[2024-01-24 11:27:04,741] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:27:04,742] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:27:04,742] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f01955d-e2a3-474c-ad86-19920343a3c1/dqc_reference
[2024-01-24 11:27:05,961] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:27:05,962] [INFO] Task started: Prodigal
[2024-01-24 11:27:05,962] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d9a4ef1-70f4-479e-b423-8ad833ae5d7a/GCF_002564005.1_ASM256400v1_genomic.fna.gz | prodigal -d GCF_002564005.1_ASM256400v1_genomic.fna/cds.fna -a GCF_002564005.1_ASM256400v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:16,068] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:16,068] [INFO] Task started: HMMsearch
[2024-01-24 11:27:16,069] [INFO] Running command: hmmsearch --tblout GCF_002564005.1_ASM256400v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f01955d-e2a3-474c-ad86-19920343a3c1/dqc_reference/reference_markers.hmm GCF_002564005.1_ASM256400v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:16,330] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:16,332] [INFO] Found 6/6 markers.
[2024-01-24 11:27:16,363] [INFO] Query marker FASTA was written to GCF_002564005.1_ASM256400v1_genomic.fna/markers.fasta
[2024-01-24 11:27:16,364] [INFO] Task started: Blastn
[2024-01-24 11:27:16,364] [INFO] Running command: blastn -query GCF_002564005.1_ASM256400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f01955d-e2a3-474c-ad86-19920343a3c1/dqc_reference/reference_markers.fasta -out GCF_002564005.1_ASM256400v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:17,491] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:17,495] [INFO] Selected 17 target genomes.
[2024-01-24 11:27:17,495] [INFO] Target genome list was writen to GCF_002564005.1_ASM256400v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:17,500] [INFO] Task started: fastANI
[2024-01-24 11:27:17,500] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d9a4ef1-70f4-479e-b423-8ad833ae5d7a/GCF_002564005.1_ASM256400v1_genomic.fna.gz --refList GCF_002564005.1_ASM256400v1_genomic.fna/target_genomes.txt --output GCF_002564005.1_ASM256400v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:30,091] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:30,092] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f01955d-e2a3-474c-ad86-19920343a3c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:30,092] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f01955d-e2a3-474c-ad86-19920343a3c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:30,108] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:30,108] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:30,109] [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
Sanguibacter antarcticus	strain=DSM 18966	GCA_002564005.1	372484	372484	type	True	100.0	1170	1173	95	conclusive
Sanguibacter suaedae	strain=YZGR15	GCA_016342785.1	2795737	2795737	type	True	80.6733	601	1173	95	below_threshold
Sanguibacter keddieii	strain=DSM 10542	GCA_000024925.1	60920	60920	type	True	80.6381	587	1173	95	below_threshold
Sanguibacter suarezii	strain=NBRC 16159	GCA_001552735.1	60921	60921	type	True	80.3703	572	1173	95	below_threshold
Sanguibacter gelidistatuariae	strain=ISLP-3	GCA_900096585.1	1814289	1814289	type	True	80.342	615	1173	95	below_threshold
Sanguibacter inulinus	strain=DSM 100099	GCA_013415325.1	60922	60922	type	True	80.3125	576	1173	95	below_threshold
Oerskovia enterophila	strain=DSM 43852	GCA_001692445.1	43678	43678	type	True	79.2679	463	1173	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	79.1695	466	1173	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	79.0117	487	1173	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	78.976	480	1173	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	78.9315	507	1173	95	below_threshold
Sediminihabitans luteus	strain=DSM 25478	GCA_002797595.1	1138585	1138585	type	True	78.8224	471	1173	95	below_threshold
Sediminihabitans luteus	strain=NBRC 108568	GCA_016863455.1	1138585	1138585	type	True	78.8211	465	1173	95	below_threshold
Cellulomonas cellasea	strain=NBRC 3753	GCA_006538745.1	43670	43670	type	True	78.6148	512	1173	95	below_threshold
Cellulomonas cellasea	strain=DSM 20118	GCA_000767135.1	43670	43670	type	True	78.5844	433	1173	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	78.4048	443	1173	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	78.3973	451	1173	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:30,120] [INFO] DFAST Taxonomy check result was written to GCF_002564005.1_ASM256400v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:30,120] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:30,121] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:30,121] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f01955d-e2a3-474c-ad86-19920343a3c1/dqc_reference/checkm_data
[2024-01-24 11:27:30,123] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:30,160] [INFO] Task started: CheckM
[2024-01-24 11:27:30,160] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002564005.1_ASM256400v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002564005.1_ASM256400v1_genomic.fna/checkm_input GCF_002564005.1_ASM256400v1_genomic.fna/checkm_result
[2024-01-24 11:28:22,013] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:22,015] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:22,030] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:22,031] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:22,031] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002564005.1_ASM256400v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:22,031] [INFO] Task started: Blastn
[2024-01-24 11:28:22,032] [INFO] Running command: blastn -query GCF_002564005.1_ASM256400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f01955d-e2a3-474c-ad86-19920343a3c1/dqc_reference/reference_markers_gtdb.fasta -out GCF_002564005.1_ASM256400v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:23,828] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:23,832] [INFO] Selected 12 target genomes.
[2024-01-24 11:28:23,832] [INFO] Target genome list was writen to GCF_002564005.1_ASM256400v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:23,844] [INFO] Task started: fastANI
[2024-01-24 11:28:23,844] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d9a4ef1-70f4-479e-b423-8ad833ae5d7a/GCF_002564005.1_ASM256400v1_genomic.fna.gz --refList GCF_002564005.1_ASM256400v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002564005.1_ASM256400v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:34,033] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:34,046] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:34,046] [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_002564005.1	s__Sanguibacter antarcticus	100.0	1170	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016342785.1	s__Sanguibacter sp016342785	80.6907	599	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024925.1	s__Sanguibacter keddieii	80.6062	587	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552735.1	s__Sanguibacter suarezii	80.3908	570	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900096585.1	s__Sanguibacter gelidistatuariae	80.3547	613	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013415325.1	s__Sanguibacter inulinus	80.3294	575	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	98.94	97.89	0.97	0.94	3	-
GCF_001692445.1	s__Oerskovia enterophila	79.2886	461	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	98.35	97.89	0.90	0.89	4	-
GCF_014836755.1	s__Oerskovia sp014836755	78.9577	482	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797595.1	s__Sediminihabitans luteus	78.8317	470	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sediminihabitans	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003052455.1	s__Cellulosimicrobium cinnabarinum	78.816	517	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	96.0261	97.94	97.40	0.92	0.90	4	-
GCF_900046455.1	s__Cellulomonas timonensis	78.607	402	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_006538745.1	s__Cellulomonas cellasea	78.5917	515	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	97.79	95.59	0.95	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:34,048] [INFO] GTDB search result was written to GCF_002564005.1_ASM256400v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:34,048] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:34,052] [INFO] DFAST_QC result json was written to GCF_002564005.1_ASM256400v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:34,052] [INFO] DFAST_QC completed!
[2024-01-24 11:28:34,052] [INFO] Total running time: 0h1m29s