[2024-01-24 13:01:39,990] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:39,992] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:39,992] [INFO] DQC Reference Directory: /var/lib/cwl/stg07e07e95-38a9-452b-9390-b8f5a0978d2a/dqc_reference
[2024-01-24 13:01:41,562] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:41,562] [INFO] Task started: Prodigal
[2024-01-24 13:01:41,563] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6a91a7f-7e57-4d2a-bde3-aa3fd056319f/GCF_004153545.1_ASM415354v1_genomic.fna.gz | prodigal -d GCF_004153545.1_ASM415354v1_genomic.fna/cds.fna -a GCF_004153545.1_ASM415354v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:51,588] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:51,588] [INFO] Task started: HMMsearch
[2024-01-24 13:01:51,588] [INFO] Running command: hmmsearch --tblout GCF_004153545.1_ASM415354v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg07e07e95-38a9-452b-9390-b8f5a0978d2a/dqc_reference/reference_markers.hmm GCF_004153545.1_ASM415354v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:51,868] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:51,869] [INFO] Found 6/6 markers.
[2024-01-24 13:01:51,907] [INFO] Query marker FASTA was written to GCF_004153545.1_ASM415354v1_genomic.fna/markers.fasta
[2024-01-24 13:01:51,907] [INFO] Task started: Blastn
[2024-01-24 13:01:51,907] [INFO] Running command: blastn -query GCF_004153545.1_ASM415354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07e07e95-38a9-452b-9390-b8f5a0978d2a/dqc_reference/reference_markers.fasta -out GCF_004153545.1_ASM415354v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:53,231] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:53,242] [INFO] Selected 12 target genomes.
[2024-01-24 13:01:53,242] [INFO] Target genome list was writen to GCF_004153545.1_ASM415354v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:53,247] [INFO] Task started: fastANI
[2024-01-24 13:01:53,247] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6a91a7f-7e57-4d2a-bde3-aa3fd056319f/GCF_004153545.1_ASM415354v1_genomic.fna.gz --refList GCF_004153545.1_ASM415354v1_genomic.fna/target_genomes.txt --output GCF_004153545.1_ASM415354v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:04,168] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:04,169] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg07e07e95-38a9-452b-9390-b8f5a0978d2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:04,169] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg07e07e95-38a9-452b-9390-b8f5a0978d2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:04,235] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:04,236] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:04,236] [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
Serinicoccus sediminis	strain=GP-T3-3	GCA_004153545.1	2306021	2306021	type	True	100.0	1151	1154	95	conclusive
Serinicoccus chungangensis	strain=CCUG 59777	GCA_006337125.1	767452	767452	type	True	89.1389	972	1154	95	below_threshold
Serinicoccus profundi	strain=CGMCC 4.5582	GCA_008001015.1	1078471	1078471	type	True	85.597	902	1154	95	below_threshold
Serinicoccus profundi	strain=MCCC 1A05965	GCA_000224715.2	1078471	1078471	type	True	85.5165	866	1154	95	below_threshold
Serinicoccus marinus	strain=DSM 15273	GCA_000421245.1	247333	247333	type	True	85.4517	851	1154	95	below_threshold
Serinicoccus marinus	strain=DSM 15273	GCA_008386315.1	247333	247333	type	True	85.3766	863	1154	95	below_threshold
Serinicoccus hydrothermalis	strain=JLT9	GCA_001685415.1	1758689	1758689	type	True	85.1046	893	1154	95	below_threshold
Serinicoccus kebangsaanensis	strain=P2D13-UKM	GCA_008919445.1	2602069	2602069	type	True	83.8586	845	1154	95	below_threshold
Ornithinimicrobium pekingense	strain=DSM 21552	GCA_000421185.1	384677	384677	type	True	81.3994	704	1154	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	81.1296	655	1154	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	79.7796	526	1154	95	below_threshold
Ornithinimicrobium murale	strain=DSM 22056	GCA_003352835.1	1050153	1050153	type	True	78.6963	328	1154	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:04,238] [INFO] DFAST Taxonomy check result was written to GCF_004153545.1_ASM415354v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:04,240] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:04,240] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:04,240] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg07e07e95-38a9-452b-9390-b8f5a0978d2a/dqc_reference/checkm_data
[2024-01-24 13:02:04,242] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:04,285] [INFO] Task started: CheckM
[2024-01-24 13:02:04,286] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004153545.1_ASM415354v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004153545.1_ASM415354v1_genomic.fna/checkm_input GCF_004153545.1_ASM415354v1_genomic.fna/checkm_result
[2024-01-24 13:02:55,362] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:55,364] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:55,388] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:55,388] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:55,389] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004153545.1_ASM415354v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:55,389] [INFO] Task started: Blastn
[2024-01-24 13:02:55,390] [INFO] Running command: blastn -query GCF_004153545.1_ASM415354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07e07e95-38a9-452b-9390-b8f5a0978d2a/dqc_reference/reference_markers_gtdb.fasta -out GCF_004153545.1_ASM415354v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:57,365] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:57,368] [INFO] Selected 8 target genomes.
[2024-01-24 13:02:57,368] [INFO] Target genome list was writen to GCF_004153545.1_ASM415354v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:57,374] [INFO] Task started: fastANI
[2024-01-24 13:02:57,375] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6a91a7f-7e57-4d2a-bde3-aa3fd056319f/GCF_004153545.1_ASM415354v1_genomic.fna.gz --refList GCF_004153545.1_ASM415354v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004153545.1_ASM415354v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:04,489] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:04,505] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:04,505] [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_004153545.1	s__Serinicoccus sediminis	100.0	1151	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006337125.1	s__Serinicoccus chungangensis	89.1389	972	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001483745.1	s__Serinicoccus chungangensis_A	89.1298	963	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008001015.1	s__Serinicoccus profundi	85.607	901	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	99.17	98.35	0.97	0.94	3	-
GCF_008386315.1	s__Serinicoccus marinus	85.4019	861	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	98.28	97.42	0.92	0.87	4	-
GCF_001685415.1	s__Serinicoccus hydrothermalis	85.1138	892	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008919445.1	s__Serinicoccus sp008919445	83.8393	847	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001942405.1	s__Ornithinimicrobium sp001942405	81.1873	661	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	97.63	97.63	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:04,506] [INFO] GTDB search result was written to GCF_004153545.1_ASM415354v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:04,507] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:04,511] [INFO] DFAST_QC result json was written to GCF_004153545.1_ASM415354v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:04,511] [INFO] DFAST_QC completed!
[2024-01-24 13:03:04,511] [INFO] Total running time: 0h1m25s