[2024-01-24 12:06:24,819] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:24,821] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:24,821] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6676c32-0704-4b30-b14a-bc7d64678acd/dqc_reference
[2024-01-24 12:06:26,104] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:26,105] [INFO] Task started: Prodigal
[2024-01-24 12:06:26,106] [INFO] Running command: gunzip -c /var/lib/cwl/stgbda787c1-8134-4e0f-bd16-15e4c542be39/GCF_030161615.1_ASM3016161v1_genomic.fna.gz | prodigal -d GCF_030161615.1_ASM3016161v1_genomic.fna/cds.fna -a GCF_030161615.1_ASM3016161v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:35,927] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:35,927] [INFO] Task started: HMMsearch
[2024-01-24 12:06:35,928] [INFO] Running command: hmmsearch --tblout GCF_030161615.1_ASM3016161v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6676c32-0704-4b30-b14a-bc7d64678acd/dqc_reference/reference_markers.hmm GCF_030161615.1_ASM3016161v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:36,136] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:36,137] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgbda787c1-8134-4e0f-bd16-15e4c542be39/GCF_030161615.1_ASM3016161v1_genomic.fna.gz]
[2024-01-24 12:06:36,165] [INFO] Query marker FASTA was written to GCF_030161615.1_ASM3016161v1_genomic.fna/markers.fasta
[2024-01-24 12:06:36,166] [INFO] Task started: Blastn
[2024-01-24 12:06:36,166] [INFO] Running command: blastn -query GCF_030161615.1_ASM3016161v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6676c32-0704-4b30-b14a-bc7d64678acd/dqc_reference/reference_markers.fasta -out GCF_030161615.1_ASM3016161v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:36,984] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:36,989] [INFO] Selected 15 target genomes.
[2024-01-24 12:06:36,989] [INFO] Target genome list was writen to GCF_030161615.1_ASM3016161v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:36,995] [INFO] Task started: fastANI
[2024-01-24 12:06:36,995] [INFO] Running command: fastANI --query /var/lib/cwl/stgbda787c1-8134-4e0f-bd16-15e4c542be39/GCF_030161615.1_ASM3016161v1_genomic.fna.gz --refList GCF_030161615.1_ASM3016161v1_genomic.fna/target_genomes.txt --output GCF_030161615.1_ASM3016161v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:46,452] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:46,452] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6676c32-0704-4b30-b14a-bc7d64678acd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:46,453] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6676c32-0704-4b30-b14a-bc7d64678acd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:46,465] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:06:46,465] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:06:46,466] [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 maris	strain=NBRC 109392	GCA_000971155.1	1638982	1638982	type	True	80.2215	433	1005	95	below_threshold
Demequina phytophila	strain=NBRC 109391	GCA_000971135.1	1638981	1638981	type	True	80.1597	430	1005	95	below_threshold
Demequina soli	strain=NBRC 109394	GCA_000971195.1	1638987	1638987	type	True	80.0981	445	1005	95	below_threshold
Demequina iriomotensis	strain=NBRC 109399	GCA_000971395.1	1536641	1536641	type	True	79.9817	424	1005	95	below_threshold
Demequina subtropica	strain=NBRC 109396	GCA_000971235.1	1638989	1638989	type	True	79.8785	438	1005	95	below_threshold
Demequina gelatinilytica	strain=NBRC 109390	GCA_000971115.1	1638980	1638980	type	True	79.7958	452	1005	95	below_threshold
Demequina pelophila	strain=NBRC 109393	GCA_000971175.1	1638984	1638984	type	True	79.6996	389	1005	95	below_threshold
Demequina salsinemoris	strain=NBRC 105323	GCA_000974805.1	577470	577470	type	True	79.6494	398	1005	95	below_threshold
Demequina globuliformis	strain=NBRC 106266	GCA_000975155.1	676202	676202	type	True	79.5111	394	1005	95	below_threshold
Demequina flava	strain=NBRC 105854	GCA_000975035.1	1095025	1095025	type	True	79.448	354	1005	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	77.3997	230	1005	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	77.3461	258	1005	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	77.2708	242	1005	95	below_threshold
Occultella aeris	strain=CIP 111667	GCA_902703175.1	2761496	2761496	type	True	76.7308	193	1005	95	below_threshold
Occultella gossypii	strain=N2-46	GCA_019947135.1	2800820	2800820	type	True	76.6906	181	1005	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:46,467] [INFO] DFAST Taxonomy check result was written to GCF_030161615.1_ASM3016161v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:46,468] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:46,468] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:46,468] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6676c32-0704-4b30-b14a-bc7d64678acd/dqc_reference/checkm_data
[2024-01-24 12:06:46,470] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:46,502] [INFO] Task started: CheckM
[2024-01-24 12:06:46,503] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030161615.1_ASM3016161v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030161615.1_ASM3016161v1_genomic.fna/checkm_input GCF_030161615.1_ASM3016161v1_genomic.fna/checkm_result
[2024-01-24 12:07:20,367] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:20,368] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:20,383] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:20,383] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:20,383] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030161615.1_ASM3016161v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:20,384] [INFO] Task started: Blastn
[2024-01-24 12:07:20,384] [INFO] Running command: blastn -query GCF_030161615.1_ASM3016161v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6676c32-0704-4b30-b14a-bc7d64678acd/dqc_reference/reference_markers_gtdb.fasta -out GCF_030161615.1_ASM3016161v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:21,515] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:21,519] [INFO] Selected 8 target genomes.
[2024-01-24 12:07:21,520] [INFO] Target genome list was writen to GCF_030161615.1_ASM3016161v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:21,526] [INFO] Task started: fastANI
[2024-01-24 12:07:21,526] [INFO] Running command: fastANI --query /var/lib/cwl/stgbda787c1-8134-4e0f-bd16-15e4c542be39/GCF_030161615.1_ASM3016161v1_genomic.fna.gz --refList GCF_030161615.1_ASM3016161v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030161615.1_ASM3016161v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:26,624] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:26,632] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:07:26,633] [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_002090175.1	s__Demequina sp002090175	85.1786	719	1005	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	83.0688	622	1005	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	82.6705	646	1005	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	80.7206	517	1005	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	79.8416	441	1005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971115.1	s__Demequina gelatinilytica	79.7724	454	1005	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	79.6627	397	1005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002090115.1	s__Demequina sp002090115	79.6424	391	1005	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 12:07:26,635] [INFO] GTDB search result was written to GCF_030161615.1_ASM3016161v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:26,635] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:26,639] [INFO] DFAST_QC result json was written to GCF_030161615.1_ASM3016161v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:26,640] [INFO] DFAST_QC completed!
[2024-01-24 12:07:26,640] [INFO] Total running time: 0h1m2s