[2024-01-25 20:21:35,687] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:21:35,688] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:21:35,688] [INFO] DQC Reference Directory: /var/lib/cwl/stg5858d7b5-e664-47cf-8132-25c18bc42371/dqc_reference
[2024-01-25 20:21:36,841] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:21:36,842] [INFO] Task started: Prodigal
[2024-01-25 20:21:36,842] [INFO] Running command: gunzip -c /var/lib/cwl/stgbc2323fb-3868-45fe-b4d8-cd17d93c9bf6/GCF_002154335.2_ASM215433v2_genomic.fna.gz | prodigal -d GCF_002154335.2_ASM215433v2_genomic.fna/cds.fna -a GCF_002154335.2_ASM215433v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:21:45,729] [INFO] Task succeeded: Prodigal
[2024-01-25 20:21:45,730] [INFO] Task started: HMMsearch
[2024-01-25 20:21:45,730] [INFO] Running command: hmmsearch --tblout GCF_002154335.2_ASM215433v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5858d7b5-e664-47cf-8132-25c18bc42371/dqc_reference/reference_markers.hmm GCF_002154335.2_ASM215433v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:21:45,941] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:21:45,942] [INFO] Found 6/6 markers.
[2024-01-25 20:21:45,974] [INFO] Query marker FASTA was written to GCF_002154335.2_ASM215433v2_genomic.fna/markers.fasta
[2024-01-25 20:21:45,974] [INFO] Task started: Blastn
[2024-01-25 20:21:45,974] [INFO] Running command: blastn -query GCF_002154335.2_ASM215433v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg5858d7b5-e664-47cf-8132-25c18bc42371/dqc_reference/reference_markers.fasta -out GCF_002154335.2_ASM215433v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:47,001] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:47,004] [INFO] Selected 15 target genomes.
[2024-01-25 20:21:47,004] [INFO] Target genome list was writen to GCF_002154335.2_ASM215433v2_genomic.fna/target_genomes.txt
[2024-01-25 20:21:47,010] [INFO] Task started: fastANI
[2024-01-25 20:21:47,010] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc2323fb-3868-45fe-b4d8-cd17d93c9bf6/GCF_002154335.2_ASM215433v2_genomic.fna.gz --refList GCF_002154335.2_ASM215433v2_genomic.fna/target_genomes.txt --output GCF_002154335.2_ASM215433v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:21:57,306] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:57,306] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5858d7b5-e664-47cf-8132-25c18bc42371/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:21:57,306] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5858d7b5-e664-47cf-8132-25c18bc42371/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:21:57,316] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:21:57,316] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:21:57,316] [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 succiniciruminis	strain=AM4	GCA_900002405.2	1522002	1522002	type	True	89.2342	814	1085	95	below_threshold
Actinomyces ruminicola	strain=DSM 27982	GCA_900103885.1	332524	332524	type	True	88.9748	802	1085	95	below_threshold
Actinomyces procaprae	strain=dk561	GCA_004798665.1	2560010	2560010	type	True	86.5672	856	1085	95	below_threshold
Actinomyces qiguomingii	strain=410	GCA_004102025.1	2057800	2057800	type	True	84.7064	817	1085	95	below_threshold
Actinomyces israelii	strain=DSM 43320	GCA_000711965.1	1659	1659	type	True	81.0886	543	1085	95	below_threshold
Actinomyces dentalis	strain=DSM 19115	GCA_000429225.1	272548	272548	type	True	81.0275	519	1085	95	below_threshold
Actinomyces viscosus	strain=CCUG 14476	GCA_004525795.1	1656	1656	type	True	80.7942	452	1085	95	below_threshold
Actinomyces bowdenii	strain=DSM 15435	GCA_017592395.1	131109	131109	type	True	80.4903	455	1085	95	below_threshold
Actinomyces radicidentis	strain=CCUG 36733	GCA_001553565.1	111015	111015	type	True	80.3457	479	1085	95	below_threshold
Actinomyces urogenitalis	strain=DSM 15434	GCA_000159035.1	103621	103621	type	True	80.2934	415	1085	95	below_threshold
Actinomyces marmotae	strain=zg-325	GCA_009829655.1	2737173	2737173	type	True	80.2803	367	1085	95	below_threshold
Actinomyces denticolens	strain=DSM 20671	GCA_002072185.1	52767	52767	type	True	80.2395	419	1085	95	below_threshold
Ruania suaedae	strain=LR1S40	GCA_021049265.1	2897774	2897774	type	True	77.0207	174	1085	95	below_threshold
Ruania zhangjianzhongii	strain=HY168	GCA_008000995.1	2603206	2603206	type	True	76.6689	151	1085	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	76.6302	173	1085	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:21:57,318] [INFO] DFAST Taxonomy check result was written to GCF_002154335.2_ASM215433v2_genomic.fna/tc_result.tsv
[2024-01-25 20:21:57,318] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:21:57,318] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:21:57,319] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5858d7b5-e664-47cf-8132-25c18bc42371/dqc_reference/checkm_data
[2024-01-25 20:21:57,319] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:21:57,356] [INFO] Task started: CheckM
[2024-01-25 20:21:57,356] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002154335.2_ASM215433v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002154335.2_ASM215433v2_genomic.fna/checkm_input GCF_002154335.2_ASM215433v2_genomic.fna/checkm_result
[2024-01-25 20:22:25,747] [INFO] Task succeeded: CheckM
[2024-01-25 20:22:25,748] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:22:25,767] [INFO] ===== Completeness check finished =====
[2024-01-25 20:22:25,768] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:22:25,768] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002154335.2_ASM215433v2_genomic.fna/markers.fasta)
[2024-01-25 20:22:25,769] [INFO] Task started: Blastn
[2024-01-25 20:22:25,769] [INFO] Running command: blastn -query GCF_002154335.2_ASM215433v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg5858d7b5-e664-47cf-8132-25c18bc42371/dqc_reference/reference_markers_gtdb.fasta -out GCF_002154335.2_ASM215433v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:27,511] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:27,514] [INFO] Selected 7 target genomes.
[2024-01-25 20:22:27,515] [INFO] Target genome list was writen to GCF_002154335.2_ASM215433v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:22:27,534] [INFO] Task started: fastANI
[2024-01-25 20:22:27,534] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc2323fb-3868-45fe-b4d8-cd17d93c9bf6/GCF_002154335.2_ASM215433v2_genomic.fna.gz --refList GCF_002154335.2_ASM215433v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002154335.2_ASM215433v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:22:33,728] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:33,734] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:22:33,734] [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_002154335.2	s__Actinomyces sp002154335	100.0	1080	1085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900002405.1	s__Actinomyces succiniciruminis	89.2342	814	1085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	96.3414	98.30	98.26	0.87	0.86	3	-
GCF_900098745.1	s__Actinomyces glycerinitolerans	89.1263	906	1085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	96.3414	98.41	98.38	0.91	0.91	4	-
GCF_900103885.1	s__Actinomyces ruminicola	88.9698	801	1085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	96.80	96.66	0.89	0.87	3	-
GCF_004798665.1	s__Actinomyces procaprae	86.5831	854	1085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.28	98.28	0.91	0.91	2	-
GCF_009930875.1	s__Actinomyces sp009930875	86.2646	745	1085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.69	98.69	0.97	0.97	2	-
GCF_004102025.1	s__Actinomyces qiguomingii	84.7187	816	1085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.95	99.95	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:22:33,735] [INFO] GTDB search result was written to GCF_002154335.2_ASM215433v2_genomic.fna/result_gtdb.tsv
[2024-01-25 20:22:33,736] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:22:33,742] [INFO] DFAST_QC result json was written to GCF_002154335.2_ASM215433v2_genomic.fna/dqc_result.json
[2024-01-25 20:22:33,743] [INFO] DFAST_QC completed!
[2024-01-25 20:22:33,743] [INFO] Total running time: 0h0m58s