[2024-01-25 19:51:35,545] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:51:35,546] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:51:35,546] [INFO] DQC Reference Directory: /var/lib/cwl/stg42d7390e-5676-4c83-8274-487380e308d4/dqc_reference
[2024-01-25 19:51:36,663] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:51:36,664] [INFO] Task started: Prodigal
[2024-01-25 19:51:36,664] [INFO] Running command: gunzip -c /var/lib/cwl/stg85a18e7a-09b8-4f57-8141-6295da2a58c4/GCF_014646195.1_ASM1464619v1_genomic.fna.gz | prodigal -d GCF_014646195.1_ASM1464619v1_genomic.fna/cds.fna -a GCF_014646195.1_ASM1464619v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:51:49,845] [INFO] Task succeeded: Prodigal
[2024-01-25 19:51:49,845] [INFO] Task started: HMMsearch
[2024-01-25 19:51:49,845] [INFO] Running command: hmmsearch --tblout GCF_014646195.1_ASM1464619v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg42d7390e-5676-4c83-8274-487380e308d4/dqc_reference/reference_markers.hmm GCF_014646195.1_ASM1464619v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:51:50,149] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:51:50,152] [INFO] Found 6/6 markers.
[2024-01-25 19:51:50,206] [INFO] Query marker FASTA was written to GCF_014646195.1_ASM1464619v1_genomic.fna/markers.fasta
[2024-01-25 19:51:50,206] [INFO] Task started: Blastn
[2024-01-25 19:51:50,206] [INFO] Running command: blastn -query GCF_014646195.1_ASM1464619v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg42d7390e-5676-4c83-8274-487380e308d4/dqc_reference/reference_markers.fasta -out GCF_014646195.1_ASM1464619v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:51,280] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:51,283] [INFO] Selected 17 target genomes.
[2024-01-25 19:51:51,284] [INFO] Target genome list was writen to GCF_014646195.1_ASM1464619v1_genomic.fna/target_genomes.txt
[2024-01-25 19:51:51,297] [INFO] Task started: fastANI
[2024-01-25 19:51:51,297] [INFO] Running command: fastANI --query /var/lib/cwl/stg85a18e7a-09b8-4f57-8141-6295da2a58c4/GCF_014646195.1_ASM1464619v1_genomic.fna.gz --refList GCF_014646195.1_ASM1464619v1_genomic.fna/target_genomes.txt --output GCF_014646195.1_ASM1464619v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:52:08,730] [INFO] Task succeeded: fastANI
[2024-01-25 19:52:08,730] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg42d7390e-5676-4c83-8274-487380e308d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:52:08,731] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg42d7390e-5676-4c83-8274-487380e308d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:52:08,742] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:52:08,742] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:52:08,742] [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 endophyticus	strain=CGMCC 4.7306	GCA_014646195.1	1716077	1716077	type	True	100.0	1681	1682	95	conclusive
Microlunatus elymi	strain=KUDC0627	GCA_007362775.1	2596828	2596828	type	True	80.0909	787	1682	95	below_threshold
Microlunatus soli	strain=DSM 21800	GCA_900105385.1	630515	630515	type	True	79.7264	815	1682	95	below_threshold
Microlunatus kandeliicorticis	strain=DSM 100723	GCA_014137855.1	1759536	1759536	type	True	78.5946	548	1682	95	below_threshold
Microlunatus panaciterrae	strain=DSM 18662	GCA_016907535.1	400768	400768	type	True	78.1361	410	1682	95	below_threshold
Microlunatus parietis	strain=DSM 22083	GCA_013407955.1	682979	682979	type	True	78.1134	540	1682	95	below_threshold
Microlunatus phosphovorus	strain=NM-1	GCA_000270245.1	29405	29405	type	True	78.0232	363	1682	95	below_threshold
Microlunatus sagamiharensis	strain=DSM 21743	GCA_900105785.1	546874	546874	type	True	77.9892	395	1682	95	below_threshold
Microlunatus speluncae	strain=SYSU K12189	GCA_009299835.1	2594267	2594267	type	True	77.901	548	1682	95	below_threshold
Auraticoccus cholistanensis	strain=F435	GCA_009742705.1	2656650	2656650	type	True	77.8116	378	1682	95	below_threshold
Enemella evansiae	strain=NML 020265	GCA_002250705.1	2016499	2016499	type	True	77.6765	355	1682	95	below_threshold
Microlunatus antarcticus	strain=DSM 11053	GCA_014193425.1	53388	53388	type	True	77.5832	362	1682	95	below_threshold
Naumannella cuiyingiana	strain=DSM 103164	GCA_013408305.1	1347891	1347891	type	True	77.5174	331	1682	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	77.0939	328	1682	95	below_threshold
Kribbella capetownensis	strain=YM53	GCA_004331485.1	1572659	1572659	type	True	77.085	336	1682	95	below_threshold
Kribbella turkmenica	strain=16K104	GCA_004348725.1	2530375	2530375	type	True	77.0301	341	1682	95	below_threshold
Kribbella jiaozuonensis	strain=NEAU-THZ27	GCA_005233875.1	2575441	2575441	type	True	76.7772	324	1682	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:52:08,745] [INFO] DFAST Taxonomy check result was written to GCF_014646195.1_ASM1464619v1_genomic.fna/tc_result.tsv
[2024-01-25 19:52:08,746] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:52:08,746] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:52:08,746] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg42d7390e-5676-4c83-8274-487380e308d4/dqc_reference/checkm_data
[2024-01-25 19:52:08,747] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:52:08,795] [INFO] Task started: CheckM
[2024-01-25 19:52:08,796] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014646195.1_ASM1464619v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014646195.1_ASM1464619v1_genomic.fna/checkm_input GCF_014646195.1_ASM1464619v1_genomic.fna/checkm_result
[2024-01-25 19:52:55,177] [INFO] Task succeeded: CheckM
[2024-01-25 19:52:55,178] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:52:55,206] [INFO] ===== Completeness check finished =====
[2024-01-25 19:52:55,206] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:52:55,206] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014646195.1_ASM1464619v1_genomic.fna/markers.fasta)
[2024-01-25 19:52:55,207] [INFO] Task started: Blastn
[2024-01-25 19:52:55,207] [INFO] Running command: blastn -query GCF_014646195.1_ASM1464619v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg42d7390e-5676-4c83-8274-487380e308d4/dqc_reference/reference_markers_gtdb.fasta -out GCF_014646195.1_ASM1464619v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:52:56,824] [INFO] Task succeeded: Blastn
[2024-01-25 19:52:56,834] [INFO] Selected 11 target genomes.
[2024-01-25 19:52:56,834] [INFO] Target genome list was writen to GCF_014646195.1_ASM1464619v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:52:56,848] [INFO] Task started: fastANI
[2024-01-25 19:52:56,848] [INFO] Running command: fastANI --query /var/lib/cwl/stg85a18e7a-09b8-4f57-8141-6295da2a58c4/GCF_014646195.1_ASM1464619v1_genomic.fna.gz --refList GCF_014646195.1_ASM1464619v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014646195.1_ASM1464619v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:53:08,835] [INFO] Task succeeded: fastANI
[2024-01-25 19:53:08,843] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:53:08,844] [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_014646195.1	s__Microlunatus_A endophyticus	100.0	1681	1682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009707365.1	s__Microlunatus_A sp009707365	81.3249	968	1682	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_013408315.1	s__Microlunatus_A terrae	80.5427	811	1682	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	80.133	781	1682	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_900105385.1	s__Microlunatus_A soli	79.746	812	1682	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_014137855.1	s__Friedmanniella_A endophytica	78.5909	549	1682	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_016907535.1	s__Microlunatus_C panaciterrae	78.1479	408	1682	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_000270245.1	s__Microlunatus phosphovorus	78.0229	363	1682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105785.1	s__Friedmanniella sagamiharensis	77.974	398	1682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009299835.1	s__Microlunatus_B speluncae	77.9073	546	1682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805915.1	s__CADCUO01 sp902805915	77.5161	253	1682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__CADCUO01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:53:08,845] [INFO] GTDB search result was written to GCF_014646195.1_ASM1464619v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:53:08,846] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:53:08,848] [INFO] DFAST_QC result json was written to GCF_014646195.1_ASM1464619v1_genomic.fna/dqc_result.json
[2024-01-25 19:53:08,849] [INFO] DFAST_QC completed!
[2024-01-25 19:53:08,849] [INFO] Total running time: 0h1m33s