[2024-01-25 18:49:50,658] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:49:50,660] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:49:50,660] [INFO] DQC Reference Directory: /var/lib/cwl/stg6db3a535-cea3-4fbc-a41d-9aeea425a01f/dqc_reference
[2024-01-25 18:49:51,835] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:49:51,835] [INFO] Task started: Prodigal
[2024-01-25 18:49:51,836] [INFO] Running command: gunzip -c /var/lib/cwl/stg69cc26d7-9928-4851-9a8b-18f66a687f1f/GCF_014191795.1_ASM1419179v1_genomic.fna.gz | prodigal -d GCF_014191795.1_ASM1419179v1_genomic.fna/cds.fna -a GCF_014191795.1_ASM1419179v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:50:05,319] [INFO] Task succeeded: Prodigal
[2024-01-25 18:50:05,319] [INFO] Task started: HMMsearch
[2024-01-25 18:50:05,319] [INFO] Running command: hmmsearch --tblout GCF_014191795.1_ASM1419179v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6db3a535-cea3-4fbc-a41d-9aeea425a01f/dqc_reference/reference_markers.hmm GCF_014191795.1_ASM1419179v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:50:05,609] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:50:05,610] [INFO] Found 6/6 markers.
[2024-01-25 18:50:05,661] [INFO] Query marker FASTA was written to GCF_014191795.1_ASM1419179v1_genomic.fna/markers.fasta
[2024-01-25 18:50:05,661] [INFO] Task started: Blastn
[2024-01-25 18:50:05,662] [INFO] Running command: blastn -query GCF_014191795.1_ASM1419179v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6db3a535-cea3-4fbc-a41d-9aeea425a01f/dqc_reference/reference_markers.fasta -out GCF_014191795.1_ASM1419179v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:06,820] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:06,823] [INFO] Selected 12 target genomes.
[2024-01-25 18:50:06,824] [INFO] Target genome list was writen to GCF_014191795.1_ASM1419179v1_genomic.fna/target_genomes.txt
[2024-01-25 18:50:06,832] [INFO] Task started: fastANI
[2024-01-25 18:50:06,832] [INFO] Running command: fastANI --query /var/lib/cwl/stg69cc26d7-9928-4851-9a8b-18f66a687f1f/GCF_014191795.1_ASM1419179v1_genomic.fna.gz --refList GCF_014191795.1_ASM1419179v1_genomic.fna/target_genomes.txt --output GCF_014191795.1_ASM1419179v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:50:25,073] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:25,074] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6db3a535-cea3-4fbc-a41d-9aeea425a01f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:50:25,074] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6db3a535-cea3-4fbc-a41d-9aeea425a01f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:50:25,083] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:50:25,083] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:50:25,083] [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
Geodermatophilus sabuli	strain=CECT 8820	GCA_014191795.1	1564158	1564158	type	True	100.0	1832	1833	95	conclusive
Geodermatophilus sabuli	strain=DSM 46844	GCA_900215145.1	1564158	1564158	type	True	99.9971	1824	1833	95	conclusive
Geodermatophilus siccatus	strain=DSM 45419	GCA_900103785.1	1137991	1137991	type	True	85.2225	1169	1833	95	below_threshold
Geodermatophilus poikilotrophus	strain=DSM 44209	GCA_900111455.1	1333667	1333667	type	True	84.9663	1134	1833	95	below_threshold
Geodermatophilus chilensis	strain=B12	GCA_002802985.1	2035835	2035835	type	True	84.9583	1026	1833	95	below_threshold
Geodermatophilus obscurus	strain=DSM 43160	GCA_000025345.1	1861	1861	type	True	84.8967	1158	1833	95	below_threshold
Geodermatophilus africanus	strain=DSM 45422	GCA_900107105.1	1137993	1137993	type	True	84.7119	1143	1833	95	below_threshold
Geodermatophilus pulveris	strain=DSM 46839	GCA_900188375.1	1564159	1564159	type	True	84.5053	1042	1833	95	below_threshold
Geodermatophilus tzadiensis	strain=DSM 45416	GCA_003002915.1	1137988	1137988	type	True	83.7705	1055	1833	95	below_threshold
Geodermatophilus saharensis	strain=DSM 45423	GCA_900188205.1	1137994	1137994	type	True	83.5344	1071	1833	95	below_threshold
Geodermatophilus normandii	strain=DSM 45417	GCA_003182485.1	1137989	1137989	type	True	83.316	1040	1833	95	below_threshold
Geodermatophilus daqingensis	strain=DSM 104001	GCA_013408985.1	2026353	2026353	type	True	82.6406	1058	1833	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:50:25,086] [INFO] DFAST Taxonomy check result was written to GCF_014191795.1_ASM1419179v1_genomic.fna/tc_result.tsv
[2024-01-25 18:50:25,087] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:50:25,087] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:50:25,087] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6db3a535-cea3-4fbc-a41d-9aeea425a01f/dqc_reference/checkm_data
[2024-01-25 18:50:25,088] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:50:25,139] [INFO] Task started: CheckM
[2024-01-25 18:50:25,139] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014191795.1_ASM1419179v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014191795.1_ASM1419179v1_genomic.fna/checkm_input GCF_014191795.1_ASM1419179v1_genomic.fna/checkm_result
[2024-01-25 18:51:58,566] [INFO] Task succeeded: CheckM
[2024-01-25 18:51:58,567] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:51:58,589] [INFO] ===== Completeness check finished =====
[2024-01-25 18:51:58,589] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:51:58,590] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014191795.1_ASM1419179v1_genomic.fna/markers.fasta)
[2024-01-25 18:51:58,590] [INFO] Task started: Blastn
[2024-01-25 18:51:58,590] [INFO] Running command: blastn -query GCF_014191795.1_ASM1419179v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6db3a535-cea3-4fbc-a41d-9aeea425a01f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014191795.1_ASM1419179v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:00,343] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:00,347] [INFO] Selected 16 target genomes.
[2024-01-25 18:52:00,347] [INFO] Target genome list was writen to GCF_014191795.1_ASM1419179v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:52:00,363] [INFO] Task started: fastANI
[2024-01-25 18:52:00,364] [INFO] Running command: fastANI --query /var/lib/cwl/stg69cc26d7-9928-4851-9a8b-18f66a687f1f/GCF_014191795.1_ASM1419179v1_genomic.fna.gz --refList GCF_014191795.1_ASM1419179v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014191795.1_ASM1419179v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:52:23,580] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:23,591] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:52:23,591] [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_900215145.1	s__Geodermatophilus sabuli	99.9971	1824	1833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900103785.1	s__Geodermatophilus siccatus	85.2572	1166	1833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104025.1	s__Geodermatophilus sp900104025	85.01	1126	1833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002802985.1	s__Geodermatophilus chilensis	84.9817	1024	1833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111455.1	s__Geodermatophilus poikilotrophus	84.9516	1135	1833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025345.1	s__Geodermatophilus obscurus	84.933	1153	1833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143215.1	s__Geodermatophilus obscurus_A	84.91	1145	1833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004571065.1	s__Geodermatophilus sp004571065	84.8502	952	1833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107105.1	s__Geodermatophilus africanus	84.7441	1138	1833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188375.1	s__Geodermatophilus pulveris	84.5179	1041	1833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124535.1	s__Geodermatophilus sp008124535	84.1392	1011	1833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002915.1	s__Geodermatophilus tzadiensis	83.7824	1052	1833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182485.1	s__Geodermatophilus normandii	83.3437	1036	1833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003319185.1	s__Blastococcus sp003319185	83.3281	968	1833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003319125.1	s__Geodermatophilus sp003319125	83.069	1006	1833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408985.1	s__Geodermatophilus_A daqingensis	82.6071	1062	1833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:52:23,593] [INFO] GTDB search result was written to GCF_014191795.1_ASM1419179v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:52:23,593] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:52:23,598] [INFO] DFAST_QC result json was written to GCF_014191795.1_ASM1419179v1_genomic.fna/dqc_result.json
[2024-01-25 18:52:23,598] [INFO] DFAST_QC completed!
[2024-01-25 18:52:23,598] [INFO] Total running time: 0h2m33s