[2024-01-24 13:18:46,269] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:46,271] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:46,271] [INFO] DQC Reference Directory: /var/lib/cwl/stg178ccaef-7718-4d2b-9260-45c5efd20850/dqc_reference
[2024-01-24 13:18:47,642] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:47,643] [INFO] Task started: Prodigal
[2024-01-24 13:18:47,643] [INFO] Running command: gunzip -c /var/lib/cwl/stg010b9ef1-1339-48c6-8310-b49ccd9705aa/GCF_014190805.1_ASM1419080v1_genomic.fna.gz | prodigal -d GCF_014190805.1_ASM1419080v1_genomic.fna/cds.fna -a GCF_014190805.1_ASM1419080v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:03,822] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:03,822] [INFO] Task started: HMMsearch
[2024-01-24 13:19:03,822] [INFO] Running command: hmmsearch --tblout GCF_014190805.1_ASM1419080v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg178ccaef-7718-4d2b-9260-45c5efd20850/dqc_reference/reference_markers.hmm GCF_014190805.1_ASM1419080v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:04,101] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:04,102] [INFO] Found 6/6 markers.
[2024-01-24 13:19:04,143] [INFO] Query marker FASTA was written to GCF_014190805.1_ASM1419080v1_genomic.fna/markers.fasta
[2024-01-24 13:19:04,143] [INFO] Task started: Blastn
[2024-01-24 13:19:04,144] [INFO] Running command: blastn -query GCF_014190805.1_ASM1419080v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg178ccaef-7718-4d2b-9260-45c5efd20850/dqc_reference/reference_markers.fasta -out GCF_014190805.1_ASM1419080v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:05,360] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:05,364] [INFO] Selected 14 target genomes.
[2024-01-24 13:19:05,364] [INFO] Target genome list was writen to GCF_014190805.1_ASM1419080v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:05,379] [INFO] Task started: fastANI
[2024-01-24 13:19:05,379] [INFO] Running command: fastANI --query /var/lib/cwl/stg010b9ef1-1339-48c6-8310-b49ccd9705aa/GCF_014190805.1_ASM1419080v1_genomic.fna.gz --refList GCF_014190805.1_ASM1419080v1_genomic.fna/target_genomes.txt --output GCF_014190805.1_ASM1419080v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:16,767] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:16,768] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg178ccaef-7718-4d2b-9260-45c5efd20850/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:16,768] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg178ccaef-7718-4d2b-9260-45c5efd20850/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:16,780] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:16,780] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:16,780] [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 oryzae	strain=DSM 105369	GCA_014190805.1	1794944	1794944	type	True	100.0	1659	1661	95	conclusive
Flexivirga endophytica	strain=KCTC 39536	GCA_014652735.1	1849103	1849103	type	True	82.734	961	1661	95	below_threshold
Flexivirga caeni	strain=BO-16	GCA_003724155.1	2294115	2294115	type	True	82.7035	888	1661	95	below_threshold
Flexivirga endophytica	strain=CGMCC 1.15085	GCA_014640635.1	1849103	1849103	type	True	82.6861	976	1661	95	below_threshold
Flexivirga aerilata	strain=ID2601S	GCA_013002715.1	1656889	1656889	type	True	81.9725	815	1661	95	below_threshold
Luteipulveratus halotolerans	strain=C296001	GCA_001247745.1	1631356	1631356	type	True	79.4732	544	1661	95	below_threshold
Branchiibius hedensis	strain=DSM 22951	GCA_900108585.1	672460	672460	type	True	78.629	445	1661	95	below_threshold
Branchiibius hedensis	strain=DSM 22951	GCA_003149195.1	672460	672460	type	True	78.6163	447	1661	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	78.4619	340	1661	95	below_threshold
Knoellia remsis	strain=ATCC BAA-1496	GCA_003002895.1	407159	407159	type	True	78.3377	360	1661	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	78.2835	331	1661	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	78.2197	351	1661	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	77.9733	316	1661	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	77.9594	322	1661	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:16,782] [INFO] DFAST Taxonomy check result was written to GCF_014190805.1_ASM1419080v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:16,783] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:16,783] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:16,783] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg178ccaef-7718-4d2b-9260-45c5efd20850/dqc_reference/checkm_data
[2024-01-24 13:19:16,784] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:16,832] [INFO] Task started: CheckM
[2024-01-24 13:19:16,832] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014190805.1_ASM1419080v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014190805.1_ASM1419080v1_genomic.fna/checkm_input GCF_014190805.1_ASM1419080v1_genomic.fna/checkm_result
[2024-01-24 13:20:19,042] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:19,044] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:19,063] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:19,063] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:19,064] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014190805.1_ASM1419080v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:19,064] [INFO] Task started: Blastn
[2024-01-24 13:20:19,064] [INFO] Running command: blastn -query GCF_014190805.1_ASM1419080v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg178ccaef-7718-4d2b-9260-45c5efd20850/dqc_reference/reference_markers_gtdb.fasta -out GCF_014190805.1_ASM1419080v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:20,998] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:21,001] [INFO] Selected 12 target genomes.
[2024-01-24 13:20:21,001] [INFO] Target genome list was writen to GCF_014190805.1_ASM1419080v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:21,024] [INFO] Task started: fastANI
[2024-01-24 13:20:21,024] [INFO] Running command: fastANI --query /var/lib/cwl/stg010b9ef1-1339-48c6-8310-b49ccd9705aa/GCF_014190805.1_ASM1419080v1_genomic.fna.gz --refList GCF_014190805.1_ASM1419080v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014190805.1_ASM1419080v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:31,440] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:31,450] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:31,451] [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_014190805.1	s__Flexivirga oryzae	100.0	1658	1661	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003724155.1	s__Flexivirga caeni	82.7006	888	1661	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640635.1	s__Flexivirga endophytica	82.6858	976	1661	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013002715.1	s__Flexivirga aerilata	81.9725	815	1661	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	79.6875	583	1661	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Rudaeicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001247745.1	s__Luteipulveratus halotolerans	79.4647	545	1661	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Luteipulveratus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013135345.1	s__Yimella sp013135345	79.387	503	1661	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Yimella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001594145.1	s__Branchiibius sp001594145	78.9296	422	1661	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Branchiibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001190945.1	s__Luteipulveratus mongoliensis	78.9273	479	1661	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Luteipulveratus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007845645.1	s__Leekyejoonella antrihumi	78.7792	520	1661	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Leekyejoonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716185.1	s__Ornithinicoccus hortensis	78.4805	376	1661	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	99.99	99.99	1.00	1.00	2	-
GCA_012838445.1	s__F2B08 sp012838445	77.6461	299	1661	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__F2B08	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:31,453] [INFO] GTDB search result was written to GCF_014190805.1_ASM1419080v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:31,454] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:31,457] [INFO] DFAST_QC result json was written to GCF_014190805.1_ASM1419080v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:31,457] [INFO] DFAST_QC completed!
[2024-01-24 13:20:31,458] [INFO] Total running time: 0h1m45s