[2024-01-24 14:05:53,618] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:53,620] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:53,620] [INFO] DQC Reference Directory: /var/lib/cwl/stge77e86db-0e64-4236-96e7-ce4d9d1b3c78/dqc_reference
[2024-01-24 14:05:55,014] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:55,015] [INFO] Task started: Prodigal
[2024-01-24 14:05:55,015] [INFO] Running command: gunzip -c /var/lib/cwl/stge84fb357-0621-490c-8c25-c84d8f941253/GCF_004025845.1_ASM402584v1_genomic.fna.gz | prodigal -d GCF_004025845.1_ASM402584v1_genomic.fna/cds.fna -a GCF_004025845.1_ASM402584v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:04,473] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:04,473] [INFO] Task started: HMMsearch
[2024-01-24 14:06:04,473] [INFO] Running command: hmmsearch --tblout GCF_004025845.1_ASM402584v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge77e86db-0e64-4236-96e7-ce4d9d1b3c78/dqc_reference/reference_markers.hmm GCF_004025845.1_ASM402584v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:04,753] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:04,755] [INFO] Found 6/6 markers.
[2024-01-24 14:06:04,791] [INFO] Query marker FASTA was written to GCF_004025845.1_ASM402584v1_genomic.fna/markers.fasta
[2024-01-24 14:06:04,792] [INFO] Task started: Blastn
[2024-01-24 14:06:04,792] [INFO] Running command: blastn -query GCF_004025845.1_ASM402584v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge77e86db-0e64-4236-96e7-ce4d9d1b3c78/dqc_reference/reference_markers.fasta -out GCF_004025845.1_ASM402584v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:06,209] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:06,212] [INFO] Selected 12 target genomes.
[2024-01-24 14:06:06,212] [INFO] Target genome list was writen to GCF_004025845.1_ASM402584v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:06,252] [INFO] Task started: fastANI
[2024-01-24 14:06:06,252] [INFO] Running command: fastANI --query /var/lib/cwl/stge84fb357-0621-490c-8c25-c84d8f941253/GCF_004025845.1_ASM402584v1_genomic.fna.gz --refList GCF_004025845.1_ASM402584v1_genomic.fna/target_genomes.txt --output GCF_004025845.1_ASM402584v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:16,311] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:16,311] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge77e86db-0e64-4236-96e7-ce4d9d1b3c78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:16,312] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge77e86db-0e64-4236-96e7-ce4d9d1b3c78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:16,326] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:06:16,326] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:16,326] [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
Janibacter hoylei	strain=PVAS-1	GCA_004025845.1	364298	364298	type	True	100.0	1023	1023	95	conclusive
Janibacter hoylei	strain=PVAS-1	GCA_000297495.1	364298	364298	type	True	99.9109	974	1023	95	conclusive
Janibacter indicus	strain=CGMCC 1.12511	GCA_900176385.1	857417	857417	type	True	88.9831	872	1023	95	below_threshold
Janibacter anophelis	strain=NBRC 107843	GCA_001570945.1	319054	319054	type	True	86.9696	812	1023	95	below_threshold
Janibacter terrae	strain=NBRC 107853	GCA_001591405.1	103817	103817	type	True	86.3673	812	1023	95	below_threshold
Janibacter limosus	strain=NBRC 16128	GCA_001570985.1	53458	53458	type	True	85.3313	788	1023	95	below_threshold
Janibacter cremeus	strain=DSM 26154	GCA_013409205.1	1285192	1285192	type	True	83.0931	691	1023	95	below_threshold
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	82.2159	603	1023	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	82.0116	677	1023	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	78.9246	393	1023	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	78.7512	402	1023	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	78.6942	374	1023	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:16,328] [INFO] DFAST Taxonomy check result was written to GCF_004025845.1_ASM402584v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:16,329] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:16,329] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:16,329] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge77e86db-0e64-4236-96e7-ce4d9d1b3c78/dqc_reference/checkm_data
[2024-01-24 14:06:16,330] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:16,364] [INFO] Task started: CheckM
[2024-01-24 14:06:16,365] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004025845.1_ASM402584v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004025845.1_ASM402584v1_genomic.fna/checkm_input GCF_004025845.1_ASM402584v1_genomic.fna/checkm_result
[2024-01-24 14:07:02,684] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:02,685] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:02,707] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:02,708] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:02,708] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004025845.1_ASM402584v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:02,708] [INFO] Task started: Blastn
[2024-01-24 14:07:02,709] [INFO] Running command: blastn -query GCF_004025845.1_ASM402584v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge77e86db-0e64-4236-96e7-ce4d9d1b3c78/dqc_reference/reference_markers_gtdb.fasta -out GCF_004025845.1_ASM402584v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:04,777] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:04,780] [INFO] Selected 8 target genomes.
[2024-01-24 14:07:04,780] [INFO] Target genome list was writen to GCF_004025845.1_ASM402584v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:04,786] [INFO] Task started: fastANI
[2024-01-24 14:07:04,787] [INFO] Running command: fastANI --query /var/lib/cwl/stge84fb357-0621-490c-8c25-c84d8f941253/GCF_004025845.1_ASM402584v1_genomic.fna.gz --refList GCF_004025845.1_ASM402584v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004025845.1_ASM402584v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:11,138] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:11,154] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:11,155] [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_000297495.1	s__Janibacter hoylei	99.9109	974	1023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	99.95	99.95	0.99	0.99	2	conclusive
GCF_900176385.1	s__Janibacter indicus	88.9893	871	1023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	97.60	97.16	0.90	0.88	4	-
GCF_001570945.1	s__Janibacter anophelis	86.9696	812	1023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	96.19	96.19	0.85	0.85	2	-
GCF_001591405.1	s__Janibacter terrae	86.3521	813	1023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	98.98	98.88	0.95	0.93	4	-
GCF_004295485.1	s__Janibacter limosus_A	86.0252	837	1023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570985.1	s__Janibacter limosus	85.3313	788	1023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409205.1	s__Janibacter cremeus	83.0555	694	1023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002384765.1	s__Demequina sp002384765	75.854	67	1023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	99.28	99.28	0.64	0.64	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:11,157] [INFO] GTDB search result was written to GCF_004025845.1_ASM402584v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:11,157] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:11,161] [INFO] DFAST_QC result json was written to GCF_004025845.1_ASM402584v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:11,162] [INFO] DFAST_QC completed!
[2024-01-24 14:07:11,162] [INFO] Total running time: 0h1m18s