[2024-01-24 12:36:58,672] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:58,674] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:58,674] [INFO] DQC Reference Directory: /var/lib/cwl/stg560c4e3c-2b54-462b-a9ef-2ae7c68cc82c/dqc_reference
[2024-01-24 12:37:00,029] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:00,030] [INFO] Task started: Prodigal
[2024-01-24 12:37:00,030] [INFO] Running command: gunzip -c /var/lib/cwl/stg517ce081-03b0-44af-827c-32a2566b4abc/GCF_003606385.1_ASM360638v1_genomic.fna.gz | prodigal -d GCF_003606385.1_ASM360638v1_genomic.fna/cds.fna -a GCF_003606385.1_ASM360638v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:09,490] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:09,490] [INFO] Task started: HMMsearch
[2024-01-24 12:37:09,490] [INFO] Running command: hmmsearch --tblout GCF_003606385.1_ASM360638v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg560c4e3c-2b54-462b-a9ef-2ae7c68cc82c/dqc_reference/reference_markers.hmm GCF_003606385.1_ASM360638v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:09,772] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:09,773] [INFO] Found 6/6 markers.
[2024-01-24 12:37:09,803] [INFO] Query marker FASTA was written to GCF_003606385.1_ASM360638v1_genomic.fna/markers.fasta
[2024-01-24 12:37:09,803] [INFO] Task started: Blastn
[2024-01-24 12:37:09,803] [INFO] Running command: blastn -query GCF_003606385.1_ASM360638v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg560c4e3c-2b54-462b-a9ef-2ae7c68cc82c/dqc_reference/reference_markers.fasta -out GCF_003606385.1_ASM360638v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:10,734] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:10,737] [INFO] Selected 19 target genomes.
[2024-01-24 12:37:10,737] [INFO] Target genome list was writen to GCF_003606385.1_ASM360638v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:10,749] [INFO] Task started: fastANI
[2024-01-24 12:37:10,749] [INFO] Running command: fastANI --query /var/lib/cwl/stg517ce081-03b0-44af-827c-32a2566b4abc/GCF_003606385.1_ASM360638v1_genomic.fna.gz --refList GCF_003606385.1_ASM360638v1_genomic.fna/target_genomes.txt --output GCF_003606385.1_ASM360638v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:22,928] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:22,929] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg560c4e3c-2b54-462b-a9ef-2ae7c68cc82c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:22,929] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg560c4e3c-2b54-462b-a9ef-2ae7c68cc82c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:22,944] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:22,945] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:22,945] [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
Actinomyces lilanjuaniae	strain=2129	GCA_003606385.1	2321394	2321394	type	True	100.0	1008	1008	95	conclusive
Actinomyces wuliandei	strain=299	GCA_004010955.1	2057743	2057743	type	True	92.0302	906	1008	95	below_threshold
Actinomyces bowdenii	strain=DSM 15435	GCA_017592395.1	131109	131109	type	True	80.7267	504	1008	95	below_threshold
Actinomyces slackii	strain=NCTC11923	GCA_900637295.1	52774	52774	type	True	80.2587	504	1008	95	below_threshold
Actinomyces viscosus	strain=CCUG 14476	GCA_004525795.1	1656	1656	type	True	80.2065	491	1008	95	below_threshold
Actinomyces slackii	strain=ATCC 49928	GCA_000428685.1	52774	52774	type	True	80.1692	494	1008	95	below_threshold
Actinomyces naeslundii	strain=NCTC 10301	GCA_001956585.1	1655	1655	type	True	79.8478	456	1008	95	below_threshold
Actinomyces ruminicola	strain=DSM 27982	GCA_900103885.1	332524	332524	type	True	79.6161	410	1008	95	below_threshold
Actinomyces timonensis	strain=7400942	GCA_000295095.1	1288391	1288391	type	True	79.5097	353	1008	95	below_threshold
Actinomyces dentalis	strain=DSM 19115	GCA_000429225.1	272548	272548	type	True	79.5031	437	1008	95	below_threshold
Actinomyces denticolens	strain=DSM 20671	GCA_002072185.1	52767	52767	type	True	79.4777	361	1008	95	below_threshold
Actinomyces marmotae	strain=zg-325	GCA_009829655.1	2737173	2737173	type	True	79.4485	317	1008	95	below_threshold
Actinomyces urogenitalis	strain=DSM 15434	GCA_000159035.1	103621	103621	type	True	79.4109	335	1008	95	below_threshold
Actinomyces succiniciruminis	strain=AM4	GCA_900002405.2	1522002	1522002	type	True	79.4001	413	1008	95	below_threshold
Actinomyces respiraculi	strain=ZJ750	GCA_014595995.2	2744574	2744574	type	True	79.2733	365	1008	95	below_threshold
Actinomyces qiguomingii	strain=410	GCA_004102025.1	2057800	2057800	type	True	79.015	343	1008	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	77.0743	180	1008	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	76.9427	124	1008	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	76.1233	125	1008	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:22,946] [INFO] DFAST Taxonomy check result was written to GCF_003606385.1_ASM360638v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:22,947] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:22,948] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:22,948] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg560c4e3c-2b54-462b-a9ef-2ae7c68cc82c/dqc_reference/checkm_data
[2024-01-24 12:37:22,949] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:22,982] [INFO] Task started: CheckM
[2024-01-24 12:37:22,982] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003606385.1_ASM360638v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003606385.1_ASM360638v1_genomic.fna/checkm_input GCF_003606385.1_ASM360638v1_genomic.fna/checkm_result
[2024-01-24 12:37:54,400] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:54,401] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:54,418] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:54,419] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:54,419] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003606385.1_ASM360638v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:54,420] [INFO] Task started: Blastn
[2024-01-24 12:37:54,420] [INFO] Running command: blastn -query GCF_003606385.1_ASM360638v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg560c4e3c-2b54-462b-a9ef-2ae7c68cc82c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003606385.1_ASM360638v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:55,706] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:55,710] [INFO] Selected 15 target genomes.
[2024-01-24 12:37:55,711] [INFO] Target genome list was writen to GCF_003606385.1_ASM360638v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:55,728] [INFO] Task started: fastANI
[2024-01-24 12:37:55,729] [INFO] Running command: fastANI --query /var/lib/cwl/stg517ce081-03b0-44af-827c-32a2566b4abc/GCF_003606385.1_ASM360638v1_genomic.fna.gz --refList GCF_003606385.1_ASM360638v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003606385.1_ASM360638v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:05,455] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:05,475] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:05,475] [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_003606385.1	s__Actinomyces lilanjuaniae	100.0	1008	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.31	99.31	0.93	0.93	2	conclusive
GCF_004010955.1	s__Actinomyces wuliandei	92.0266	907	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.68	99.68	0.97	0.97	2	-
GCF_017592395.1	s__Actinomyces bowdenii	80.7268	505	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.11	99.11	0.96	0.96	2	-
GCF_013415415.1	s__Actinomyces bowdenii_B	80.4483	461	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	100.00	100.00	0.98	0.98	2	-
GCF_900637295.1	s__Actinomyces slackii	80.224	504	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001929375.1	s__Actinomyces oris_B	80.222	457	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.22	97.84	0.91	0.90	3	-
GCF_001553935.1	s__Actinomyces oris_A	80.1999	440	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	97.65	97.48	0.94	0.93	4	-
GCF_001956585.1	s__Actinomyces naeslundii	79.8478	456	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	97.74	96.59	0.92	0.89	23	-
GCF_000195595.1	s__Actinomyces sp000195595	79.7152	451	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001278845.1	s__Actinomyces sp001278845	79.6208	425	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103885.1	s__Actinomyces ruminicola	79.6052	412	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	96.80	96.66	0.89	0.87	3	-
GCF_000429225.1	s__Actinomyces dentalis	79.5205	436	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.22	98.22	0.92	0.92	2	-
GCF_000295095.1	s__Actinomyces timonensis	79.4812	355	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009930875.1	s__Actinomyces sp009930875	79.4125	382	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.69	98.69	0.97	0.97	2	-
GCF_900002405.1	s__Actinomyces succiniciruminis	79.4001	413	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	96.3414	98.30	98.26	0.87	0.86	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:05,477] [INFO] GTDB search result was written to GCF_003606385.1_ASM360638v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:05,477] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:05,482] [INFO] DFAST_QC result json was written to GCF_003606385.1_ASM360638v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:05,482] [INFO] DFAST_QC completed!
[2024-01-24 12:38:05,482] [INFO] Total running time: 0h1m7s