[2024-01-24 13:58:25,625] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:25,627] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:25,627] [INFO] DQC Reference Directory: /var/lib/cwl/stg97de288f-6a76-45e2-b0ed-5ae405253fbc/dqc_reference
[2024-01-24 13:58:26,947] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:26,947] [INFO] Task started: Prodigal
[2024-01-24 13:58:26,948] [INFO] Running command: gunzip -c /var/lib/cwl/stgadf34bc1-ec8a-42df-b475-f45ddc8fb438/GCF_001552435.1_ASM155243v1_genomic.fna.gz | prodigal -d GCF_001552435.1_ASM155243v1_genomic.fna/cds.fna -a GCF_001552435.1_ASM155243v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:36,586] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:36,587] [INFO] Task started: HMMsearch
[2024-01-24 13:58:36,587] [INFO] Running command: hmmsearch --tblout GCF_001552435.1_ASM155243v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97de288f-6a76-45e2-b0ed-5ae405253fbc/dqc_reference/reference_markers.hmm GCF_001552435.1_ASM155243v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:36,856] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:36,857] [INFO] Found 6/6 markers.
[2024-01-24 13:58:36,890] [INFO] Query marker FASTA was written to GCF_001552435.1_ASM155243v1_genomic.fna/markers.fasta
[2024-01-24 13:58:36,890] [INFO] Task started: Blastn
[2024-01-24 13:58:36,890] [INFO] Running command: blastn -query GCF_001552435.1_ASM155243v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97de288f-6a76-45e2-b0ed-5ae405253fbc/dqc_reference/reference_markers.fasta -out GCF_001552435.1_ASM155243v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:38,096] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:38,100] [INFO] Selected 23 target genomes.
[2024-01-24 13:58:38,100] [INFO] Target genome list was writen to GCF_001552435.1_ASM155243v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:38,111] [INFO] Task started: fastANI
[2024-01-24 13:58:38,112] [INFO] Running command: fastANI --query /var/lib/cwl/stgadf34bc1-ec8a-42df-b475-f45ddc8fb438/GCF_001552435.1_ASM155243v1_genomic.fna.gz --refList GCF_001552435.1_ASM155243v1_genomic.fna/target_genomes.txt --output GCF_001552435.1_ASM155243v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:51,679] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:51,680] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97de288f-6a76-45e2-b0ed-5ae405253fbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:51,680] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97de288f-6a76-45e2-b0ed-5ae405253fbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:51,703] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:58:51,703] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:58:51,704] [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 indicus	strain=CGMCC 1.12511	GCA_900176385.1	857417	857417	type	True	79.607	378	956	95	below_threshold
Janibacter anophelis	strain=NBRC 107843	GCA_001570945.1	319054	319054	type	True	79.5931	357	956	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_004025845.1	364298	364298	type	True	79.5888	349	956	95	below_threshold
Janibacter massiliensis	strain=Marseille-P4121	GCA_900289115.1	2058291	2058291	type	True	79.5495	314	956	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_000297495.1	364298	364298	type	True	79.5431	342	956	95	below_threshold
Janibacter terrae	strain=NBRC 107853	GCA_001591405.1	103817	103817	type	True	79.4806	372	956	95	below_threshold
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	79.4768	334	956	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	79.3441	366	956	95	below_threshold
Pedococcus cremeus	strain=CGMCC 1.6963	GCA_900111375.1	587636	587636	type	True	79.2545	372	956	95	below_threshold
Knoellia remsis	strain=ATCC BAA-1496	GCA_003002895.1	407159	407159	type	True	79.1962	353	956	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	79.1871	352	956	95	below_threshold
Knoellia subterranea	strain=KCTC 19937	GCA_000768685.1	184882	184882	type	True	79.173	311	956	95	below_threshold
Phycicoccus mangrovi	strain=KQZ13P-1	GCA_018729305.1	2840470	2840470	type	True	79.1041	360	956	95	below_threshold
Janibacter limosus	strain=NBRC 16128	GCA_001570985.1	53458	53458	type	True	79.0892	315	956	95	below_threshold
Pedococcus dokdonensis	strain=DSM 22329	GCA_900104525.1	443156	443156	type	True	78.997	317	956	95	below_threshold
Janibacter corallicola	strain=NBRC 107790	GCA_001570965.1	415212	415212	type	True	78.9757	292	956	95	below_threshold
Pedococcus badiiscoriae	strain=DSM 23987	GCA_013408925.1	642776	642776	type	True	78.9264	302	956	95	below_threshold
Phycicoccus flavus	strain=CMS6Z-2	GCA_004025965.2	2502783	2502783	type	True	78.6834	324	956	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	78.6357	288	956	95	below_threshold
Kineosphaera limosa	strain=NBRC 100340	GCA_000298215.1	111564	111564	type	True	78.4318	274	956	95	below_threshold
Kineosphaera limosa	strain=DSM 14548	GCA_013409325.1	111564	111564	type	True	78.3738	294	956	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	78.0959	244	956	95	below_threshold
Ornithinimicrobium murale	strain=DSM 22056	GCA_003352835.1	1050153	1050153	type	True	77.6526	162	956	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:51,705] [INFO] DFAST Taxonomy check result was written to GCF_001552435.1_ASM155243v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:51,706] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:51,706] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:51,706] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97de288f-6a76-45e2-b0ed-5ae405253fbc/dqc_reference/checkm_data
[2024-01-24 13:58:51,708] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:51,744] [INFO] Task started: CheckM
[2024-01-24 13:58:51,744] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001552435.1_ASM155243v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001552435.1_ASM155243v1_genomic.fna/checkm_input GCF_001552435.1_ASM155243v1_genomic.fna/checkm_result
[2024-01-24 13:59:40,586] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:40,587] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:40,610] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:40,610] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:40,611] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001552435.1_ASM155243v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:40,611] [INFO] Task started: Blastn
[2024-01-24 13:59:40,611] [INFO] Running command: blastn -query GCF_001552435.1_ASM155243v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97de288f-6a76-45e2-b0ed-5ae405253fbc/dqc_reference/reference_markers_gtdb.fasta -out GCF_001552435.1_ASM155243v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:42,448] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:42,453] [INFO] Selected 23 target genomes.
[2024-01-24 13:59:42,453] [INFO] Target genome list was writen to GCF_001552435.1_ASM155243v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:42,476] [INFO] Task started: fastANI
[2024-01-24 13:59:42,476] [INFO] Running command: fastANI --query /var/lib/cwl/stgadf34bc1-ec8a-42df-b475-f45ddc8fb438/GCF_001552435.1_ASM155243v1_genomic.fna.gz --refList GCF_001552435.1_ASM155243v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001552435.1_ASM155243v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:57,321] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:57,345] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:57,345] [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_001552435.1	s__Kribbia dieselivorans	100.0	949	956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Kribbia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900176385.1	s__Janibacter indicus	79.6328	376	956	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	79.6054	356	956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	96.19	96.19	0.85	0.85	2	-
GCF_900289115.1	s__Janibacter_A massiliensis	79.5423	315	956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016888335.1	s__Marihabitans sp016888335	79.4619	335	956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Marihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003721155.3	s__Marihabitans melonis	79.428	368	956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Marihabitans	95.0	99.04	97.16	0.97	0.90	16	-
GCF_006716205.1	s__Oryzihumus leptocrescens	79.3175	323	956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Oryzihumus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992835.1	s__Knoellia locipacati	79.2709	348	956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111375.1	s__Pedococcus cremeus	79.2422	373	956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	95.41	95.41	0.91	0.91	2	-
GCF_003002895.1	s__Knoellia remsis	79.2038	353	956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720925.1	s__Phycicoccus jejuensis	79.1479	355	956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	96.36	95.39	0.88	0.87	4	-
GCF_001570985.1	s__Janibacter limosus	79.0889	315	956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013041615.1	s__Pedococcus sp013041615	79.0641	345	956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409205.1	s__Janibacter cremeus	78.9793	318	956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104525.1	s__Pedococcus dokdonensis	78.9759	319	956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570965.1	s__Janibacter corallicola	78.9757	292	956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846495.1	s__Phycicoccus duodecadis	78.9669	333	956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426245.1	s__Pedococcus sp001426245	78.9414	338	956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	98.80	98.80	0.95	0.95	2	-
GCF_007991735.1	s__Terrabacter aerolatus	78.9265	331	956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006438965.1	s__Pedococcus bigeumensis	78.8292	307	956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383675.1	s__Terrabacter sp000383675	78.8107	341	956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428065.1	s__Phycicoccus sp001428065	78.7745	316	956	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	78.7478	319	956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:57,347] [INFO] GTDB search result was written to GCF_001552435.1_ASM155243v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:57,348] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:57,352] [INFO] DFAST_QC result json was written to GCF_001552435.1_ASM155243v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:57,352] [INFO] DFAST_QC completed!
[2024-01-24 13:59:57,353] [INFO] Total running time: 0h1m32s