[2024-01-24 14:19:00,236] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:00,238] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:00,239] [INFO] DQC Reference Directory: /var/lib/cwl/stg95acd2c9-5f88-44fa-ba85-7f800427253e/dqc_reference
[2024-01-24 14:19:01,659] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:01,660] [INFO] Task started: Prodigal
[2024-01-24 14:19:01,661] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f35f197-d201-41f4-8554-e8bedb70306e/GCF_020567375.1_ASM2056737v1_genomic.fna.gz | prodigal -d GCF_020567375.1_ASM2056737v1_genomic.fna/cds.fna -a GCF_020567375.1_ASM2056737v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:11,118] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:11,118] [INFO] Task started: HMMsearch
[2024-01-24 14:19:11,118] [INFO] Running command: hmmsearch --tblout GCF_020567375.1_ASM2056737v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95acd2c9-5f88-44fa-ba85-7f800427253e/dqc_reference/reference_markers.hmm GCF_020567375.1_ASM2056737v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:11,400] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:11,401] [INFO] Found 6/6 markers.
[2024-01-24 14:19:11,435] [INFO] Query marker FASTA was written to GCF_020567375.1_ASM2056737v1_genomic.fna/markers.fasta
[2024-01-24 14:19:11,435] [INFO] Task started: Blastn
[2024-01-24 14:19:11,436] [INFO] Running command: blastn -query GCF_020567375.1_ASM2056737v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95acd2c9-5f88-44fa-ba85-7f800427253e/dqc_reference/reference_markers.fasta -out GCF_020567375.1_ASM2056737v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:12,832] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:12,835] [INFO] Selected 15 target genomes.
[2024-01-24 14:19:12,835] [INFO] Target genome list was writen to GCF_020567375.1_ASM2056737v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:12,895] [INFO] Task started: fastANI
[2024-01-24 14:19:12,895] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f35f197-d201-41f4-8554-e8bedb70306e/GCF_020567375.1_ASM2056737v1_genomic.fna.gz --refList GCF_020567375.1_ASM2056737v1_genomic.fna/target_genomes.txt --output GCF_020567375.1_ASM2056737v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:26,824] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:26,824] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95acd2c9-5f88-44fa-ba85-7f800427253e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:26,825] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95acd2c9-5f88-44fa-ba85-7f800427253e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:26,838] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:26,838] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:26,838] [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 melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	100.0	1161	1161	95	conclusive
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	84.2337	729	1161	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_004025845.1	364298	364298	type	True	82.1677	666	1161	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_000297495.1	364298	364298	type	True	82.1148	637	1161	95	below_threshold
Janibacter indicus	strain=CGMCC 1.12511	GCA_900176385.1	857417	857417	type	True	82.0355	697	1161	95	below_threshold
Janibacter terrae	strain=NBRC 107853	GCA_001591405.1	103817	103817	type	True	81.8955	690	1161	95	below_threshold
Janibacter anophelis	strain=NBRC 107843	GCA_001570945.1	319054	319054	type	True	81.7656	655	1161	95	below_threshold
Janibacter limosus	strain=NBRC 16128	GCA_001570985.1	53458	53458	type	True	80.8303	599	1161	95	below_threshold
Phycicoccus mangrovi	strain=KQZ13P-1	GCA_018729305.1	2840470	2840470	type	True	80.2311	631	1161	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	80.2294	630	1161	95	below_threshold
Phycicoccus flavus	strain=CMS6Z-2	GCA_004025965.2	2502783	2502783	type	True	79.8077	571	1161	95	below_threshold
Phycicoccus duodecadis	strain=DSM 12806	GCA_002846495.1	173053	173053	type	True	79.6928	535	1161	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	78.8335	442	1161	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	78.6951	451	1161	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	78.2446	377	1161	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:26,840] [INFO] DFAST Taxonomy check result was written to GCF_020567375.1_ASM2056737v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:26,841] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:26,841] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:26,841] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95acd2c9-5f88-44fa-ba85-7f800427253e/dqc_reference/checkm_data
[2024-01-24 14:19:26,842] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:26,888] [INFO] Task started: CheckM
[2024-01-24 14:19:26,888] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020567375.1_ASM2056737v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020567375.1_ASM2056737v1_genomic.fna/checkm_input GCF_020567375.1_ASM2056737v1_genomic.fna/checkm_result
[2024-01-24 14:20:16,398] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:16,400] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:16,428] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:16,428] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:16,429] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020567375.1_ASM2056737v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:16,429] [INFO] Task started: Blastn
[2024-01-24 14:20:16,429] [INFO] Running command: blastn -query GCF_020567375.1_ASM2056737v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95acd2c9-5f88-44fa-ba85-7f800427253e/dqc_reference/reference_markers_gtdb.fasta -out GCF_020567375.1_ASM2056737v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:18,599] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:18,603] [INFO] Selected 13 target genomes.
[2024-01-24 14:20:18,603] [INFO] Target genome list was writen to GCF_020567375.1_ASM2056737v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:18,655] [INFO] Task started: fastANI
[2024-01-24 14:20:18,656] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f35f197-d201-41f4-8554-e8bedb70306e/GCF_020567375.1_ASM2056737v1_genomic.fna.gz --refList GCF_020567375.1_ASM2056737v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020567375.1_ASM2056737v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:30,090] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:30,104] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:30,104] [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_003721155.3	s__Marihabitans melonis	98.3367	1098	1161	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Marihabitans	95.0	99.04	97.16	0.97	0.90	16	conclusive
GCF_016888335.1	s__Marihabitans sp016888335	84.1802	733	1161	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Marihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007828725.1	s__Marihabitans asiaticum	82.4796	676	1161	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Marihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000297495.1	s__Janibacter hoylei	82.1042	639	1161	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	99.95	99.95	0.99	0.99	2	-
GCF_900176385.1	s__Janibacter indicus	82.0881	692	1161	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	97.60	97.16	0.90	0.88	4	-
GCF_001591405.1	s__Janibacter terrae	81.9176	688	1161	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	98.98	98.88	0.95	0.93	4	-
GCF_001570945.1	s__Janibacter anophelis	81.7252	659	1161	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	96.19	96.19	0.85	0.85	2	-
GCF_013408565.1	s__Janibacter alkaliphilus	81.5394	697	1161	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004295485.1	s__Janibacter limosus_A	81.2319	653	1161	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570985.1	s__Janibacter limosus	80.7989	602	1161	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013201035.1	s__Phycicoccus sp013201035	80.1566	631	1161	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011383005.1	s__Phycicoccus sp011383005	79.901	628	1161	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139485.1	s__Phycicoccus sp018139485	79.6741	570	1161	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 14:20:30,109] [INFO] GTDB search result was written to GCF_020567375.1_ASM2056737v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:30,110] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:30,114] [INFO] DFAST_QC result json was written to GCF_020567375.1_ASM2056737v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:30,114] [INFO] DFAST_QC completed!
[2024-01-24 14:20:30,114] [INFO] Total running time: 0h1m30s