[2024-01-24 11:12:57,046] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:57,049] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:57,049] [INFO] DQC Reference Directory: /var/lib/cwl/stg2bdece95-2b2b-4395-8b97-1efefea20add/dqc_reference
[2024-01-24 11:12:58,444] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:58,445] [INFO] Task started: Prodigal
[2024-01-24 11:12:58,446] [INFO] Running command: gunzip -c /var/lib/cwl/stg51da58ad-c403-4dfb-be1e-521b17041184/GCF_007989225.1_ASM798922v1_genomic.fna.gz | prodigal -d GCF_007989225.1_ASM798922v1_genomic.fna/cds.fna -a GCF_007989225.1_ASM798922v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:09,268] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:09,268] [INFO] Task started: HMMsearch
[2024-01-24 11:13:09,268] [INFO] Running command: hmmsearch --tblout GCF_007989225.1_ASM798922v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2bdece95-2b2b-4395-8b97-1efefea20add/dqc_reference/reference_markers.hmm GCF_007989225.1_ASM798922v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:09,576] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:09,578] [INFO] Found 6/6 markers.
[2024-01-24 11:13:09,619] [INFO] Query marker FASTA was written to GCF_007989225.1_ASM798922v1_genomic.fna/markers.fasta
[2024-01-24 11:13:09,619] [INFO] Task started: Blastn
[2024-01-24 11:13:09,619] [INFO] Running command: blastn -query GCF_007989225.1_ASM798922v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bdece95-2b2b-4395-8b97-1efefea20add/dqc_reference/reference_markers.fasta -out GCF_007989225.1_ASM798922v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:11,049] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:11,052] [INFO] Selected 19 target genomes.
[2024-01-24 11:13:11,053] [INFO] Target genome list was writen to GCF_007989225.1_ASM798922v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:11,057] [INFO] Task started: fastANI
[2024-01-24 11:13:11,057] [INFO] Running command: fastANI --query /var/lib/cwl/stg51da58ad-c403-4dfb-be1e-521b17041184/GCF_007989225.1_ASM798922v1_genomic.fna.gz --refList GCF_007989225.1_ASM798922v1_genomic.fna/target_genomes.txt --output GCF_007989225.1_ASM798922v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:29,843] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:29,844] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2bdece95-2b2b-4395-8b97-1efefea20add/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:29,844] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2bdece95-2b2b-4395-8b97-1efefea20add/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:29,858] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:13:29,859] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:29,859] [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 hominis	strain=NBRC 16055	GCA_007989225.1	156981	156981	suspected-type	True	100.0	1391	1402	95	conclusive
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	99.9963	1402	1402	95	conclusive
Cellulomonas denverensis	strain=ATCC BAA-788	GCA_012396125.1	264297	264297	type	True	81.9228	799	1402	95	below_threshold
Cellulomonas taurus	strain=P40-2	GCA_012931845.1	2729175	2729175	type	True	81.7031	734	1402	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	80.4952	734	1402	95	below_threshold
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	80.4382	689	1402	95	below_threshold
Cellulomonas fimi	strain=ATCC 484	GCA_000212695.1	1708	1708	type	True	80.4375	752	1402	95	below_threshold
Cellulomonas cellasea	strain=NBRC 3753	GCA_006538745.1	43670	43670	type	True	80.3961	738	1402	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	80.2772	683	1402	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	80.2564	703	1402	95	below_threshold
Cellulomonas composti	strain=NBRC 100758	GCA_007990245.1	266130	266130	type	True	80.2208	598	1402	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	80.2061	654	1402	95	below_threshold
Cellulomonas cellasea	strain=DSM 20118	GCA_000767135.1	43670	43670	type	True	80.1563	620	1402	95	below_threshold
Cellulomonas terrae	strain=NBRC 100819	GCA_007990265.1	311234	311234	type	True	80.1526	665	1402	95	below_threshold
Cellulomonas xylanilytica	strain=NBRC 101102	GCA_007989805.1	233583	233583	type	True	80.1456	672	1402	95	below_threshold
Cellulomonas flavigena	strain=DSM 20109	GCA_000092865.1	1711	1711	type	True	80.1318	678	1402	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	79.8176	658	1402	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	78.7319	581	1402	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	78.7123	564	1402	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:29,860] [INFO] DFAST Taxonomy check result was written to GCF_007989225.1_ASM798922v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:29,861] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:29,861] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:29,861] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2bdece95-2b2b-4395-8b97-1efefea20add/dqc_reference/checkm_data
[2024-01-24 11:13:29,862] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:29,911] [INFO] Task started: CheckM
[2024-01-24 11:13:29,911] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007989225.1_ASM798922v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007989225.1_ASM798922v1_genomic.fna/checkm_input GCF_007989225.1_ASM798922v1_genomic.fna/checkm_result
[2024-01-24 11:14:26,069] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:26,070] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:26,091] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:26,091] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:26,092] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007989225.1_ASM798922v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:26,092] [INFO] Task started: Blastn
[2024-01-24 11:14:26,092] [INFO] Running command: blastn -query GCF_007989225.1_ASM798922v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bdece95-2b2b-4395-8b97-1efefea20add/dqc_reference/reference_markers_gtdb.fasta -out GCF_007989225.1_ASM798922v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:28,329] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:28,332] [INFO] Selected 8 target genomes.
[2024-01-24 11:14:28,333] [INFO] Target genome list was writen to GCF_007989225.1_ASM798922v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:28,340] [INFO] Task started: fastANI
[2024-01-24 11:14:28,340] [INFO] Running command: fastANI --query /var/lib/cwl/stg51da58ad-c403-4dfb-be1e-521b17041184/GCF_007989225.1_ASM798922v1_genomic.fna.gz --refList GCF_007989225.1_ASM798922v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007989225.1_ASM798922v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:38,127] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:38,142] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:38,142] [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_014201095.1	s__Cellulomonas hominis	99.9963	1402	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.15	98.63	0.95	0.92	4	conclusive
GCF_011603975.1	s__Cellulomonas sp011603975	86.2894	836	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005239125.1	s__Cellulomonas hominis_A	86.1747	861	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763765.1	s__Cellulomonas sp014763765	86.168	843	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409475.1	s__Cellulomonas hominis_B	86.0979	985	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862755.1	s__Cellulomonas pakistanensis	85.9724	936	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033115.1	s__Cellulomonas sp008033115	85.8923	1002	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	96.34	96.34	0.91	0.91	2	-
GCF_007679345.1	s__Cellulomonas cellulans_A	85.8746	1000	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:38,144] [INFO] GTDB search result was written to GCF_007989225.1_ASM798922v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:38,145] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:38,148] [INFO] DFAST_QC result json was written to GCF_007989225.1_ASM798922v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:38,148] [INFO] DFAST_QC completed!
[2024-01-24 11:14:38,149] [INFO] Total running time: 0h1m41s