[2024-01-24 14:19:01,956] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:01,959] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:01,959] [INFO] DQC Reference Directory: /var/lib/cwl/stg67c211e6-7ab4-4ce0-84a4-fb274ccdb2b1/dqc_reference
[2024-01-24 14:19:03,209] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:03,210] [INFO] Task started: Prodigal
[2024-01-24 14:19:03,211] [INFO] Running command: gunzip -c /var/lib/cwl/stg59ae7bfe-c15a-43d8-8655-9d38003e589e/GCF_000021685.1_ASM2168v1_genomic.fna.gz | prodigal -d GCF_000021685.1_ASM2168v1_genomic.fna/cds.fna -a GCF_000021685.1_ASM2168v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:11,883] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:11,883] [INFO] Task started: HMMsearch
[2024-01-24 14:19:11,884] [INFO] Running command: hmmsearch --tblout GCF_000021685.1_ASM2168v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67c211e6-7ab4-4ce0-84a4-fb274ccdb2b1/dqc_reference/reference_markers.hmm GCF_000021685.1_ASM2168v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:12,129] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:12,130] [INFO] Found 6/6 markers.
[2024-01-24 14:19:12,167] [INFO] Query marker FASTA was written to GCF_000021685.1_ASM2168v1_genomic.fna/markers.fasta
[2024-01-24 14:19:12,167] [INFO] Task started: Blastn
[2024-01-24 14:19:12,167] [INFO] Running command: blastn -query GCF_000021685.1_ASM2168v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67c211e6-7ab4-4ce0-84a4-fb274ccdb2b1/dqc_reference/reference_markers.fasta -out GCF_000021685.1_ASM2168v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:12,784] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:12,787] [INFO] Selected 16 target genomes.
[2024-01-24 14:19:12,788] [INFO] Target genome list was writen to GCF_000021685.1_ASM2168v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:12,827] [INFO] Task started: fastANI
[2024-01-24 14:19:12,827] [INFO] Running command: fastANI --query /var/lib/cwl/stg59ae7bfe-c15a-43d8-8655-9d38003e589e/GCF_000021685.1_ASM2168v1_genomic.fna.gz --refList GCF_000021685.1_ASM2168v1_genomic.fna/target_genomes.txt --output GCF_000021685.1_ASM2168v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:24,539] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:24,540] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67c211e6-7ab4-4ce0-84a4-fb274ccdb2b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:24,540] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67c211e6-7ab4-4ce0-84a4-fb274ccdb2b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:24,544] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:24,544] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:24,545] [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
Thermomicrobium roseum	strain=DSM 5159	GCA_000021685.1	500	500	type	True	100.0	972	972	95	conclusive
Sphaerobacter thermophilus	strain=DSM 20745	GCA_000024985.1	2057	2057	type	True	76.2617	72	972	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:24,546] [INFO] DFAST Taxonomy check result was written to GCF_000021685.1_ASM2168v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:24,547] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:24,547] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:24,547] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67c211e6-7ab4-4ce0-84a4-fb274ccdb2b1/dqc_reference/checkm_data
[2024-01-24 14:19:24,548] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:24,581] [INFO] Task started: CheckM
[2024-01-24 14:19:24,581] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000021685.1_ASM2168v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000021685.1_ASM2168v1_genomic.fna/checkm_input GCF_000021685.1_ASM2168v1_genomic.fna/checkm_result
[2024-01-24 14:19:56,853] [INFO] Task succeeded: CheckM
[2024-01-24 14:19:56,854] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:19:56,885] [INFO] ===== Completeness check finished =====
[2024-01-24 14:19:56,885] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:19:56,885] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000021685.1_ASM2168v1_genomic.fna/markers.fasta)
[2024-01-24 14:19:56,886] [INFO] Task started: Blastn
[2024-01-24 14:19:56,886] [INFO] Running command: blastn -query GCF_000021685.1_ASM2168v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67c211e6-7ab4-4ce0-84a4-fb274ccdb2b1/dqc_reference/reference_markers_gtdb.fasta -out GCF_000021685.1_ASM2168v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:57,817] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:57,820] [INFO] Selected 19 target genomes.
[2024-01-24 14:19:57,821] [INFO] Target genome list was writen to GCF_000021685.1_ASM2168v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:19:57,842] [INFO] Task started: fastANI
[2024-01-24 14:19:57,842] [INFO] Running command: fastANI --query /var/lib/cwl/stg59ae7bfe-c15a-43d8-8655-9d38003e589e/GCF_000021685.1_ASM2168v1_genomic.fna.gz --refList GCF_000021685.1_ASM2168v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000021685.1_ASM2168v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:08,372] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:08,385] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:08,385] [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_000021685.1	s__Thermomicrobium roseum	100.0	972	972	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermomicrobiales;f__Thermomicrobiaceae;g__Thermomicrobium	95.0	98.52	98.29	0.96	0.94	6	conclusive
GCA_002898975.1	s__Thermomicrobium sp002898975	78.5836	215	972	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermomicrobiales;f__Thermomicrobiaceae;g__Thermomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002898255.1	s__Thermomicrobium sp002898255	77.2061	274	972	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermomicrobiales;f__Thermomicrobiaceae;g__Thermomicrobium	95.0	99.11	99.09	0.97	0.97	4	-
GCA_002898875.1	s__HRBIN26 sp002898875	76.8108	136	972	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermomicrobiales;f__Thermomicrobiaceae;g__HRBIN26	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014874455.1	s__HRBIN26 sp014874455	76.6121	177	972	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermomicrobiales;f__Thermomicrobiaceae;g__HRBIN26	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024985.1	s__Sphaerobacter thermophilus	76.3694	75	972	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermomicrobiales;f__Thermomicrobiaceae;g__Sphaerobacter	95.0	99.04	99.02	0.92	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:08,387] [INFO] GTDB search result was written to GCF_000021685.1_ASM2168v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:08,388] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:08,391] [INFO] DFAST_QC result json was written to GCF_000021685.1_ASM2168v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:08,391] [INFO] DFAST_QC completed!
[2024-01-24 14:20:08,391] [INFO] Total running time: 0h1m6s