[2024-01-24 12:13:52,938] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:52,940] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:52,940] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d2cd5a7-6144-4083-ac84-fbb22ebfb711/dqc_reference
[2024-01-24 12:13:54,252] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:54,252] [INFO] Task started: Prodigal
[2024-01-24 12:13:54,253] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a7f38de-03ab-4a64-9fb9-d4a26622c828/GCF_000975035.1_ASM97503v1_genomic.fna.gz | prodigal -d GCF_000975035.1_ASM97503v1_genomic.fna/cds.fna -a GCF_000975035.1_ASM97503v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:02,770] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:02,770] [INFO] Task started: HMMsearch
[2024-01-24 12:14:02,770] [INFO] Running command: hmmsearch --tblout GCF_000975035.1_ASM97503v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d2cd5a7-6144-4083-ac84-fbb22ebfb711/dqc_reference/reference_markers.hmm GCF_000975035.1_ASM97503v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:03,021] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:03,023] [INFO] Found 6/6 markers.
[2024-01-24 12:14:03,053] [INFO] Query marker FASTA was written to GCF_000975035.1_ASM97503v1_genomic.fna/markers.fasta
[2024-01-24 12:14:03,053] [INFO] Task started: Blastn
[2024-01-24 12:14:03,053] [INFO] Running command: blastn -query GCF_000975035.1_ASM97503v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d2cd5a7-6144-4083-ac84-fbb22ebfb711/dqc_reference/reference_markers.fasta -out GCF_000975035.1_ASM97503v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:04,049] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:04,053] [INFO] Selected 18 target genomes.
[2024-01-24 12:14:04,054] [INFO] Target genome list was writen to GCF_000975035.1_ASM97503v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:04,060] [INFO] Task started: fastANI
[2024-01-24 12:14:04,061] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a7f38de-03ab-4a64-9fb9-d4a26622c828/GCF_000975035.1_ASM97503v1_genomic.fna.gz --refList GCF_000975035.1_ASM97503v1_genomic.fna/target_genomes.txt --output GCF_000975035.1_ASM97503v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:14,241] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:14,242] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d2cd5a7-6144-4083-ac84-fbb22ebfb711/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:14,242] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d2cd5a7-6144-4083-ac84-fbb22ebfb711/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:14,263] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:14,263] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:14,263] [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
Demequina flava	strain=NBRC 105854	GCA_000975035.1	1095025	1095025	type	True	100.0	847	847	95	conclusive
Demequina globuliformis	strain=NBRC 106266	GCA_000975155.1	676202	676202	type	True	80.8315	471	847	95	below_threshold
Demequina sediminicola	strain=NBRC 105855	GCA_000975055.1	1095026	1095026	type	True	80.0374	349	847	95	below_threshold
Demequina activiva	strain=NBRC 110675	GCA_016862815.1	1582364	1582364	type	True	79.1278	359	847	95	below_threshold
Demequina maris	strain=NBRC 109392	GCA_000971155.1	1638982	1638982	type	True	79.0787	297	847	95	below_threshold
Demequina phytophila	strain=NBRC 109391	GCA_000971135.1	1638981	1638981	type	True	78.9641	272	847	95	below_threshold
Demequina salsinemoris	strain=NBRC 105323	GCA_000974805.1	577470	577470	type	True	78.9413	246	847	95	below_threshold
Demequina silvatica	strain=NBRC 109395	GCA_000971215.1	1638988	1638988	type	True	78.9126	295	847	95	below_threshold
Demequina mangrovi	strain=NBRC 105856	GCA_000759715.1	1043493	1043493	type	True	78.8555	297	847	95	below_threshold
Demequina pelophila	strain=NBRC 109393	GCA_000971175.1	1638984	1638984	type	True	78.7838	292	847	95	below_threshold
Demequina rhizosphaerae	strain=NBRC 109397	GCA_000971255.1	1638985	1638985	type	True	78.6959	305	847	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	77.4238	150	847	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	77.4209	132	847	95	below_threshold
Cellulomonas flavigena	strain=DSM 20109	GCA_000092865.1	1711	1711	type	True	77.363	147	847	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	76.8262	96	847	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	76.683	99	847	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	76.447	83	847	95	below_threshold
Planotetraspora kaengkrachanensis	strain=NBRC 104272	GCA_016862895.1	575193	575193	type	True	76.0871	88	847	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:14,266] [INFO] DFAST Taxonomy check result was written to GCF_000975035.1_ASM97503v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:14,267] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:14,267] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:14,267] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d2cd5a7-6144-4083-ac84-fbb22ebfb711/dqc_reference/checkm_data
[2024-01-24 12:14:14,268] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:14,294] [INFO] Task started: CheckM
[2024-01-24 12:14:14,294] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000975035.1_ASM97503v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000975035.1_ASM97503v1_genomic.fna/checkm_input GCF_000975035.1_ASM97503v1_genomic.fna/checkm_result
[2024-01-24 12:14:43,916] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:43,918] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:43,942] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:43,942] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:43,943] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000975035.1_ASM97503v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:43,943] [INFO] Task started: Blastn
[2024-01-24 12:14:43,943] [INFO] Running command: blastn -query GCF_000975035.1_ASM97503v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d2cd5a7-6144-4083-ac84-fbb22ebfb711/dqc_reference/reference_markers_gtdb.fasta -out GCF_000975035.1_ASM97503v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:45,481] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:45,485] [INFO] Selected 12 target genomes.
[2024-01-24 12:14:45,485] [INFO] Target genome list was writen to GCF_000975035.1_ASM97503v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:45,535] [INFO] Task started: fastANI
[2024-01-24 12:14:45,536] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a7f38de-03ab-4a64-9fb9-d4a26622c828/GCF_000975035.1_ASM97503v1_genomic.fna.gz --refList GCF_000975035.1_ASM97503v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000975035.1_ASM97503v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:52,966] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:52,982] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:52,983] [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_000975035.1	s__Demequina flava	100.0	847	847	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000975155.1	s__Demequina globuliformis	80.831	471	847	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000975055.1	s__Demequina sediminicola	80.0528	348	847	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002090175.1	s__Demequina sp002090175	79.9414	400	847	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002090055.1	s__Demequina sp002090055	79.8613	381	847	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002090135.1	s__Demequina sp002090135	79.7703	378	847	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002090155.1	s__Demequina sp002090155	79.3767	369	847	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002090075.1	s__Demequina sp002090075	79.3252	264	847	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002090095.1	s__Demequina sp002090095	79.3206	318	847	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862815.1	s__Demequina activiva	79.1535	357	847	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971235.1	s__Demequina subtropica	79.0118	282	847	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000974805.1	s__Demequina salsinemoris	78.9056	248	847	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:52,986] [INFO] GTDB search result was written to GCF_000975035.1_ASM97503v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:52,987] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:52,991] [INFO] DFAST_QC result json was written to GCF_000975035.1_ASM97503v1_genomic.fna/dqc_result.json
[2024-01-24 12:14:52,992] [INFO] DFAST_QC completed!
[2024-01-24 12:14:52,992] [INFO] Total running time: 0h1m0s