[2024-01-25 18:08:50,418] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:08:50,419] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:08:50,419] [INFO] DQC Reference Directory: /var/lib/cwl/stg8018c8b3-5e09-44e0-8e29-dc6f9fe836c0/dqc_reference
[2024-01-25 18:08:51,582] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:08:51,583] [INFO] Task started: Prodigal
[2024-01-25 18:08:51,583] [INFO] Running command: gunzip -c /var/lib/cwl/stg2154b946-dae7-4bd6-9150-fa528b98fca5/GCF_014640635.1_ASM1464063v1_genomic.fna.gz | prodigal -d GCF_014640635.1_ASM1464063v1_genomic.fna/cds.fna -a GCF_014640635.1_ASM1464063v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:09:04,773] [INFO] Task succeeded: Prodigal
[2024-01-25 18:09:04,773] [INFO] Task started: HMMsearch
[2024-01-25 18:09:04,773] [INFO] Running command: hmmsearch --tblout GCF_014640635.1_ASM1464063v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8018c8b3-5e09-44e0-8e29-dc6f9fe836c0/dqc_reference/reference_markers.hmm GCF_014640635.1_ASM1464063v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:09:05,052] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:09:05,053] [INFO] Found 6/6 markers.
[2024-01-25 18:09:05,091] [INFO] Query marker FASTA was written to GCF_014640635.1_ASM1464063v1_genomic.fna/markers.fasta
[2024-01-25 18:09:05,091] [INFO] Task started: Blastn
[2024-01-25 18:09:05,091] [INFO] Running command: blastn -query GCF_014640635.1_ASM1464063v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8018c8b3-5e09-44e0-8e29-dc6f9fe836c0/dqc_reference/reference_markers.fasta -out GCF_014640635.1_ASM1464063v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:06,288] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:06,291] [INFO] Selected 11 target genomes.
[2024-01-25 18:09:06,292] [INFO] Target genome list was writen to GCF_014640635.1_ASM1464063v1_genomic.fna/target_genomes.txt
[2024-01-25 18:09:06,308] [INFO] Task started: fastANI
[2024-01-25 18:09:06,308] [INFO] Running command: fastANI --query /var/lib/cwl/stg2154b946-dae7-4bd6-9150-fa528b98fca5/GCF_014640635.1_ASM1464063v1_genomic.fna.gz --refList GCF_014640635.1_ASM1464063v1_genomic.fna/target_genomes.txt --output GCF_014640635.1_ASM1464063v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:09:16,346] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:16,347] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8018c8b3-5e09-44e0-8e29-dc6f9fe836c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:09:16,347] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8018c8b3-5e09-44e0-8e29-dc6f9fe836c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:09:16,354] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:09:16,354] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:09:16,355] [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
Flexivirga endophytica	strain=CGMCC 1.15085	GCA_014640635.1	1849103	1849103	type	True	100.0	1563	1565	95	conclusive
Flexivirga endophytica	strain=KCTC 39536	GCA_014652735.1	1849103	1849103	type	True	99.9972	1549	1565	95	conclusive
Flexivirga oryzae	strain=DSM 105369	GCA_014190805.1	1794944	1794944	type	True	82.5769	972	1565	95	below_threshold
Flexivirga caeni	strain=BO-16	GCA_003724155.1	2294115	2294115	type	True	81.8031	844	1565	95	below_threshold
Flexivirga aerilata	strain=ID2601S	GCA_013002715.1	1656889	1656889	type	True	81.3751	787	1565	95	below_threshold
Luteipulveratus mongoliensis	strain=MN07-A0370	GCA_001190945.1	571913	571913	type	True	78.8065	499	1565	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	78.1588	329	1565	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	77.9581	326	1565	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	77.8553	288	1565	95	below_threshold
Serinicoccus marinus	strain=DSM 15273	GCA_008386315.1	247333	247333	type	True	77.7903	295	1565	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	77.6239	297	1565	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:09:16,356] [INFO] DFAST Taxonomy check result was written to GCF_014640635.1_ASM1464063v1_genomic.fna/tc_result.tsv
[2024-01-25 18:09:16,356] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:09:16,356] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:09:16,357] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8018c8b3-5e09-44e0-8e29-dc6f9fe836c0/dqc_reference/checkm_data
[2024-01-25 18:09:16,357] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:09:16,402] [INFO] Task started: CheckM
[2024-01-25 18:09:16,402] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014640635.1_ASM1464063v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014640635.1_ASM1464063v1_genomic.fna/checkm_input GCF_014640635.1_ASM1464063v1_genomic.fna/checkm_result
[2024-01-25 18:10:26,893] [INFO] Task succeeded: CheckM
[2024-01-25 18:10:26,894] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:10:26,920] [INFO] ===== Completeness check finished =====
[2024-01-25 18:10:26,920] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:10:26,921] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014640635.1_ASM1464063v1_genomic.fna/markers.fasta)
[2024-01-25 18:10:26,922] [INFO] Task started: Blastn
[2024-01-25 18:10:26,922] [INFO] Running command: blastn -query GCF_014640635.1_ASM1464063v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8018c8b3-5e09-44e0-8e29-dc6f9fe836c0/dqc_reference/reference_markers_gtdb.fasta -out GCF_014640635.1_ASM1464063v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:28,853] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:28,856] [INFO] Selected 10 target genomes.
[2024-01-25 18:10:28,856] [INFO] Target genome list was writen to GCF_014640635.1_ASM1464063v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:10:28,871] [INFO] Task started: fastANI
[2024-01-25 18:10:28,871] [INFO] Running command: fastANI --query /var/lib/cwl/stg2154b946-dae7-4bd6-9150-fa528b98fca5/GCF_014640635.1_ASM1464063v1_genomic.fna.gz --refList GCF_014640635.1_ASM1464063v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014640635.1_ASM1464063v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:10:38,941] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:38,948] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:10:38,949] [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_014640635.1	s__Flexivirga endophytica	100.0	1563	1565	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_014190805.1	s__Flexivirga oryzae	82.562	973	1565	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003724155.1	s__Flexivirga caeni	81.7883	845	1565	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013002715.1	s__Flexivirga aerilata	81.4075	784	1565	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829035.1	s__Rudaeicoccus suwonensis	79.7222	549	1565	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Rudaeicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001190945.1	s__Luteipulveratus mongoliensis	78.8028	500	1565	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Luteipulveratus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013041615.1	s__Pedococcus sp013041615	78.4863	397	1565	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716205.1	s__Oryzihumus leptocrescens	78.2107	405	1565	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Oryzihumus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715875.1	s__Terrabacter sp006715875	77.9233	383	1565	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000955875.1	s__Terrabacter sp000955875	77.8343	395	1565	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:10:38,950] [INFO] GTDB search result was written to GCF_014640635.1_ASM1464063v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:10:38,951] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:10:38,954] [INFO] DFAST_QC result json was written to GCF_014640635.1_ASM1464063v1_genomic.fna/dqc_result.json
[2024-01-25 18:10:38,954] [INFO] DFAST_QC completed!
[2024-01-25 18:10:38,954] [INFO] Total running time: 0h1m49s