[2024-01-24 12:06:34,914] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:34,916] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:34,916] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbfdb433-a16a-46a5-b824-3c38a2499797/dqc_reference
[2024-01-24 12:06:36,150] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:36,151] [INFO] Task started: Prodigal
[2024-01-24 12:06:36,151] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb20ba35-d2d0-4906-8dc1-568be7ef1d29/GCF_013407955.1_ASM1340795v1_genomic.fna.gz | prodigal -d GCF_013407955.1_ASM1340795v1_genomic.fna/cds.fna -a GCF_013407955.1_ASM1340795v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:55,542] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:55,543] [INFO] Task started: HMMsearch
[2024-01-24 12:06:55,543] [INFO] Running command: hmmsearch --tblout GCF_013407955.1_ASM1340795v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbfdb433-a16a-46a5-b824-3c38a2499797/dqc_reference/reference_markers.hmm GCF_013407955.1_ASM1340795v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:55,894] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:55,896] [INFO] Found 6/6 markers.
[2024-01-24 12:06:55,963] [INFO] Query marker FASTA was written to GCF_013407955.1_ASM1340795v1_genomic.fna/markers.fasta
[2024-01-24 12:06:55,964] [INFO] Task started: Blastn
[2024-01-24 12:06:55,964] [INFO] Running command: blastn -query GCF_013407955.1_ASM1340795v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbfdb433-a16a-46a5-b824-3c38a2499797/dqc_reference/reference_markers.fasta -out GCF_013407955.1_ASM1340795v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:57,279] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:57,284] [INFO] Selected 15 target genomes.
[2024-01-24 12:06:57,284] [INFO] Target genome list was writen to GCF_013407955.1_ASM1340795v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:57,292] [INFO] Task started: fastANI
[2024-01-24 12:06:57,292] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb20ba35-d2d0-4906-8dc1-568be7ef1d29/GCF_013407955.1_ASM1340795v1_genomic.fna.gz --refList GCF_013407955.1_ASM1340795v1_genomic.fna/target_genomes.txt --output GCF_013407955.1_ASM1340795v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:15,960] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:15,960] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbbfdb433-a16a-46a5-b824-3c38a2499797/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:15,960] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbbfdb433-a16a-46a5-b824-3c38a2499797/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:15,981] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:15,982] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:15,982] [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
Microlunatus parietis	strain=DSM 22083	GCA_013407955.1	682979	682979	type	True	100.0	2413	2413	95	conclusive
Microlunatus speluncae	strain=SYSU K12189	GCA_009299835.1	2594267	2594267	type	True	83.8471	1605	2413	95	below_threshold
Microlunatus panaciterrae	strain=DSM 18662	GCA_016907535.1	400768	400768	type	True	78.6306	559	2413	95	below_threshold
Microlunatus kandeliicorticis	strain=DSM 100723	GCA_014137855.1	1759536	1759536	type	True	78.6238	675	2413	95	below_threshold
Microlunatus endophyticus	strain=CGMCC 4.7306	GCA_014646195.1	1716077	1716077	type	True	78.3197	527	2413	95	below_threshold
Microlunatus elymi	strain=KUDC0627	GCA_007362775.1	2596828	2596828	type	True	78.2661	663	2413	95	below_threshold
Microlunatus phosphovorus	strain=NM-1	GCA_000270245.1	29405	29405	type	True	78.1702	522	2413	95	below_threshold
Auraticoccus cholistanensis	strain=F435	GCA_009742705.1	2656650	2656650	type	True	77.7802	551	2413	95	below_threshold
Microlunatus antarcticus	strain=DSM 11053	GCA_014193425.1	53388	53388	type	True	77.6685	546	2413	95	below_threshold
Kribbella turkmenica	strain=16K104	GCA_004348725.1	2530375	2530375	type	True	77.1161	605	2413	95	below_threshold
Granulicoccus phenolivorans	strain=DSM 17626	GCA_000423085.1	266854	266854	type	True	77.1088	381	2413	95	below_threshold
Kribbella capetownensis	strain=YM53	GCA_004331485.1	1572659	1572659	type	True	77.0595	612	2413	95	below_threshold
Kribbella jiaozuonensis	strain=NEAU-THZ27	GCA_005233875.1	2575441	2575441	type	True	76.9881	576	2413	95	below_threshold
Propioniciclava soli	strain=YIM S02567	GCA_014858005.1	2775081	2775081	type	True	76.7899	319	2413	95	below_threshold
Actinomadura rubrobrunea	strain=NBRC 15275	GCA_001552235.1	115335	115335	type	True	76.149	482	2413	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:15,985] [INFO] DFAST Taxonomy check result was written to GCF_013407955.1_ASM1340795v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:15,985] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:15,986] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:15,986] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbfdb433-a16a-46a5-b824-3c38a2499797/dqc_reference/checkm_data
[2024-01-24 12:07:15,988] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:16,055] [INFO] Task started: CheckM
[2024-01-24 12:07:16,055] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013407955.1_ASM1340795v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013407955.1_ASM1340795v1_genomic.fna/checkm_input GCF_013407955.1_ASM1340795v1_genomic.fna/checkm_result
[2024-01-24 12:08:51,845] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:51,847] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:51,875] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:51,876] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:51,876] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013407955.1_ASM1340795v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:51,877] [INFO] Task started: Blastn
[2024-01-24 12:08:51,877] [INFO] Running command: blastn -query GCF_013407955.1_ASM1340795v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbfdb433-a16a-46a5-b824-3c38a2499797/dqc_reference/reference_markers_gtdb.fasta -out GCF_013407955.1_ASM1340795v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:53,860] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:53,864] [INFO] Selected 14 target genomes.
[2024-01-24 12:08:53,865] [INFO] Target genome list was writen to GCF_013407955.1_ASM1340795v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:53,877] [INFO] Task started: fastANI
[2024-01-24 12:08:53,877] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb20ba35-d2d0-4906-8dc1-568be7ef1d29/GCF_013407955.1_ASM1340795v1_genomic.fna.gz --refList GCF_013407955.1_ASM1340795v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013407955.1_ASM1340795v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:09:12,303] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:12,319] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:09:12,319] [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_013407955.1	s__Microlunatus_B parietis	100.0	2411	2413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009299835.1	s__Microlunatus_B speluncae	83.8694	1600	2413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907535.1	s__Microlunatus_C panaciterrae	78.6263	559	2413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014137855.1	s__Friedmanniella_A endophytica	78.596	678	2413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408315.1	s__Microlunatus_A terrae	78.5927	771	2413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646195.1	s__Microlunatus_A endophyticus	78.3058	529	2413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007362775.1	s__Microlunatus_A sp007362775	78.2471	667	2413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876495.1	s__Friedmanniella capsulata	78.2219	679	2413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105065.1	s__Friedmanniella luteola	78.1815	647	2413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000270245.1	s__Microlunatus phosphovorus	78.1565	524	2413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105385.1	s__Microlunatus_A soli	78.0038	747	2413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009707365.1	s__Microlunatus_A sp009707365	77.7954	538	2413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016711205.1	s__Micropruina sp016711205	77.1474	358	2413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Micropruina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003001795.1	s__Actinomadura_B viridilutea	76.1688	507	2413	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinomadura_B	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:09:12,321] [INFO] GTDB search result was written to GCF_013407955.1_ASM1340795v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:09:12,322] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:09:12,326] [INFO] DFAST_QC result json was written to GCF_013407955.1_ASM1340795v1_genomic.fna/dqc_result.json
[2024-01-24 12:09:12,326] [INFO] DFAST_QC completed!
[2024-01-24 12:09:12,326] [INFO] Total running time: 0h2m37s