[2024-01-24 13:47:11,852] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:47:11,854] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:47:11,854] [INFO] DQC Reference Directory: /var/lib/cwl/stgc47f86ba-586e-4216-8a23-0fbdc0e4f0ef/dqc_reference
[2024-01-24 13:47:13,206] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:47:13,209] [INFO] Task started: Prodigal
[2024-01-24 13:47:13,210] [INFO] Running command: gunzip -c /var/lib/cwl/stg32ef3f1b-2663-4ee6-a6f7-c879bbd16f32/GCF_000701465.1_ASM70146v1_genomic.fna.gz | prodigal -d GCF_000701465.1_ASM70146v1_genomic.fna/cds.fna -a GCF_000701465.1_ASM70146v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:47:21,475] [INFO] Task succeeded: Prodigal
[2024-01-24 13:47:21,475] [INFO] Task started: HMMsearch
[2024-01-24 13:47:21,475] [INFO] Running command: hmmsearch --tblout GCF_000701465.1_ASM70146v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc47f86ba-586e-4216-8a23-0fbdc0e4f0ef/dqc_reference/reference_markers.hmm GCF_000701465.1_ASM70146v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:47:21,742] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:47:21,743] [INFO] Found 6/6 markers.
[2024-01-24 13:47:21,775] [INFO] Query marker FASTA was written to GCF_000701465.1_ASM70146v1_genomic.fna/markers.fasta
[2024-01-24 13:47:21,775] [INFO] Task started: Blastn
[2024-01-24 13:47:21,776] [INFO] Running command: blastn -query GCF_000701465.1_ASM70146v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc47f86ba-586e-4216-8a23-0fbdc0e4f0ef/dqc_reference/reference_markers.fasta -out GCF_000701465.1_ASM70146v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:23,073] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:23,076] [INFO] Selected 19 target genomes.
[2024-01-24 13:47:23,077] [INFO] Target genome list was writen to GCF_000701465.1_ASM70146v1_genomic.fna/target_genomes.txt
[2024-01-24 13:47:23,082] [INFO] Task started: fastANI
[2024-01-24 13:47:23,083] [INFO] Running command: fastANI --query /var/lib/cwl/stg32ef3f1b-2663-4ee6-a6f7-c879bbd16f32/GCF_000701465.1_ASM70146v1_genomic.fna.gz --refList GCF_000701465.1_ASM70146v1_genomic.fna/target_genomes.txt --output GCF_000701465.1_ASM70146v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:37,056] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:37,057] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc47f86ba-586e-4216-8a23-0fbdc0e4f0ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:37,057] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc47f86ba-586e-4216-8a23-0fbdc0e4f0ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:37,079] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:37,079] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:37,079] [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
Paraoerskovia marina	strain=DSM 21750	GCA_000701465.1	545619	545619	type	True	100.0	976	976	95	conclusive
Sediminihabitans luteus	strain=NBRC 108568	GCA_016863455.1	1138585	1138585	type	True	80.9119	606	976	95	below_threshold
Sediminihabitans luteus	strain=DSM 25478	GCA_002797595.1	1138585	1138585	type	True	80.8922	615	976	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	79.6976	512	976	95	below_threshold
Cellulosimicrobium marinum	strain=NBRC 110994	GCA_020551945.1	1638992	1638992	type	True	79.6241	530	976	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	79.5985	516	976	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	79.5846	524	976	95	below_threshold
Oerskovia enterophila	strain=DSM 43852	GCA_001692445.1	43678	43678	type	True	79.5632	526	976	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	79.5156	549	976	95	below_threshold
Cellulomonas cellasea	strain=DSM 20118	GCA_000767135.1	43670	43670	type	True	78.8584	375	976	95	below_threshold
Promicromonospora citrea	strain=ATCC 15908	GCA_013004695.1	43677	43677	type	True	78.8309	449	976	95	below_threshold
Cellulomonas cellasea	strain=NBRC 3753	GCA_006538745.1	43670	43670	type	True	78.7607	469	976	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	78.7258	440	976	95	below_threshold
Sanguibacter suaedae	strain=YZGR15	GCA_016342785.1	2795737	2795737	type	True	78.703	394	976	95	below_threshold
Sanguibacter inulinus	strain=DSM 100099	GCA_013415325.1	60922	60922	type	True	78.6913	416	976	95	below_threshold
Sanguibacter antarcticus	strain=DSM 18966	GCA_002564005.1	372484	372484	type	True	78.5431	369	976	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	78.357	445	976	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	78.3416	431	976	95	below_threshold
Motilibacter aurantiacus	strain=K478	GCA_011250645.1	2714955	2714955	type	True	76.9592	243	976	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:37,081] [INFO] DFAST Taxonomy check result was written to GCF_000701465.1_ASM70146v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:37,082] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:37,082] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:37,082] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc47f86ba-586e-4216-8a23-0fbdc0e4f0ef/dqc_reference/checkm_data
[2024-01-24 13:47:37,083] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:37,113] [INFO] Task started: CheckM
[2024-01-24 13:47:37,114] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000701465.1_ASM70146v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000701465.1_ASM70146v1_genomic.fna/checkm_input GCF_000701465.1_ASM70146v1_genomic.fna/checkm_result
[2024-01-24 13:48:06,035] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:06,037] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:06,059] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:06,060] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:06,060] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000701465.1_ASM70146v1_genomic.fna/markers.fasta)
[2024-01-24 13:48:06,061] [INFO] Task started: Blastn
[2024-01-24 13:48:06,061] [INFO] Running command: blastn -query GCF_000701465.1_ASM70146v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc47f86ba-586e-4216-8a23-0fbdc0e4f0ef/dqc_reference/reference_markers_gtdb.fasta -out GCF_000701465.1_ASM70146v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:07,983] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:07,988] [INFO] Selected 18 target genomes.
[2024-01-24 13:48:07,989] [INFO] Target genome list was writen to GCF_000701465.1_ASM70146v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:08,001] [INFO] Task started: fastANI
[2024-01-24 13:48:08,001] [INFO] Running command: fastANI --query /var/lib/cwl/stg32ef3f1b-2663-4ee6-a6f7-c879bbd16f32/GCF_000701465.1_ASM70146v1_genomic.fna.gz --refList GCF_000701465.1_ASM70146v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000701465.1_ASM70146v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:21,599] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:21,620] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:21,621] [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_000701465.1	s__Paraoerskovia marina	100.0	976	976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Paraoerskovia	95.0	98.25	98.25	0.95	0.95	2	conclusive
GCF_002797595.1	s__Sediminihabitans luteus	80.8849	615	976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sediminihabitans	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003752595.1	s__Sediminihabitans sp003752595	80.3792	557	976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sediminihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001942335.1	s__Cellulosimicrobium sp001942335	79.8313	517	976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010287905.1	s__Cellulosimicrobium fucosivorans	79.8098	537	976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	98.84	98.55	0.94	0.90	6	-
GCF_016907365.1	s__Oerskovia paurometabola	79.7234	527	976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	99.20	99.20	0.97	0.97	2	-
GCF_001722485.1	s__Cellulosimicrobium cellulans_A	79.7216	464	976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005937995.2	s__Oerskovia sp005937995	79.7182	501	976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	96.13	96.13	0.91	0.91	2	-
GCA_014803435.1	s__Cellulosimicrobium terreum	79.536	530	976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001019615.1	s__Cellulosimicrobium cellulans_E	79.5243	559	976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	98.64	98.58	0.94	0.93	3	-
GCF_006539945.1	s__Cellulosimicrobium cellulans	79.4238	560	976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009663185.1	s__Isoptericola sp009663185	79.1668	442	976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009429125.1	s__Luteimicrobium xylanilyticum	79.0361	443	976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Luteimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003244315.1	s__Xylanimonas oleitrophica	79.007	417	976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167525.1	s__Isoptericola flava	79.0015	498	976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006386485.1	s__Cellulomonas oligotrophica	78.5812	431	976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	1.00	1.00	3	-
GCA_017744555.1	s__Cellulomonas sp017744555	78.4829	401	976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715865.1	s__Cellulomonas sp006715865	78.4716	441	976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:21,623] [INFO] GTDB search result was written to GCF_000701465.1_ASM70146v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:21,624] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:21,631] [INFO] DFAST_QC result json was written to GCF_000701465.1_ASM70146v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:21,631] [INFO] DFAST_QC completed!
[2024-01-24 13:48:21,632] [INFO] Total running time: 0h1m10s