[2024-01-24 13:40:43,887] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:43,892] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:43,892] [INFO] DQC Reference Directory: /var/lib/cwl/stg9de5a971-ce53-4f63-b71b-e931d4795efc/dqc_reference
[2024-01-24 13:40:45,104] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:45,105] [INFO] Task started: Prodigal
[2024-01-24 13:40:45,105] [INFO] Running command: gunzip -c /var/lib/cwl/stg492be16e-4287-4cad-b6b2-7d5bac08fed1/GCF_007989805.1_ASM798980v1_genomic.fna.gz | prodigal -d GCF_007989805.1_ASM798980v1_genomic.fna/cds.fna -a GCF_007989805.1_ASM798980v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:57,320] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:57,321] [INFO] Task started: HMMsearch
[2024-01-24 13:40:57,321] [INFO] Running command: hmmsearch --tblout GCF_007989805.1_ASM798980v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9de5a971-ce53-4f63-b71b-e931d4795efc/dqc_reference/reference_markers.hmm GCF_007989805.1_ASM798980v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:57,612] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:57,614] [INFO] Found 6/6 markers.
[2024-01-24 13:40:57,660] [INFO] Query marker FASTA was written to GCF_007989805.1_ASM798980v1_genomic.fna/markers.fasta
[2024-01-24 13:40:57,661] [INFO] Task started: Blastn
[2024-01-24 13:40:57,661] [INFO] Running command: blastn -query GCF_007989805.1_ASM798980v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9de5a971-ce53-4f63-b71b-e931d4795efc/dqc_reference/reference_markers.fasta -out GCF_007989805.1_ASM798980v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:58,988] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:58,991] [INFO] Selected 16 target genomes.
[2024-01-24 13:40:58,992] [INFO] Target genome list was writen to GCF_007989805.1_ASM798980v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:59,064] [INFO] Task started: fastANI
[2024-01-24 13:40:59,065] [INFO] Running command: fastANI --query /var/lib/cwl/stg492be16e-4287-4cad-b6b2-7d5bac08fed1/GCF_007989805.1_ASM798980v1_genomic.fna.gz --refList GCF_007989805.1_ASM798980v1_genomic.fna/target_genomes.txt --output GCF_007989805.1_ASM798980v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:14,317] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:14,318] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9de5a971-ce53-4f63-b71b-e931d4795efc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:14,319] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9de5a971-ce53-4f63-b71b-e931d4795efc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:14,336] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:14,336] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:14,336] [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 xylanilytica	strain=NBRC 101102	GCA_007989805.1	233583	233583	type	True	100.0	1466	1468	95	conclusive
Cellulomonas terrae	strain=NBRC 100819	GCA_007990265.1	311234	311234	type	True	89.0619	1180	1468	95	below_threshold
Cellulomonas humilata	strain=ATCC 25174	GCA_013359775.1	144055	144055	type	True	86.4743	1096	1468	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	82.0186	803	1468	95	below_threshold
Cellulomonas rhizosphaerae	strain=NEAU-TCZ24	GCA_003470205.1	2293719	2293719	type	True	82.0182	716	1468	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	81.7767	871	1468	95	below_threshold
Cellulomonas fimi	strain=ATCC 484	GCA_000212695.1	1708	1708	type	True	81.7104	889	1468	95	below_threshold
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	81.0172	697	1468	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	80.9321	752	1468	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	80.9101	746	1468	95	below_threshold
Cellulomonas uda	strain=NBRC 3747	GCA_006538705.1	1714	1714	type	True	80.8699	702	1468	95	below_threshold
Cellulomonas persica	strain=NBRC 101101	GCA_007989825.1	76861	76861	type	True	80.8138	712	1468	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	80.3034	744	1468	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	80.201	679	1468	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	79.3649	676	1468	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	79.2445	561	1468	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:14,338] [INFO] DFAST Taxonomy check result was written to GCF_007989805.1_ASM798980v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:14,338] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:14,339] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:14,339] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9de5a971-ce53-4f63-b71b-e931d4795efc/dqc_reference/checkm_data
[2024-01-24 13:41:14,340] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:14,380] [INFO] Task started: CheckM
[2024-01-24 13:41:14,381] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007989805.1_ASM798980v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007989805.1_ASM798980v1_genomic.fna/checkm_input GCF_007989805.1_ASM798980v1_genomic.fna/checkm_result
[2024-01-24 13:42:18,206] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:18,207] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:18,229] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:18,229] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:18,230] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007989805.1_ASM798980v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:18,230] [INFO] Task started: Blastn
[2024-01-24 13:42:18,230] [INFO] Running command: blastn -query GCF_007989805.1_ASM798980v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9de5a971-ce53-4f63-b71b-e931d4795efc/dqc_reference/reference_markers_gtdb.fasta -out GCF_007989805.1_ASM798980v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:20,371] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:20,376] [INFO] Selected 11 target genomes.
[2024-01-24 13:42:20,376] [INFO] Target genome list was writen to GCF_007989805.1_ASM798980v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:20,421] [INFO] Task started: fastANI
[2024-01-24 13:42:20,422] [INFO] Running command: fastANI --query /var/lib/cwl/stg492be16e-4287-4cad-b6b2-7d5bac08fed1/GCF_007989805.1_ASM798980v1_genomic.fna.gz --refList GCF_007989805.1_ASM798980v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007989805.1_ASM798980v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:33,307] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:33,327] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:33,327] [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_007989805.1	s__Cellulomonas xylanilytica	100.0	1466	1468	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001426705.1	s__Cellulomonas sp001426705	89.2426	1195	1468	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	89.1869	1240	1468	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	89.0616	1180	1468	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	88.5952	1081	1468	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001429255.1	s__Cellulomonas sp001429255	86.6464	1099	1468	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.79	98.79	0.94	0.94	2	-
GCF_018388465.1	s__Cellulomonas sp018388465	85.4413	1011	1468	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.65	99.29	0.98	0.97	3	-
GCF_000426185.1	s__Cellulomonas sp000426185	82.2339	858	1468	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862675.1	s__Cellulomonas chitinilytica	82.0425	927	1468	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	81.6924	891	1468	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	99.99	1.00	1.00	3	-
GCF_013409305.1	s__Cellulomonas soli	80.9584	703	1468	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 13:42:33,331] [INFO] GTDB search result was written to GCF_007989805.1_ASM798980v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:33,332] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:33,335] [INFO] DFAST_QC result json was written to GCF_007989805.1_ASM798980v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:33,336] [INFO] DFAST_QC completed!
[2024-01-24 13:42:33,336] [INFO] Total running time: 0h1m49s