[2024-01-24 14:50:03,796] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:50:03,807] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:50:03,808] [INFO] DQC Reference Directory: /var/lib/cwl/stg44909c99-1bc0-4486-a92a-e3dcb8dbaa72/dqc_reference
[2024-01-24 14:50:05,259] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:50:05,260] [INFO] Task started: Prodigal
[2024-01-24 14:50:05,260] [INFO] Running command: gunzip -c /var/lib/cwl/stg35908258-48cd-4a5f-979f-5d3edcb7eb7c/GCF_004136555.1_ASM413655v1_genomic.fna.gz | prodigal -d GCF_004136555.1_ASM413655v1_genomic.fna/cds.fna -a GCF_004136555.1_ASM413655v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:50:17,325] [INFO] Task succeeded: Prodigal
[2024-01-24 14:50:17,325] [INFO] Task started: HMMsearch
[2024-01-24 14:50:17,325] [INFO] Running command: hmmsearch --tblout GCF_004136555.1_ASM413655v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44909c99-1bc0-4486-a92a-e3dcb8dbaa72/dqc_reference/reference_markers.hmm GCF_004136555.1_ASM413655v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:50:17,610] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:50:17,612] [INFO] Found 6/6 markers.
[2024-01-24 14:50:17,644] [INFO] Query marker FASTA was written to GCF_004136555.1_ASM413655v1_genomic.fna/markers.fasta
[2024-01-24 14:50:17,645] [INFO] Task started: Blastn
[2024-01-24 14:50:17,645] [INFO] Running command: blastn -query GCF_004136555.1_ASM413655v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44909c99-1bc0-4486-a92a-e3dcb8dbaa72/dqc_reference/reference_markers.fasta -out GCF_004136555.1_ASM413655v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:50:18,793] [INFO] Task succeeded: Blastn
[2024-01-24 14:50:18,796] [INFO] Selected 13 target genomes.
[2024-01-24 14:50:18,797] [INFO] Target genome list was writen to GCF_004136555.1_ASM413655v1_genomic.fna/target_genomes.txt
[2024-01-24 14:50:18,804] [INFO] Task started: fastANI
[2024-01-24 14:50:18,804] [INFO] Running command: fastANI --query /var/lib/cwl/stg35908258-48cd-4a5f-979f-5d3edcb7eb7c/GCF_004136555.1_ASM413655v1_genomic.fna.gz --refList GCF_004136555.1_ASM413655v1_genomic.fna/target_genomes.txt --output GCF_004136555.1_ASM413655v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:50:27,521] [INFO] Task succeeded: fastANI
[2024-01-24 14:50:27,521] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44909c99-1bc0-4486-a92a-e3dcb8dbaa72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:50:27,521] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44909c99-1bc0-4486-a92a-e3dcb8dbaa72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:50:27,534] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:50:27,535] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:50:27,535] [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
Kocuria carniphila	strain=CCM 132	GCA_004136555.1	262208	262208	type	True	100.0	1117	1117	95	conclusive
Kocuria indica	strain=NIO-1021	GCA_900177335.1	1049583	1049583	type	True	81.3421	577	1117	95	below_threshold
Kocuria indica	strain=DSM 25126	GCA_002237805.1	1049583	1049583	type	True	81.3332	577	1117	95	below_threshold
Kocuria indica	strain=NIO-1021	GCA_003667205.1	1049583	1049583	type	True	81.3072	571	1117	95	below_threshold
Kocuria rhizophila	strain=TA68	GCA_003667225.1	72000	72000	type	True	80.6225	499	1117	95	below_threshold
Kocuria tytonis	strain=442	GCA_003226895.2	2054280	2054280	type	True	80.5928	536	1117	95	below_threshold
Kocuria tytonicola	strain=DSM 104133	GCA_003687455.1	2055946	2055946	type	True	80.4773	476	1117	95	below_threshold
Kocuria varians	strain=NBRC 15358	GCA_006539885.1	1272	1272	type	True	80.459	531	1117	95	below_threshold
Micrococcus flavus	strain=DSM 19079	GCA_022348285.1	384602	384602	type	True	77.7064	200	1117	95	below_threshold
Arthrobacter stackebrandtii	strain=DSM 16005	GCA_017876675.1	272161	272161	type	True	77.6134	164	1117	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	77.4605	151	1117	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	77.4325	207	1117	95	below_threshold
Sinomonas notoginsengisoli	strain=KCTC 29237	GCA_021554725.1	1457311	1457311	type	True	77.0752	145	1117	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:50:27,538] [INFO] DFAST Taxonomy check result was written to GCF_004136555.1_ASM413655v1_genomic.fna/tc_result.tsv
[2024-01-24 14:50:27,538] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:50:27,539] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:50:27,539] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44909c99-1bc0-4486-a92a-e3dcb8dbaa72/dqc_reference/checkm_data
[2024-01-24 14:50:27,541] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:50:27,581] [INFO] Task started: CheckM
[2024-01-24 14:50:27,582] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004136555.1_ASM413655v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004136555.1_ASM413655v1_genomic.fna/checkm_input GCF_004136555.1_ASM413655v1_genomic.fna/checkm_result
[2024-01-24 14:51:05,921] [INFO] Task succeeded: CheckM
[2024-01-24 14:51:05,922] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:51:05,939] [INFO] ===== Completeness check finished =====
[2024-01-24 14:51:05,940] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:51:05,940] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004136555.1_ASM413655v1_genomic.fna/markers.fasta)
[2024-01-24 14:51:05,941] [INFO] Task started: Blastn
[2024-01-24 14:51:05,941] [INFO] Running command: blastn -query GCF_004136555.1_ASM413655v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44909c99-1bc0-4486-a92a-e3dcb8dbaa72/dqc_reference/reference_markers_gtdb.fasta -out GCF_004136555.1_ASM413655v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:51:07,611] [INFO] Task succeeded: Blastn
[2024-01-24 14:51:07,618] [INFO] Selected 10 target genomes.
[2024-01-24 14:51:07,618] [INFO] Target genome list was writen to GCF_004136555.1_ASM413655v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:51:07,642] [INFO] Task started: fastANI
[2024-01-24 14:51:07,643] [INFO] Running command: fastANI --query /var/lib/cwl/stg35908258-48cd-4a5f-979f-5d3edcb7eb7c/GCF_004136555.1_ASM413655v1_genomic.fna.gz --refList GCF_004136555.1_ASM413655v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004136555.1_ASM413655v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:51:14,489] [INFO] Task succeeded: fastANI
[2024-01-24 14:51:14,499] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:51:14,499] [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_004136555.1	s__Kocuria carniphila	100.0	1117	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	97.73	97.73	0.89	0.89	2	conclusive
GCA_000286355.1	s__Kocuria atrinae	91.0105	800	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014698015.1	s__Kocuria sp014698015	85.7227	806	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.68	98.68	0.92	0.92	2	-
GCF_000786655.1	s__Kocuria marina_A	81.3502	604	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.811	96.52	96.52	0.87	0.87	2	-
GCA_014652975.1	s__Kocuria marina	81.2497	563	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.811	98.16	96.52	0.91	0.86	16	-
GCF_003667225.1	s__Kocuria rhizophila	80.6281	499	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	97.80	97.11	0.92	0.85	19	-
GCF_003226895.2	s__Kocuria tytonis	80.6101	535	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010285.1	s__Kocuria rhizophila_A	80.4909	536	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.71	97.98	0.95	0.89	9	-
GCF_003687455.1	s__Kocuria tytonicola	80.4773	476	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.95	98.95	0.94	0.94	2	-
GCF_006539885.1	s__Kocuria varians	80.459	531	1117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	99.47	99.47	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:51:14,501] [INFO] GTDB search result was written to GCF_004136555.1_ASM413655v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:51:14,501] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:51:14,505] [INFO] DFAST_QC result json was written to GCF_004136555.1_ASM413655v1_genomic.fna/dqc_result.json
[2024-01-24 14:51:14,505] [INFO] DFAST_QC completed!
[2024-01-24 14:51:14,505] [INFO] Total running time: 0h1m11s