[2024-01-24 13:56:59,355] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:59,357] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:59,357] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d11770d-e227-4ac5-9362-32bca0ecee0b/dqc_reference
[2024-01-24 13:57:00,671] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:00,672] [INFO] Task started: Prodigal
[2024-01-24 13:57:00,672] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d7f2a8d-caa6-439e-baf6-b0adb6ee34fd/GCF_026626635.1_ASM2662663v1_genomic.fna.gz | prodigal -d GCF_026626635.1_ASM2662663v1_genomic.fna/cds.fna -a GCF_026626635.1_ASM2662663v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:22,648] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:22,649] [INFO] Task started: HMMsearch
[2024-01-24 13:58:22,649] [INFO] Running command: hmmsearch --tblout GCF_026626635.1_ASM2662663v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d11770d-e227-4ac5-9362-32bca0ecee0b/dqc_reference/reference_markers.hmm GCF_026626635.1_ASM2662663v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:23,304] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:23,305] [INFO] Found 6/6 markers.
[2024-01-24 13:58:23,414] [INFO] Query marker FASTA was written to GCF_026626635.1_ASM2662663v1_genomic.fna/markers.fasta
[2024-01-24 13:58:23,415] [INFO] Task started: Blastn
[2024-01-24 13:58:23,415] [INFO] Running command: blastn -query GCF_026626635.1_ASM2662663v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d11770d-e227-4ac5-9362-32bca0ecee0b/dqc_reference/reference_markers.fasta -out GCF_026626635.1_ASM2662663v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:24,153] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:24,156] [INFO] Selected 22 target genomes.
[2024-01-24 13:58:24,157] [INFO] Target genome list was writen to GCF_026626635.1_ASM2662663v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:24,164] [INFO] Task started: fastANI
[2024-01-24 13:58:24,165] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d7f2a8d-caa6-439e-baf6-b0adb6ee34fd/GCF_026626635.1_ASM2662663v1_genomic.fna.gz --refList GCF_026626635.1_ASM2662663v1_genomic.fna/target_genomes.txt --output GCF_026626635.1_ASM2662663v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:11,265] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:11,265] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d11770d-e227-4ac5-9362-32bca0ecee0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:11,266] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d11770d-e227-4ac5-9362-32bca0ecee0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:11,294] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:59:11,294] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:59:11,294] [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
Archangium gephyra	strain=DSM 2261	GCA_003387095.1	48	48	type	True	89.1335	3124	4610	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_001027285.1	48	48	type	True	89.1166	3150	4610	95	below_threshold
Archangium violaceum	strain=Cb vi76	GCA_000733295.1	83451	83451	type	True	89.0188	3082	4610	95	below_threshold
Pyxidicoccus fallax	strain=DSM 14698	GCA_012933655.1	394095	394095	type	True	80.4929	1885	4610	95	below_threshold
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	80.4289	1966	4610	95	below_threshold
Stigmatella aurantiaca	strain=DSM 17044	GCA_900109545.1	41	41	type	True	80.4177	1568	4610	95	below_threshold
Stigmatella hybrida	strain=DSM 14722	GCA_020103775.1	394097	394097	type	True	80.3823	1539	4610	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	80.2327	2022	4610	95	below_threshold
Myxococcus virescens	strain=NBRC 100334	GCA_007989405.1	83456	83456	type	True	79.9907	1444	4610	95	below_threshold
Myxococcus virescens	strain=DSM 2260	GCA_900101905.1	83456	83456	type	True	79.9723	1468	4610	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	79.8683	1554	4610	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	79.8525	1510	4610	95	below_threshold
Myxococcus stipitatus	strain=DSM 14675	GCA_000331735.1	83455	83455	neotype	True	79.576	1539	4610	95	below_threshold
Thiohalorhabdus denitrificans	strain=HL 19	GCA_900101365.1	381306	381306	type	True	75.1786	123	4610	95	below_threshold
Actinomyces denticolens	strain=DSM 20671	GCA_002072185.1	52767	52767	type	True	75.1159	106	4610	95	below_threshold
Rhodococcus tukisamuensis	strain=NBRC 100609	GCA_001894985.1	168276	168276	type	True	75.0925	166	4610	95	below_threshold
Rhodococcus tukisamuensis	strain=JCM 11308	GCA_900101735.1	168276	168276	type	True	75.0775	171	4610	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	75.0766	393	4610	95	below_threshold
Streptomyces megasporus	strain=NRRL B-16372	GCA_000718985.1	44060	44060	type	True	75.0347	246	4610	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	75.0313	405	4610	95	below_threshold
Albimonas pacifica	strain=CGMCC 1.11030	GCA_900113695.1	1114924	1114924	type	True	74.9701	264	4610	95	below_threshold
Actinomyces dentalis	strain=DSM 19115	GCA_000429225.1	272548	272548	type	True	74.8328	152	4610	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:11,297] [INFO] DFAST Taxonomy check result was written to GCF_026626635.1_ASM2662663v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:11,298] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:11,298] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:11,298] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d11770d-e227-4ac5-9362-32bca0ecee0b/dqc_reference/checkm_data
[2024-01-24 13:59:11,300] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:11,427] [INFO] Task started: CheckM
[2024-01-24 13:59:11,428] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026626635.1_ASM2662663v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026626635.1_ASM2662663v1_genomic.fna/checkm_input GCF_026626635.1_ASM2662663v1_genomic.fna/checkm_result
[2024-01-24 14:04:52,376] [INFO] Task succeeded: CheckM
[2024-01-24 14:04:52,379] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:04:52,409] [INFO] ===== Completeness check finished =====
[2024-01-24 14:04:52,410] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:04:52,411] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026626635.1_ASM2662663v1_genomic.fna/markers.fasta)
[2024-01-24 14:04:52,411] [INFO] Task started: Blastn
[2024-01-24 14:04:52,412] [INFO] Running command: blastn -query GCF_026626635.1_ASM2662663v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d11770d-e227-4ac5-9362-32bca0ecee0b/dqc_reference/reference_markers_gtdb.fasta -out GCF_026626635.1_ASM2662663v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:04:53,672] [INFO] Task succeeded: Blastn
[2024-01-24 14:04:53,675] [INFO] Selected 7 target genomes.
[2024-01-24 14:04:53,675] [INFO] Target genome list was writen to GCF_026626635.1_ASM2662663v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:04:53,699] [INFO] Task started: fastANI
[2024-01-24 14:04:53,699] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d7f2a8d-caa6-439e-baf6-b0adb6ee34fd/GCF_026626635.1_ASM2662663v1_genomic.fna.gz --refList GCF_026626635.1_ASM2662663v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026626635.1_ASM2662663v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:05:22,807] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:22,814] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:05:22,814] [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_001027285.1	s__Archangium gephyra	89.1293	3148	4610	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Archangium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000733295.1	s__Archangium violaceum	89.0468	3075	4610	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Archangium	95.0	95.60	95.60	0.86	0.86	2	-
GCF_003044305.1	s__Archangium sp003044305	86.4672	3053	4610	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Archangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016859125.1	s__Archangium violaceum_A	86.43	2728	4610	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Archangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016887565.1	s__Archangium violaceum_B	85.8853	2878	4610	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Archangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001887355.1	s__Cystobacter ferrugineus	83.4482	2320	4610	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Cystobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000335475.2	s__Cystobacter fuscus	83.1773	2292	4610	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Cystobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:05:22,816] [INFO] GTDB search result was written to GCF_026626635.1_ASM2662663v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:05:22,817] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:05:22,822] [INFO] DFAST_QC result json was written to GCF_026626635.1_ASM2662663v1_genomic.fna/dqc_result.json
[2024-01-24 14:05:22,822] [INFO] DFAST_QC completed!
[2024-01-24 14:05:22,822] [INFO] Total running time: 0h8m23s