[2024-01-24 11:12:36,752] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:36,754] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:36,754] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a65ee9c-62ca-45f7-b5a4-6c17c1d4db55/dqc_reference
[2024-01-24 11:12:37,999] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:38,000] [INFO] Task started: Prodigal
[2024-01-24 11:12:38,000] [INFO] Running command: gunzip -c /var/lib/cwl/stg0452db39-89b2-4ea4-9fb5-203f3374c506/GCF_017582035.1_ASM1758203v1_genomic.fna.gz | prodigal -d GCF_017582035.1_ASM1758203v1_genomic.fna/cds.fna -a GCF_017582035.1_ASM1758203v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:49,189] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:49,189] [INFO] Task started: HMMsearch
[2024-01-24 11:12:49,189] [INFO] Running command: hmmsearch --tblout GCF_017582035.1_ASM1758203v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a65ee9c-62ca-45f7-b5a4-6c17c1d4db55/dqc_reference/reference_markers.hmm GCF_017582035.1_ASM1758203v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:49,467] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:49,469] [INFO] Found 6/6 markers.
[2024-01-24 11:12:49,508] [INFO] Query marker FASTA was written to GCF_017582035.1_ASM1758203v1_genomic.fna/markers.fasta
[2024-01-24 11:12:49,508] [INFO] Task started: Blastn
[2024-01-24 11:12:49,508] [INFO] Running command: blastn -query GCF_017582035.1_ASM1758203v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a65ee9c-62ca-45f7-b5a4-6c17c1d4db55/dqc_reference/reference_markers.fasta -out GCF_017582035.1_ASM1758203v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:50,869] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:50,872] [INFO] Selected 16 target genomes.
[2024-01-24 11:12:50,873] [INFO] Target genome list was writen to GCF_017582035.1_ASM1758203v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:50,882] [INFO] Task started: fastANI
[2024-01-24 11:12:50,882] [INFO] Running command: fastANI --query /var/lib/cwl/stg0452db39-89b2-4ea4-9fb5-203f3374c506/GCF_017582035.1_ASM1758203v1_genomic.fna.gz --refList GCF_017582035.1_ASM1758203v1_genomic.fna/target_genomes.txt --output GCF_017582035.1_ASM1758203v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:05,744] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:05,745] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a65ee9c-62ca-45f7-b5a4-6c17c1d4db55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:05,745] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a65ee9c-62ca-45f7-b5a4-6c17c1d4db55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:05,758] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:13:05,758] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:13:05,758] [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
Cellulomonas humilata	strain=ATCC 25174	GCA_013359775.1	144055	144055	type	True	85.7018	989	1322	95	below_threshold
Cellulomonas terrae	strain=NBRC 100819	GCA_007990265.1	311234	311234	type	True	85.5378	973	1322	95	below_threshold
Cellulomonas xylanilytica	strain=NBRC 101102	GCA_007989805.1	233583	233583	type	True	85.4617	996	1322	95	below_threshold
Cellulomonas rhizosphaerae	strain=NEAU-TCZ24	GCA_003470205.1	2293719	2293719	type	True	81.9131	666	1322	95	below_threshold
Cellulomonas fimi	strain=ATCC 484	GCA_000212695.1	1708	1708	type	True	81.4643	852	1322	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	81.4639	842	1322	95	below_threshold
Cellulomonas massiliensis	strain=JC225	GCA_000312005.1	1465811	1465811	type	True	80.8783	687	1322	95	below_threshold
Cellulomonas uda	strain=NBRC 3747	GCA_006538705.1	1714	1714	type	True	80.8128	675	1322	95	below_threshold
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	80.8066	709	1322	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	80.7904	731	1322	95	below_threshold
Cellulomonas persica	strain=NBRC 101101	GCA_007989825.1	76861	76861	type	True	80.7364	680	1322	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	80.6846	731	1322	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	80.2686	736	1322	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	80.2514	670	1322	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	79.3442	636	1322	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	78.9685	537	1322	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:05,761] [INFO] DFAST Taxonomy check result was written to GCF_017582035.1_ASM1758203v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:05,762] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:05,762] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:05,763] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a65ee9c-62ca-45f7-b5a4-6c17c1d4db55/dqc_reference/checkm_data
[2024-01-24 11:13:05,764] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:05,810] [INFO] Task started: CheckM
[2024-01-24 11:13:05,811] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017582035.1_ASM1758203v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017582035.1_ASM1758203v1_genomic.fna/checkm_input GCF_017582035.1_ASM1758203v1_genomic.fna/checkm_result
[2024-01-24 11:14:03,950] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:03,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:03,972] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:03,973] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:03,973] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017582035.1_ASM1758203v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:03,974] [INFO] Task started: Blastn
[2024-01-24 11:14:03,974] [INFO] Running command: blastn -query GCF_017582035.1_ASM1758203v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a65ee9c-62ca-45f7-b5a4-6c17c1d4db55/dqc_reference/reference_markers_gtdb.fasta -out GCF_017582035.1_ASM1758203v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:06,163] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:06,166] [INFO] Selected 12 target genomes.
[2024-01-24 11:14:06,166] [INFO] Target genome list was writen to GCF_017582035.1_ASM1758203v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:06,175] [INFO] Task started: fastANI
[2024-01-24 11:14:06,175] [INFO] Running command: fastANI --query /var/lib/cwl/stg0452db39-89b2-4ea4-9fb5-203f3374c506/GCF_017582035.1_ASM1758203v1_genomic.fna.gz --refList GCF_017582035.1_ASM1758203v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017582035.1_ASM1758203v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:18,082] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:18,103] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:18,103] [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_018388465.1	s__Cellulomonas sp018388465	99.9988	1320	1322	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.65	99.29	0.98	0.97	3	conclusive
GCA_001429255.1	s__Cellulomonas sp001429255	85.9794	959	1322	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.79	98.79	0.94	0.94	2	-
GCF_001426705.1	s__Cellulomonas sp001426705	85.7503	993	1322	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013359775.1	s__Cellulomonas humilata	85.6684	992	1322	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424195.1	s__Cellulomonas sp001424195	85.6239	992	1322	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424125.1	s__Cellulomonas sp001424125	85.592	931	1322	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007990265.1	s__Cellulomonas terrae	85.5318	974	1322	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007989805.1	s__Cellulomonas xylanilytica	85.4704	995	1322	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003470205.1	s__Cellulomonas rhizosphaerae	81.909	667	1322	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000212695.1	s__Cellulomonas fimi	81.4516	854	1322	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	99.99	1.00	1.00	3	-
GCF_000312005.1	s__Cellulomonas massiliensis	80.864	689	1322	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013409305.1	s__Cellulomonas soli	80.8065	708	1322	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:18,105] [INFO] GTDB search result was written to GCF_017582035.1_ASM1758203v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:18,106] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:18,110] [INFO] DFAST_QC result json was written to GCF_017582035.1_ASM1758203v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:18,110] [INFO] DFAST_QC completed!
[2024-01-24 11:14:18,110] [INFO] Total running time: 0h1m41s