[2024-01-25 20:22:50,713] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:22:50,719] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:22:50,719] [INFO] DQC Reference Directory: /var/lib/cwl/stgad5a8007-6540-4efb-81ab-cec1e94bb7a4/dqc_reference
[2024-01-25 20:22:51,855] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:22:51,856] [INFO] Task started: Prodigal
[2024-01-25 20:22:51,856] [INFO] Running command: gunzip -c /var/lib/cwl/stg185b5789-8b82-41c9-ad58-cb6d039e1fcf/GCF_000421245.1_ASM42124v1_genomic.fna.gz | prodigal -d GCF_000421245.1_ASM42124v1_genomic.fna/cds.fna -a GCF_000421245.1_ASM42124v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:23:00,347] [INFO] Task succeeded: Prodigal
[2024-01-25 20:23:00,347] [INFO] Task started: HMMsearch
[2024-01-25 20:23:00,347] [INFO] Running command: hmmsearch --tblout GCF_000421245.1_ASM42124v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad5a8007-6540-4efb-81ab-cec1e94bb7a4/dqc_reference/reference_markers.hmm GCF_000421245.1_ASM42124v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:23:00,564] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:23:00,565] [INFO] Found 6/6 markers.
[2024-01-25 20:23:00,610] [INFO] Query marker FASTA was written to GCF_000421245.1_ASM42124v1_genomic.fna/markers.fasta
[2024-01-25 20:23:00,610] [INFO] Task started: Blastn
[2024-01-25 20:23:00,610] [INFO] Running command: blastn -query GCF_000421245.1_ASM42124v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad5a8007-6540-4efb-81ab-cec1e94bb7a4/dqc_reference/reference_markers.fasta -out GCF_000421245.1_ASM42124v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:01,734] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:01,737] [INFO] Selected 11 target genomes.
[2024-01-25 20:23:01,737] [INFO] Target genome list was writen to GCF_000421245.1_ASM42124v1_genomic.fna/target_genomes.txt
[2024-01-25 20:23:01,747] [INFO] Task started: fastANI
[2024-01-25 20:23:01,747] [INFO] Running command: fastANI --query /var/lib/cwl/stg185b5789-8b82-41c9-ad58-cb6d039e1fcf/GCF_000421245.1_ASM42124v1_genomic.fna.gz --refList GCF_000421245.1_ASM42124v1_genomic.fna/target_genomes.txt --output GCF_000421245.1_ASM42124v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:23:10,760] [INFO] Task succeeded: fastANI
[2024-01-25 20:23:10,760] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad5a8007-6540-4efb-81ab-cec1e94bb7a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:23:10,761] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad5a8007-6540-4efb-81ab-cec1e94bb7a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:23:10,769] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:23:10,769] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:23:10,769] [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 marinus	strain=DSM 15273	GCA_000421245.1	247333	247333	type	True	100.0	1119	1119	95	conclusive
Serinicoccus marinus	strain=DSM 15273	GCA_008386315.1	247333	247333	type	True	99.9662	1118	1119	95	conclusive
Serinicoccus hydrothermalis	strain=JLT9	GCA_001685415.1	1758689	1758689	type	True	89.4208	959	1119	95	below_threshold
Serinicoccus sediminis	strain=GP-T3-3	GCA_004153545.1	2306021	2306021	type	True	85.4765	855	1119	95	below_threshold
Serinicoccus kebangsaanensis	strain=P2D13-UKM	GCA_008919445.1	2602069	2602069	type	True	85.4028	870	1119	95	below_threshold
Serinicoccus chungangensis	strain=CCUG 59777	GCA_006337125.1	767452	767452	type	True	84.978	866	1119	95	below_threshold
Serinicoccus profundi	strain=MCCC 1A05965	GCA_000224715.2	1078471	1078471	type	True	84.6936	840	1119	95	below_threshold
Serinicoccus profundi	strain=CGMCC 4.5582	GCA_008001015.1	1078471	1078471	type	True	84.6428	860	1119	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	81.175	656	1119	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	79.6073	534	1119	95	below_threshold
Ornithinimicrobium murale	strain=DSM 22056	GCA_003352835.1	1050153	1050153	type	True	78.6927	336	1119	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:23:10,770] [INFO] DFAST Taxonomy check result was written to GCF_000421245.1_ASM42124v1_genomic.fna/tc_result.tsv
[2024-01-25 20:23:10,771] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:23:10,771] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:23:10,771] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad5a8007-6540-4efb-81ab-cec1e94bb7a4/dqc_reference/checkm_data
[2024-01-25 20:23:10,772] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:23:10,807] [INFO] Task started: CheckM
[2024-01-25 20:23:10,807] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000421245.1_ASM42124v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000421245.1_ASM42124v1_genomic.fna/checkm_input GCF_000421245.1_ASM42124v1_genomic.fna/checkm_result
[2024-01-25 20:23:56,887] [INFO] Task succeeded: CheckM
[2024-01-25 20:23:56,888] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:23:56,905] [INFO] ===== Completeness check finished =====
[2024-01-25 20:23:56,905] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:23:56,906] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000421245.1_ASM42124v1_genomic.fna/markers.fasta)
[2024-01-25 20:23:56,906] [INFO] Task started: Blastn
[2024-01-25 20:23:56,906] [INFO] Running command: blastn -query GCF_000421245.1_ASM42124v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad5a8007-6540-4efb-81ab-cec1e94bb7a4/dqc_reference/reference_markers_gtdb.fasta -out GCF_000421245.1_ASM42124v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:58,755] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:58,758] [INFO] Selected 9 target genomes.
[2024-01-25 20:23:58,759] [INFO] Target genome list was writen to GCF_000421245.1_ASM42124v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:23:58,768] [INFO] Task started: fastANI
[2024-01-25 20:23:58,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg185b5789-8b82-41c9-ad58-cb6d039e1fcf/GCF_000421245.1_ASM42124v1_genomic.fna.gz --refList GCF_000421245.1_ASM42124v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000421245.1_ASM42124v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:24:06,627] [INFO] Task succeeded: fastANI
[2024-01-25 20:24:06,634] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:24:06,634] [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_008386315.1	s__Serinicoccus marinus	99.9662	1118	1119	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	98.28	97.42	0.92	0.87	4	conclusive
GCF_001685415.1	s__Serinicoccus hydrothermalis	89.4208	959	1119	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004153545.1	s__Serinicoccus sediminis	85.4792	855	1119	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	85.4124	869	1119	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	85.1449	874	1119	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006337125.1	s__Serinicoccus chungangensis	84.9838	865	1119	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	84.6782	857	1119	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	99.17	98.35	0.97	0.94	3	-
GCF_004526345.1	s__Serinicoccus flavus	81.1728	697	1119	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014636495.1	s__Ornithinimicrobium tianjinense	81.0572	645	1119	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:24:06,636] [INFO] GTDB search result was written to GCF_000421245.1_ASM42124v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:24:06,636] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:24:06,639] [INFO] DFAST_QC result json was written to GCF_000421245.1_ASM42124v1_genomic.fna/dqc_result.json
[2024-01-25 20:24:06,639] [INFO] DFAST_QC completed!
[2024-01-25 20:24:06,639] [INFO] Total running time: 0h1m16s