[2024-01-24 12:30:52,395] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:52,397] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:52,397] [INFO] DQC Reference Directory: /var/lib/cwl/stg1114c395-8b4c-47cc-a870-457056bd599b/dqc_reference
[2024-01-24 12:30:53,672] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:53,673] [INFO] Task started: Prodigal
[2024-01-24 12:30:53,673] [INFO] Running command: gunzip -c /var/lib/cwl/stgc65c7f14-907c-4e46-aa16-f04f9c59e6f8/GCF_004563975.1_ASM456397v1_genomic.fna.gz | prodigal -d GCF_004563975.1_ASM456397v1_genomic.fna/cds.fna -a GCF_004563975.1_ASM456397v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:01,376] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:01,377] [INFO] Task started: HMMsearch
[2024-01-24 12:31:01,377] [INFO] Running command: hmmsearch --tblout GCF_004563975.1_ASM456397v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1114c395-8b4c-47cc-a870-457056bd599b/dqc_reference/reference_markers.hmm GCF_004563975.1_ASM456397v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:01,681] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:01,683] [INFO] Found 6/6 markers.
[2024-01-24 12:31:01,712] [INFO] Query marker FASTA was written to GCF_004563975.1_ASM456397v1_genomic.fna/markers.fasta
[2024-01-24 12:31:01,713] [INFO] Task started: Blastn
[2024-01-24 12:31:01,713] [INFO] Running command: blastn -query GCF_004563975.1_ASM456397v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1114c395-8b4c-47cc-a870-457056bd599b/dqc_reference/reference_markers.fasta -out GCF_004563975.1_ASM456397v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:02,978] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:02,986] [INFO] Selected 14 target genomes.
[2024-01-24 12:31:02,987] [INFO] Target genome list was writen to GCF_004563975.1_ASM456397v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:02,994] [INFO] Task started: fastANI
[2024-01-24 12:31:02,994] [INFO] Running command: fastANI --query /var/lib/cwl/stgc65c7f14-907c-4e46-aa16-f04f9c59e6f8/GCF_004563975.1_ASM456397v1_genomic.fna.gz --refList GCF_004563975.1_ASM456397v1_genomic.fna/target_genomes.txt --output GCF_004563975.1_ASM456397v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:11,322] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:11,323] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1114c395-8b4c-47cc-a870-457056bd599b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:11,323] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1114c395-8b4c-47cc-a870-457056bd599b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:11,335] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:11,335] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:11,335] [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
Micrococcus lylae	strain=NBRC 15355	GCA_001570885.1	1273	1273	type	True	99.9283	806	860	95	conclusive
Micrococcus endophyticus	strain=DSM 17945	GCA_014205115.1	455343	455343	type	True	83.171	564	860	95	below_threshold
Micrococcus luteus	strain=ATCC 4698	GCA_003417425.1	1270	1270	type	True	83.0507	442	860	95	below_threshold
Micrococcus luteus	strain=ATCC 4698	GCA_008868275.1	1270	1270	type	True	83.0251	497	860	95	below_threshold
Micrococcus luteus	strain=NCTC 2665	GCA_000023205.1	1270	1270	type	True	82.8708	545	860	95	below_threshold
Micrococcus luteus	strain=NCTC2665	GCA_900475555.1	1270	1270	type	True	82.8639	556	860	95	below_threshold
Micrococcus flavus	strain=CGMCC 1.5361	GCA_014644875.1	384602	384602	type	True	82.6384	529	860	95	below_threshold
Micrococcus flavus	strain=DSM 19079	GCA_022348285.1	384602	384602	type	True	82.4857	541	860	95	below_threshold
Micrococcus flavus	strain=DSM 19079	GCA_014204815.1	384602	384602	type	True	82.4726	545	860	95	below_threshold
Citricoccus zhacaiensis	strain=CGMCC 1.7064	GCA_014645315.1	489142	489142	type	True	79.6879	422	860	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	77.6122	246	860	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	77.2323	215	860	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	76.9367	199	860	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.8968	209	860	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:11,337] [INFO] DFAST Taxonomy check result was written to GCF_004563975.1_ASM456397v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:11,338] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:11,338] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:11,338] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1114c395-8b4c-47cc-a870-457056bd599b/dqc_reference/checkm_data
[2024-01-24 12:31:11,339] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:11,369] [INFO] Task started: CheckM
[2024-01-24 12:31:11,369] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004563975.1_ASM456397v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004563975.1_ASM456397v1_genomic.fna/checkm_input GCF_004563975.1_ASM456397v1_genomic.fna/checkm_result
[2024-01-24 12:31:55,815] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:55,817] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:55,835] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:55,835] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:55,835] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004563975.1_ASM456397v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:55,836] [INFO] Task started: Blastn
[2024-01-24 12:31:55,836] [INFO] Running command: blastn -query GCF_004563975.1_ASM456397v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1114c395-8b4c-47cc-a870-457056bd599b/dqc_reference/reference_markers_gtdb.fasta -out GCF_004563975.1_ASM456397v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:57,938] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:57,941] [INFO] Selected 9 target genomes.
[2024-01-24 12:31:57,941] [INFO] Target genome list was writen to GCF_004563975.1_ASM456397v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:57,948] [INFO] Task started: fastANI
[2024-01-24 12:31:57,948] [INFO] Running command: fastANI --query /var/lib/cwl/stgc65c7f14-907c-4e46-aa16-f04f9c59e6f8/GCF_004563975.1_ASM456397v1_genomic.fna.gz --refList GCF_004563975.1_ASM456397v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004563975.1_ASM456397v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:03,680] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:03,693] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:03,693] [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_001570885.1	s__Micrococcus lylae	99.9283	806	860	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Micrococcus	95.0	98.72	97.35	0.93	0.90	6	conclusive
GCF_014205115.1	s__Micrococcus endophyticus	83.1555	565	860	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Micrococcus	95.0	97.47	97.28	0.90	0.88	4	-
GCF_000023205.1	s__Micrococcus luteus	82.7834	550	860	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Micrococcus	95.0	97.15	95.98	0.88	0.78	124	-
GCF_014204815.1	s__Micrococcus flavus	82.5075	543	860	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Micrococcus	95.0	99.99	99.99	1.00	1.00	3	-
GCF_014205175.1	s__Micrococcus cohnii	81.4664	483	860	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Micrococcus	95.0	99.00	98.97	0.96	0.96	3	-
GCF_005877055.1	s__Citricoccus sp005877055	80.5371	460	860	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Citricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116905.1	s__Citricoccus terreus	80.2285	438	860	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Citricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000224415.1	s__Citricoccus sp000224415	80.1777	433	860	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Citricoccus	95.0	96.24	96.24	0.87	0.87	2	-
GCF_014645315.1	s__Citricoccus zhacaiensis	79.7055	421	860	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Citricoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:03,695] [INFO] GTDB search result was written to GCF_004563975.1_ASM456397v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:03,696] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:03,699] [INFO] DFAST_QC result json was written to GCF_004563975.1_ASM456397v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:03,699] [INFO] DFAST_QC completed!
[2024-01-24 12:32:03,699] [INFO] Total running time: 0h1m11s