[2024-01-24 13:24:12,789] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:24:12,791] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:24:12,791] [INFO] DQC Reference Directory: /var/lib/cwl/stgde6c95b2-2819-482f-b087-88710559d203/dqc_reference
[2024-01-24 13:24:13,982] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:24:13,983] [INFO] Task started: Prodigal
[2024-01-24 13:24:13,983] [INFO] Running command: gunzip -c /var/lib/cwl/stg16e723a8-e757-4c51-91f4-9c32e3422ea2/GCF_002564025.1_ASM256402v1_genomic.fna.gz | prodigal -d GCF_002564025.1_ASM256402v1_genomic.fna/cds.fna -a GCF_002564025.1_ASM256402v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:24:21,509] [INFO] Task succeeded: Prodigal
[2024-01-24 13:24:21,510] [INFO] Task started: HMMsearch
[2024-01-24 13:24:21,510] [INFO] Running command: hmmsearch --tblout GCF_002564025.1_ASM256402v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde6c95b2-2819-482f-b087-88710559d203/dqc_reference/reference_markers.hmm GCF_002564025.1_ASM256402v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:24:21,702] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:24:21,704] [INFO] Found 6/6 markers.
[2024-01-24 13:24:21,730] [INFO] Query marker FASTA was written to GCF_002564025.1_ASM256402v1_genomic.fna/markers.fasta
[2024-01-24 13:24:21,731] [INFO] Task started: Blastn
[2024-01-24 13:24:21,731] [INFO] Running command: blastn -query GCF_002564025.1_ASM256402v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde6c95b2-2819-482f-b087-88710559d203/dqc_reference/reference_markers.fasta -out GCF_002564025.1_ASM256402v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:22,987] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:22,990] [INFO] Selected 19 target genomes.
[2024-01-24 13:24:22,991] [INFO] Target genome list was writen to GCF_002564025.1_ASM256402v1_genomic.fna/target_genomes.txt
[2024-01-24 13:24:23,005] [INFO] Task started: fastANI
[2024-01-24 13:24:23,006] [INFO] Running command: fastANI --query /var/lib/cwl/stg16e723a8-e757-4c51-91f4-9c32e3422ea2/GCF_002564025.1_ASM256402v1_genomic.fna.gz --refList GCF_002564025.1_ASM256402v1_genomic.fna/target_genomes.txt --output GCF_002564025.1_ASM256402v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:24:37,016] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:37,017] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde6c95b2-2819-482f-b087-88710559d203/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:24:37,017] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde6c95b2-2819-482f-b087-88710559d203/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:24:37,031] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:24:37,031] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:24:37,031] [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
Flavimobilis marinus	strain=DSM 19083	GCA_900113055.1	285351	285351	type	True	80.9364	562	962	95	below_threshold
Flavimobilis marinus	strain=CGMCC 1.3457	GCA_014653315.1	285351	285351	type	True	80.8669	569	962	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	80.038	569	962	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	79.9942	523	962	95	below_threshold
Cellulosimicrobium funkei	strain=JCM 14302	GCA_004519295.1	264251	264251	suspected-type	True	79.9551	591	962	95	below_threshold
Oerskovia turbata	strain=JCM3160	GCA_004121315.1	1713	1713	type	True	79.9304	542	962	95	below_threshold
Oerskovia turbata	strain=NRRL B-8019	GCA_000718325.1	1713	1713	type	True	79.9259	534	962	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	79.9174	517	962	95	below_threshold
Sanguibacter keddieii	strain=DSM 10542	GCA_000024925.1	60920	60920	type	True	79.8527	542	962	95	below_threshold
Oerskovia jenensis	strain=DSM 46000	GCA_016907235.1	162169	162169	type	True	79.8451	527	962	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	79.8017	515	962	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	79.7614	534	962	95	below_threshold
Sanguibacter suarezii	strain=NBRC 16159	GCA_001552735.1	60921	60921	type	True	79.5297	466	962	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	79.4807	557	962	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	79.3531	501	962	95	below_threshold
Cellulomonas hominis	strain=NBRC 16055	GCA_007989225.1	156981	156981	suspected-type	True	79.327	479	962	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	79.2546	521	962	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	79.192	508	962	95	below_threshold
Cellulomonas endophytica	strain=SYSUP0004	GCA_004123805.1	2494735	2494735	type	True	78.4968	458	962	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:24:37,033] [INFO] DFAST Taxonomy check result was written to GCF_002564025.1_ASM256402v1_genomic.fna/tc_result.tsv
[2024-01-24 13:24:37,034] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:24:37,034] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:24:37,034] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde6c95b2-2819-482f-b087-88710559d203/dqc_reference/checkm_data
[2024-01-24 13:24:37,035] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:24:37,063] [INFO] Task started: CheckM
[2024-01-24 13:24:37,063] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002564025.1_ASM256402v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002564025.1_ASM256402v1_genomic.fna/checkm_input GCF_002564025.1_ASM256402v1_genomic.fna/checkm_result
[2024-01-24 13:25:14,601] [INFO] Task succeeded: CheckM
[2024-01-24 13:25:14,602] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:25:14,617] [INFO] ===== Completeness check finished =====
[2024-01-24 13:25:14,618] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:25:14,618] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002564025.1_ASM256402v1_genomic.fna/markers.fasta)
[2024-01-24 13:25:14,618] [INFO] Task started: Blastn
[2024-01-24 13:25:14,618] [INFO] Running command: blastn -query GCF_002564025.1_ASM256402v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde6c95b2-2819-482f-b087-88710559d203/dqc_reference/reference_markers_gtdb.fasta -out GCF_002564025.1_ASM256402v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:16,592] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:16,596] [INFO] Selected 16 target genomes.
[2024-01-24 13:25:16,596] [INFO] Target genome list was writen to GCF_002564025.1_ASM256402v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:25:16,621] [INFO] Task started: fastANI
[2024-01-24 13:25:16,621] [INFO] Running command: fastANI --query /var/lib/cwl/stg16e723a8-e757-4c51-91f4-9c32e3422ea2/GCF_002564025.1_ASM256402v1_genomic.fna.gz --refList GCF_002564025.1_ASM256402v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002564025.1_ASM256402v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:25:28,722] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:28,735] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:25:28,735] [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_002564025.1	s__Flavimobilis soli	100.0	960	962	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Flavimobilis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_012396185.1	s__Flavimobilis hominis	90.1874	852	962	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Flavimobilis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011300875.1	s__Flavimobilis sp011300875	82.2038	657	962	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Flavimobilis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014852685.1	s__Flavimobilis rhizosphaerae	81.7691	633	962	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Flavimobilis	95.0	95.20	95.20	0.83	0.83	2	-
GCF_900113055.1	s__Flavimobilis marinus	80.9104	565	962	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Flavimobilis	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005937995.2	s__Oerskovia sp005937995	80.1415	516	962	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	96.13	96.13	0.91	0.91	2	-
GCA_003052455.1	s__Cellulosimicrobium cinnabarinum	80.1284	564	962	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	96.0261	97.94	97.40	0.92	0.90	4	-
GCF_016907365.1	s__Oerskovia paurometabola	79.985	532	962	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	99.20	99.20	0.97	0.97	2	-
GCF_012396155.1	s__Cellulomonas septica	79.9846	375	962	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718325.1	s__Oerskovia turbata	79.9099	536	962	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	99.78	99.34	0.96	0.90	4	-
GCF_001552375.1	s__Cellulomonas iranensis	79.772	518	962	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.21	97.89	0.91	0.88	6	-
GCF_001462455.1	s__Cellulomonas sp001462455	79.5673	526	962	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552735.1	s__Sanguibacter suarezii	79.5623	465	962	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005239125.1	s__Cellulomonas hominis_A	79.3971	463	962	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007679345.1	s__Cellulomonas cellulans_A	79.2295	495	962	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002441315.1	s__Cellulomonas sp002441315	78.4257	350	962	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 13:25:28,738] [INFO] GTDB search result was written to GCF_002564025.1_ASM256402v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:25:28,738] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:25:28,742] [INFO] DFAST_QC result json was written to GCF_002564025.1_ASM256402v1_genomic.fna/dqc_result.json
[2024-01-24 13:25:28,743] [INFO] DFAST_QC completed!
[2024-01-24 13:25:28,743] [INFO] Total running time: 0h1m16s