actinoplanes sp003999975	75.242	58	549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744955.1	s__Dokdonella_A sp017744955	74.8706	55	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003220225.1	s__AR12 sp003220225	74.8699	73	549	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__AR12	95.0	99.31	99.31	0.91	0.91	2	-
GCA_004143945.1	s__Dokdonella_A sp004143945	74.8316	50	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 18:15:48,078] [INFO] GTDB search result was written to GCA_005883465.1_ASM588346v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:15:48,079] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:15:48,082] [INFO] DFAST_QC result json was written to GCA_005883465.1_ASM588346v1_genomic.fna/dqc_result.json
[2023-06-28 18:15:48,082] [INFO] DFAST_QC completed!
[2023-06-28 18:15:48,082] [INFO] Total running time: 0h1m7s