[2024-01-24 13:28:11,886] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:11,889] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:11,889] [INFO] DQC Reference Directory: /var/lib/cwl/stg7827d282-667c-455a-99bc-17a090e835cc/dqc_reference
[2024-01-24 13:28:13,169] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:13,170] [INFO] Task started: Prodigal
[2024-01-24 13:28:13,170] [INFO] Running command: gunzip -c /var/lib/cwl/stg348ba759-197c-4974-a508-c48363500848/GCF_013868055.1_ASM1386805v1_genomic.fna.gz | prodigal -d GCF_013868055.1_ASM1386805v1_genomic.fna/cds.fna -a GCF_013868055.1_ASM1386805v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:22,219] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:22,220] [INFO] Task started: HMMsearch
[2024-01-24 13:28:22,221] [INFO] Running command: hmmsearch --tblout GCF_013868055.1_ASM1386805v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7827d282-667c-455a-99bc-17a090e835cc/dqc_reference/reference_markers.hmm GCF_013868055.1_ASM1386805v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:22,480] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:22,482] [INFO] Found 6/6 markers.
[2024-01-24 13:28:22,515] [INFO] Query marker FASTA was written to GCF_013868055.1_ASM1386805v1_genomic.fna/markers.fasta
[2024-01-24 13:28:22,515] [INFO] Task started: Blastn
[2024-01-24 13:28:22,515] [INFO] Running command: blastn -query GCF_013868055.1_ASM1386805v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7827d282-667c-455a-99bc-17a090e835cc/dqc_reference/reference_markers.fasta -out GCF_013868055.1_ASM1386805v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:23,137] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:23,141] [INFO] Selected 20 target genomes.
[2024-01-24 13:28:23,141] [INFO] Target genome list was writen to GCF_013868055.1_ASM1386805v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:23,154] [INFO] Task started: fastANI
[2024-01-24 13:28:23,154] [INFO] Running command: fastANI --query /var/lib/cwl/stg348ba759-197c-4974-a508-c48363500848/GCF_013868055.1_ASM1386805v1_genomic.fna.gz --refList GCF_013868055.1_ASM1386805v1_genomic.fna/target_genomes.txt --output GCF_013868055.1_ASM1386805v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:35,995] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:35,996] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7827d282-667c-455a-99bc-17a090e835cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:35,996] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7827d282-667c-455a-99bc-17a090e835cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:36,009] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:36,009] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:36,010] [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
Thermoactinomyces mirandus	strain=AMNI-1	GCA_013868055.1	2756294	2756294	type	True	100.0	1081	1084	95	conclusive
Thermoactinomyces vulgaris	strain=DSM 43016	GCA_003688725.1	2026	2026	type	True	77.8188	260	1084	95	below_threshold
Thermoactinomyces intermedius	strain=NRRL B-16979	GCA_013912365.1	2024	2024	type	True	77.701	272	1084	95	below_threshold
Laceyella sacchari	strain=DSM 43356	GCA_004343255.1	37482	37482	type	True	77.0291	74	1084	95	below_threshold
Laceyella sediminis	strain=RHA1	GCA_003003125.1	573074	573074	type	True	76.8712	78	1084	95	below_threshold
Thermoflavimicrobium dichotomicum	strain=DSM 44778	GCA_900114055.1	46223	46223	type	True	76.6132	61	1084	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:36,011] [INFO] DFAST Taxonomy check result was written to GCF_013868055.1_ASM1386805v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:36,012] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:36,012] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:36,013] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7827d282-667c-455a-99bc-17a090e835cc/dqc_reference/checkm_data
[2024-01-24 13:28:36,014] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:36,048] [INFO] Task started: CheckM
[2024-01-24 13:28:36,049] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013868055.1_ASM1386805v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013868055.1_ASM1386805v1_genomic.fna/checkm_input GCF_013868055.1_ASM1386805v1_genomic.fna/checkm_result
[2024-01-24 13:29:07,872] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:07,874] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:07,901] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:07,901] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:07,902] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013868055.1_ASM1386805v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:07,902] [INFO] Task started: Blastn
[2024-01-24 13:29:07,902] [INFO] Running command: blastn -query GCF_013868055.1_ASM1386805v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7827d282-667c-455a-99bc-17a090e835cc/dqc_reference/reference_markers_gtdb.fasta -out GCF_013868055.1_ASM1386805v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:08,697] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:08,701] [INFO] Selected 20 target genomes.
[2024-01-24 13:29:08,701] [INFO] Target genome list was writen to GCF_013868055.1_ASM1386805v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:08,925] [INFO] Task started: fastANI
[2024-01-24 13:29:08,925] [INFO] Running command: fastANI --query /var/lib/cwl/stg348ba759-197c-4974-a508-c48363500848/GCF_013868055.1_ASM1386805v1_genomic.fna.gz --refList GCF_013868055.1_ASM1386805v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013868055.1_ASM1386805v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:21,666] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:21,677] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:21,677] [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_013868055.1	s__Thermoactinomyces mirandus	100.0	1081	1084	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Thermoactinomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003688725.1	s__Thermoactinomyces vulgaris	77.8098	260	1084	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Thermoactinomyces	95.0	98.49	95.03	0.97	0.93	17	-
GCF_004343255.1	s__Laceyella sacchari	77.0291	74	1084	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Laceyella	95.237	96.84	96.83	0.94	0.94	3	-
GCF_003003125.1	s__Laceyella sediminis	76.8712	78	1084	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Laceyella	95.237	97.79	97.73	0.93	0.93	3	-
GCF_900114055.1	s__Thermoflavimicrobium dichotomicum	76.6132	61	1084	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Thermoflavimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:21,679] [INFO] GTDB search result was written to GCF_013868055.1_ASM1386805v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:21,680] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:21,695] [INFO] DFAST_QC result json was written to GCF_013868055.1_ASM1386805v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:21,695] [INFO] DFAST_QC completed!
[2024-01-24 13:29:21,695] [INFO] Total running time: 0h1m10s