[2024-01-24 14:46:57,691] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:57,693] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:57,694] [INFO] DQC Reference Directory: /var/lib/cwl/stg9e9db1a8-a5e7-4f89-9e0c-f6b72f64bf4a/dqc_reference
[2024-01-24 14:46:59,007] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:59,008] [INFO] Task started: Prodigal
[2024-01-24 14:46:59,009] [INFO] Running command: gunzip -c /var/lib/cwl/stgb1cb9582-0130-4bdf-a7e4-c61b7733a56d/GCF_003702705.1_ASM370270v1_genomic.fna.gz | prodigal -d GCF_003702705.1_ASM370270v1_genomic.fna/cds.fna -a GCF_003702705.1_ASM370270v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:09,956] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:09,957] [INFO] Task started: HMMsearch
[2024-01-24 14:47:09,957] [INFO] Running command: hmmsearch --tblout GCF_003702705.1_ASM370270v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9e9db1a8-a5e7-4f89-9e0c-f6b72f64bf4a/dqc_reference/reference_markers.hmm GCF_003702705.1_ASM370270v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:10,284] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:10,286] [INFO] Found 6/6 markers.
[2024-01-24 14:47:10,320] [INFO] Query marker FASTA was written to GCF_003702705.1_ASM370270v1_genomic.fna/markers.fasta
[2024-01-24 14:47:10,321] [INFO] Task started: Blastn
[2024-01-24 14:47:10,321] [INFO] Running command: blastn -query GCF_003702705.1_ASM370270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e9db1a8-a5e7-4f89-9e0c-f6b72f64bf4a/dqc_reference/reference_markers.fasta -out GCF_003702705.1_ASM370270v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:11,588] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:11,591] [INFO] Selected 13 target genomes.
[2024-01-24 14:47:11,592] [INFO] Target genome list was writen to GCF_003702705.1_ASM370270v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:11,599] [INFO] Task started: fastANI
[2024-01-24 14:47:11,599] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1cb9582-0130-4bdf-a7e4-c61b7733a56d/GCF_003702705.1_ASM370270v1_genomic.fna.gz --refList GCF_003702705.1_ASM370270v1_genomic.fna/target_genomes.txt --output GCF_003702705.1_ASM370270v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:23,876] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:23,877] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9e9db1a8-a5e7-4f89-9e0c-f6b72f64bf4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:23,877] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9e9db1a8-a5e7-4f89-9e0c-f6b72f64bf4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:23,889] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:23,889] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:23,890] [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
Ornithinimicrobium cerasi	strain=CPCC 203383	GCA_003702705.1	2248773	2248773	type	True	100.0	1240	1242	95	conclusive
Ornithinimicrobium tianjinense	strain=CGMCC 1.12160	GCA_014636495.1	1195761	1195761	type	True	82.8506	771	1242	95	below_threshold
Ornithinimicrobium pekingense	strain=DSM 21552	GCA_000421185.1	384677	384677	type	True	82.3116	802	1242	95	below_threshold
Ornithinimicrobium pekingense	strain=CGMCC 1.5362	GCA_014644955.1	384677	384677	type	True	82.2791	799	1242	95	below_threshold
Ornithinimicrobium humiphilum	strain=DSM 12362	GCA_006716885.1	125288	125288	type	True	82.0893	723	1242	95	below_threshold
Ornithinimicrobium avium	strain=AMA3305	GCA_003351765.1	2283195	2283195	type	True	81.7951	734	1242	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	81.7622	719	1242	95	below_threshold
Ornithinimicrobium flavum	strain=CPCC 203535	GCA_004526345.1	1288636	1288636	type	True	81.7172	749	1242	95	below_threshold
Serinicoccus marinus	strain=DSM 15273	GCA_000421245.1	247333	247333	type	True	80.7885	664	1242	95	below_threshold
Serinicoccus marinus	strain=DSM 15273	GCA_008386315.1	247333	247333	type	True	80.7305	657	1242	95	below_threshold
Serinicoccus kebangsaanensis	strain=P2D13-UKM	GCA_008919445.1	2602069	2602069	type	True	80.7115	628	1242	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	79.7366	522	1242	95	below_threshold
Ornithinimicrobium murale	strain=DSM 22056	GCA_003352835.1	1050153	1050153	type	True	78.5939	327	1242	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:23,891] [INFO] DFAST Taxonomy check result was written to GCF_003702705.1_ASM370270v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:23,892] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:23,892] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:23,892] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9e9db1a8-a5e7-4f89-9e0c-f6b72f64bf4a/dqc_reference/checkm_data
[2024-01-24 14:47:23,893] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:23,932] [INFO] Task started: CheckM
[2024-01-24 14:47:23,932] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003702705.1_ASM370270v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003702705.1_ASM370270v1_genomic.fna/checkm_input GCF_003702705.1_ASM370270v1_genomic.fna/checkm_result
[2024-01-24 14:48:24,636] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:24,638] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:24,658] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:24,659] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:24,659] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003702705.1_ASM370270v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:24,659] [INFO] Task started: Blastn
[2024-01-24 14:48:24,660] [INFO] Running command: blastn -query GCF_003702705.1_ASM370270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e9db1a8-a5e7-4f89-9e0c-f6b72f64bf4a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003702705.1_ASM370270v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:26,522] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:26,526] [INFO] Selected 11 target genomes.
[2024-01-24 14:48:26,526] [INFO] Target genome list was writen to GCF_003702705.1_ASM370270v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:26,537] [INFO] Task started: fastANI
[2024-01-24 14:48:26,538] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1cb9582-0130-4bdf-a7e4-c61b7733a56d/GCF_003702705.1_ASM370270v1_genomic.fna.gz --refList GCF_003702705.1_ASM370270v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003702705.1_ASM370270v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:36,096] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:36,113] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:36,113] [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_003702705.1	s__Ornithinimicrobium cerasi	100.0	1240	1242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	96.64	96.64	0.85	0.85	2	conclusive
GCF_014636495.1	s__Ornithinimicrobium tianjinense	82.8399	772	1242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421185.1	s__Ornithinimicrobium pekingense	82.3313	800	1242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006716885.1	s__Ornithinimicrobium humiphilum	82.0829	724	1242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001942405.1	s__Ornithinimicrobium sp001942405	81.8958	728	1242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	97.63	97.63	0.88	0.88	2	-
GCF_003351765.1	s__Ornithinimicrobium sp003351765	81.795	734	1242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004526345.1	s__Serinicoccus flavus	81.7102	750	1242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003577095.1	s__Ornithinimicrobium sp003577095	81.5878	567	1242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006337125.1	s__Serinicoccus chungangensis	81.0785	683	1242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004322775.1	s__Serinicoccus sp004322775	81.0621	717	1242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_008386315.1	s__Serinicoccus marinus	80.7395	656	1242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	98.28	97.42	0.92	0.87	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:36,115] [INFO] GTDB search result was written to GCF_003702705.1_ASM370270v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:36,116] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:36,122] [INFO] DFAST_QC result json was written to GCF_003702705.1_ASM370270v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:36,122] [INFO] DFAST_QC completed!
[2024-01-24 14:48:36,122] [INFO] Total running time: 0h1m38s