[2024-01-24 13:57:32,276] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:32,278] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:32,278] [INFO] DQC Reference Directory: /var/lib/cwl/stg7aeddc0a-6ea8-47ab-8a83-429cb8ee09d6/dqc_reference
[2024-01-24 13:57:33,625] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:33,626] [INFO] Task started: Prodigal
[2024-01-24 13:57:33,626] [INFO] Running command: gunzip -c /var/lib/cwl/stg094d91e4-2517-4037-ba88-be2ac2e607c2/GCF_011492945.1_ASM1149294v1_genomic.fna.gz | prodigal -d GCF_011492945.1_ASM1149294v1_genomic.fna/cds.fna -a GCF_011492945.1_ASM1149294v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:46,129] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:46,129] [INFO] Task started: HMMsearch
[2024-01-24 13:57:46,129] [INFO] Running command: hmmsearch --tblout GCF_011492945.1_ASM1149294v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7aeddc0a-6ea8-47ab-8a83-429cb8ee09d6/dqc_reference/reference_markers.hmm GCF_011492945.1_ASM1149294v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:46,400] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:46,402] [INFO] Found 6/6 markers.
[2024-01-24 13:57:46,442] [INFO] Query marker FASTA was written to GCF_011492945.1_ASM1149294v1_genomic.fna/markers.fasta
[2024-01-24 13:57:46,442] [INFO] Task started: Blastn
[2024-01-24 13:57:46,442] [INFO] Running command: blastn -query GCF_011492945.1_ASM1149294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7aeddc0a-6ea8-47ab-8a83-429cb8ee09d6/dqc_reference/reference_markers.fasta -out GCF_011492945.1_ASM1149294v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:47,136] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:47,139] [INFO] Selected 13 target genomes.
[2024-01-24 13:57:47,139] [INFO] Target genome list was writen to GCF_011492945.1_ASM1149294v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:47,144] [INFO] Task started: fastANI
[2024-01-24 13:57:47,144] [INFO] Running command: fastANI --query /var/lib/cwl/stg094d91e4-2517-4037-ba88-be2ac2e607c2/GCF_011492945.1_ASM1149294v1_genomic.fna.gz --refList GCF_011492945.1_ASM1149294v1_genomic.fna/target_genomes.txt --output GCF_011492945.1_ASM1149294v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:01,063] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:01,063] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7aeddc0a-6ea8-47ab-8a83-429cb8ee09d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:01,063] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7aeddc0a-6ea8-47ab-8a83-429cb8ee09d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:01,075] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:01,075] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:01,075] [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
Rubrobacter tropicus	strain=SCSIO 52909	GCA_011492945.1	2653851	2653851	type	True	100.0	1527	1527	95	conclusive
Rubrobacter marinus	strain=SCSIO 52915	GCA_011492965.1	2653852	2653852	type	True	79.0002	548	1527	95	below_threshold
Rubrobacter radiotolerans	strain=DSM 5868	GCA_900175965.1	42256	42256	type	True	77.8257	337	1527	95	below_threshold
Rubrobacter aplysinae	strain=RV113	GCA_001029505.1	909625	909625	type	True	77.6124	297	1527	95	below_threshold
Rubrobacter indicoceani	strain=SCSIO 08198	GCA_003568865.1	2051957	2051957	type	True	77.1432	247	1527	95	below_threshold
Streptomyces decoyicus	strain=NRRL 2666	GCA_001270575.1	249567	249567	type	True	75.2727	112	1527	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	75.2086	130	1527	95	below_threshold
Actinoplanes utahensis	strain=NBRC 13244	GCA_016862455.1	1869	1869	type	True	74.9944	130	1527	95	below_threshold
Actinomadura viridis	strain=DSM 43175	GCA_015751755.1	58110	58110	type	True	74.9765	138	1527	95	below_threshold
Deinococcus metalli	strain=DSM 27521	GCA_014201805.1	1141878	1141878	type	True	74.9632	58	1527	95	below_threshold
Thermomonospora echinospora	strain=DSM 43163	GCA_900108175.1	1992	1992	type	True	74.9284	127	1527	95	below_threshold
Streptomyces sedi	strain=JCM 16909	GCA_006335015.1	555059	555059	type	True	74.9052	107	1527	95	below_threshold
Streptomyces radicis	strain=DS1-2	GCA_003626575.1	1750517	1750517	type	True	74.8121	137	1527	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:01,077] [INFO] DFAST Taxonomy check result was written to GCF_011492945.1_ASM1149294v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:01,078] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:01,078] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:01,078] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7aeddc0a-6ea8-47ab-8a83-429cb8ee09d6/dqc_reference/checkm_data
[2024-01-24 13:58:01,079] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:01,124] [INFO] Task started: CheckM
[2024-01-24 13:58:01,124] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011492945.1_ASM1149294v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011492945.1_ASM1149294v1_genomic.fna/checkm_input GCF_011492945.1_ASM1149294v1_genomic.fna/checkm_result
[2024-01-24 13:58:37,329] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:37,332] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:37,365] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:37,365] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:37,366] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011492945.1_ASM1149294v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:37,366] [INFO] Task started: Blastn
[2024-01-24 13:58:37,366] [INFO] Running command: blastn -query GCF_011492945.1_ASM1149294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7aeddc0a-6ea8-47ab-8a83-429cb8ee09d6/dqc_reference/reference_markers_gtdb.fasta -out GCF_011492945.1_ASM1149294v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:38,382] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:38,385] [INFO] Selected 8 target genomes.
[2024-01-24 13:58:38,385] [INFO] Target genome list was writen to GCF_011492945.1_ASM1149294v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:38,401] [INFO] Task started: fastANI
[2024-01-24 13:58:38,401] [INFO] Running command: fastANI --query /var/lib/cwl/stg094d91e4-2517-4037-ba88-be2ac2e607c2/GCF_011492945.1_ASM1149294v1_genomic.fna.gz --refList GCF_011492945.1_ASM1149294v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011492945.1_ASM1149294v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:46,034] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:46,042] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:46,043] [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_011492945.1	s__SCSIO-52909 sp011492945	100.0	1527	1527	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902806085.1	s__SCSIO-52909 sp902806085	85.1787	915	1527	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013815575.1	s__SCSIO-52909 sp013815575	84.2976	476	1527	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	97.69	97.69	0.64	0.64	2	-
GCA_902805975.1	s__SCSIO-52909 sp902805975	83.6028	706	1527	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805985.1	s__SCSIO-52909 sp902805985	83.5718	641	1527	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806015.1	s__SCSIO-52909 sp902806015	83.4287	601	1527	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016781725.1	s__SCSIO-52909 sp016781725	79.9969	403	1527	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	98.84	98.84	0.72	0.72	2	-
GCA_013812245.1	s__JACDGB01 sp013812245	78.3881	330	1527	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__JACDGB01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:46,046] [INFO] GTDB search result was written to GCF_011492945.1_ASM1149294v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:46,048] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:46,053] [INFO] DFAST_QC result json was written to GCF_011492945.1_ASM1149294v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:46,054] [INFO] DFAST_QC completed!
[2024-01-24 13:58:46,054] [INFO] Total running time: 0h1m14s