[2024-01-24 14:21:50,727] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:21:50,731] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:21:50,733] [INFO] DQC Reference Directory: /var/lib/cwl/stg960db137-a8bc-46ea-81d3-a9ed7d4b3fea/dqc_reference
[2024-01-24 14:21:52,157] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:21:52,159] [INFO] Task started: Prodigal
[2024-01-24 14:21:52,159] [INFO] Running command: gunzip -c /var/lib/cwl/stga70a6efa-f664-4b72-af53-e79a81ce334b/GCF_002798405.1_ASM279840v1_genomic.fna.gz | prodigal -d GCF_002798405.1_ASM279840v1_genomic.fna/cds.fna -a GCF_002798405.1_ASM279840v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:04,585] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:04,586] [INFO] Task started: HMMsearch
[2024-01-24 14:22:04,586] [INFO] Running command: hmmsearch --tblout GCF_002798405.1_ASM279840v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg960db137-a8bc-46ea-81d3-a9ed7d4b3fea/dqc_reference/reference_markers.hmm GCF_002798405.1_ASM279840v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:04,868] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:04,869] [INFO] Found 6/6 markers.
[2024-01-24 14:22:04,910] [INFO] Query marker FASTA was written to GCF_002798405.1_ASM279840v1_genomic.fna/markers.fasta
[2024-01-24 14:22:04,910] [INFO] Task started: Blastn
[2024-01-24 14:22:04,910] [INFO] Running command: blastn -query GCF_002798405.1_ASM279840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg960db137-a8bc-46ea-81d3-a9ed7d4b3fea/dqc_reference/reference_markers.fasta -out GCF_002798405.1_ASM279840v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:06,221] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:06,224] [INFO] Selected 8 target genomes.
[2024-01-24 14:22:06,225] [INFO] Target genome list was writen to GCF_002798405.1_ASM279840v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:06,229] [INFO] Task started: fastANI
[2024-01-24 14:22:06,229] [INFO] Running command: fastANI --query /var/lib/cwl/stga70a6efa-f664-4b72-af53-e79a81ce334b/GCF_002798405.1_ASM279840v1_genomic.fna.gz --refList GCF_002798405.1_ASM279840v1_genomic.fna/target_genomes.txt --output GCF_002798405.1_ASM279840v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:17,215] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:17,216] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg960db137-a8bc-46ea-81d3-a9ed7d4b3fea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:17,216] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg960db137-a8bc-46ea-81d3-a9ed7d4b3fea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:17,225] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:17,225] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:17,225] [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
Glycomyces xiaoerkulensis	strain=TRM 41368	GCA_002798405.1	2038139	2038139	type	True	100.0	1436	1439	95	conclusive
Glycomyces salinus	strain=YIM 93776	GCA_016428645.1	980294	980294	type	True	84.0446	977	1439	95	below_threshold
Glycomyces tenuis	strain=NRRL B-16895	GCA_000715885.1	58116	58116	type	True	83.9994	1008	1439	95	below_threshold
Glycomyces tenuis	strain=DSM 44171	GCA_000427885.1	58116	58116	type	True	83.9771	1010	1439	95	below_threshold
Glycomyces arizonensis	strain=DSM 44726	GCA_000482705.1	256035	256035	type	True	83.9141	973	1439	95	below_threshold
Glycomyces terrestris	strain=YIM 121974	GCA_003933745.1	2493553	2493553	type	True	82.2132	910	1439	95	below_threshold
Glycomyces albidus	strain=NEAU-7082	GCA_009451885.1	2656774	2656774	type	True	82.016	907	1439	95	below_threshold
Glycomyces dulcitolivorans	strain=SJ-25	GCA_003265355.1	2200759	2200759	type	True	81.9571	817	1439	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:17,227] [INFO] DFAST Taxonomy check result was written to GCF_002798405.1_ASM279840v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:17,227] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:17,227] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:17,228] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg960db137-a8bc-46ea-81d3-a9ed7d4b3fea/dqc_reference/checkm_data
[2024-01-24 14:22:17,229] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:17,277] [INFO] Task started: CheckM
[2024-01-24 14:22:17,277] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002798405.1_ASM279840v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002798405.1_ASM279840v1_genomic.fna/checkm_input GCF_002798405.1_ASM279840v1_genomic.fna/checkm_result
[2024-01-24 14:22:55,031] [INFO] Task succeeded: CheckM
[2024-01-24 14:22:55,032] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:22:55,053] [INFO] ===== Completeness check finished =====
[2024-01-24 14:22:55,053] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:22:55,053] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002798405.1_ASM279840v1_genomic.fna/markers.fasta)
[2024-01-24 14:22:55,054] [INFO] Task started: Blastn
[2024-01-24 14:22:55,054] [INFO] Running command: blastn -query GCF_002798405.1_ASM279840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg960db137-a8bc-46ea-81d3-a9ed7d4b3fea/dqc_reference/reference_markers_gtdb.fasta -out GCF_002798405.1_ASM279840v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:56,887] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:56,891] [INFO] Selected 11 target genomes.
[2024-01-24 14:22:56,892] [INFO] Target genome list was writen to GCF_002798405.1_ASM279840v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:22:56,900] [INFO] Task started: fastANI
[2024-01-24 14:22:56,901] [INFO] Running command: fastANI --query /var/lib/cwl/stga70a6efa-f664-4b72-af53-e79a81ce334b/GCF_002798405.1_ASM279840v1_genomic.fna.gz --refList GCF_002798405.1_ASM279840v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002798405.1_ASM279840v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:10,505] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:10,523] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:10,523] [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_002798405.1	s__Glycomyces xiaoerkulensis	100.0	1435	1439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016428645.1	s__Glycomyces sp016428645	84.0367	977	1439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427885.1	s__Glycomyces tenuis	83.9764	1010	1439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482705.1	s__Glycomyces arizonensis	83.9562	968	1439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719515.1	s__Glycomyces sp000719515	82.414	895	1439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004912275.1	s__Glycomyces buryatensis	82.3525	898	1439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003933745.1	s__Glycomyces terrestris	82.1578	917	1439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102815.1	s__Glycomyces sambucus	82.0441	881	1439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009451885.1	s__Glycomyces albidus	82.0432	905	1439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003265355.1	s__Glycomyces dulcitolivorans	81.9329	822	1439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002955.1	s__Glycomyces artemisiae	81.4789	897	1439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	97.80	97.80	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:10,527] [INFO] GTDB search result was written to GCF_002798405.1_ASM279840v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:10,528] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:10,531] [INFO] DFAST_QC result json was written to GCF_002798405.1_ASM279840v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:10,531] [INFO] DFAST_QC completed!
[2024-01-24 14:23:10,531] [INFO] Total running time: 0h1m20s