[2023-07-01 06:51:05,563] [INFO] DFAST_QC pipeline started.
[2023-07-01 06:51:05,566] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 06:51:05,566] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d846e4d-941c-409b-a064-3f8d9a2975c5/dqc_reference
[2023-07-01 06:51:06,864] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 06:51:06,864] [INFO] Task started: Prodigal
[2023-07-01 06:51:06,865] [INFO] Running command: gunzip -c /var/lib/cwl/stg99402e67-4a51-46bf-b52f-b6620169adcc/GCA_024636005.1_ASM2463600v1_genomic.fna.gz | prodigal -d GCA_024636005.1_ASM2463600v1_genomic.fna/cds.fna -a GCA_024636005.1_ASM2463600v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 06:51:12,674] [INFO] Task succeeded: Prodigal
[2023-07-01 06:51:12,675] [INFO] Task started: HMMsearch
[2023-07-01 06:51:12,675] [INFO] Running command: hmmsearch --tblout GCA_024636005.1_ASM2463600v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d846e4d-941c-409b-a064-3f8d9a2975c5/dqc_reference/reference_markers.hmm GCA_024636005.1_ASM2463600v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 06:51:12,927] [INFO] Task succeeded: HMMsearch
[2023-07-01 06:51:12,929] [INFO] Found 6/6 markers.
[2023-07-01 06:51:12,988] [INFO] Query marker FASTA was written to GCA_024636005.1_ASM2463600v1_genomic.fna/markers.fasta
[2023-07-01 06:51:12,989] [INFO] Task started: Blastn
[2023-07-01 06:51:12,989] [INFO] Running command: blastn -query GCA_024636005.1_ASM2463600v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d846e4d-941c-409b-a064-3f8d9a2975c5/dqc_reference/reference_markers.fasta -out GCA_024636005.1_ASM2463600v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 06:51:13,577] [INFO] Task succeeded: Blastn
[2023-07-01 06:51:13,600] [INFO] Selected 25 target genomes.
[2023-07-01 06:51:13,601] [INFO] Target genome list was writen to GCA_024636005.1_ASM2463600v1_genomic.fna/target_genomes.txt
[2023-07-01 06:51:13,608] [INFO] Task started: fastANI
[2023-07-01 06:51:13,609] [INFO] Running command: fastANI --query /var/lib/cwl/stg99402e67-4a51-46bf-b52f-b6620169adcc/GCA_024636005.1_ASM2463600v1_genomic.fna.gz --refList GCA_024636005.1_ASM2463600v1_genomic.fna/target_genomes.txt --output GCA_024636005.1_ASM2463600v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 06:51:27,059] [INFO] Task succeeded: fastANI
[2023-07-01 06:51:27,059] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d846e4d-941c-409b-a064-3f8d9a2975c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 06:51:27,060] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d846e4d-941c-409b-a064-3f8d9a2975c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 06:51:27,064] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 06:51:27,064] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 06:51:27,065] [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
Fusibacter tunisiensis	strain=DSM 24436	GCA_016908355.1	1008308	1008308	type	True	77.4635	73	758	95	below_threshold
Fusibacter ferrireducens	strain=Q10-2	GCA_015352425.1	2785058	2785058	type	True	77.1411	58	758	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 06:51:27,067] [INFO] DFAST Taxonomy check result was written to GCA_024636005.1_ASM2463600v1_genomic.fna/tc_result.tsv
[2023-07-01 06:51:27,067] [INFO] ===== Taxonomy check completed =====
[2023-07-01 06:51:27,067] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 06:51:27,068] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d846e4d-941c-409b-a064-3f8d9a2975c5/dqc_reference/checkm_data
[2023-07-01 06:51:27,069] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 06:51:27,101] [INFO] Task started: CheckM
[2023-07-01 06:51:27,101] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024636005.1_ASM2463600v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024636005.1_ASM2463600v1_genomic.fna/checkm_input GCA_024636005.1_ASM2463600v1_genomic.fna/checkm_result
[2023-07-01 06:51:52,444] [INFO] Task succeeded: CheckM
[2023-07-01 06:51:52,446] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 06:51:52,467] [INFO] ===== Completeness check finished =====
[2023-07-01 06:51:52,468] [INFO] ===== Start GTDB Search =====
[2023-07-01 06:51:52,468] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024636005.1_ASM2463600v1_genomic.fna/markers.fasta)
[2023-07-01 06:51:52,469] [INFO] Task started: Blastn
[2023-07-01 06:51:52,469] [INFO] Running command: blastn -query GCA_024636005.1_ASM2463600v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d846e4d-941c-409b-a064-3f8d9a2975c5/dqc_reference/reference_markers_gtdb.fasta -out GCA_024636005.1_ASM2463600v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 06:51:53,297] [INFO] Task succeeded: Blastn
[2023-07-01 06:51:53,302] [INFO] Selected 19 target genomes.
[2023-07-01 06:51:53,302] [INFO] Target genome list was writen to GCA_024636005.1_ASM2463600v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 06:51:53,331] [INFO] Task started: fastANI
[2023-07-01 06:51:53,332] [INFO] Running command: fastANI --query /var/lib/cwl/stg99402e67-4a51-46bf-b52f-b6620169adcc/GCA_024636005.1_ASM2463600v1_genomic.fna.gz --refList GCA_024636005.1_ASM2463600v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024636005.1_ASM2463600v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 06:52:03,644] [INFO] Task succeeded: fastANI
[2023-07-01 06:52:03,653] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-07-01 06:52:03,654] [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
GCA_014859095.1	s__Fusibacter_C sp014859095	84.1895	529	758	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Acidaminobacteraceae;g__Fusibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002412775.1	s__Fusibacter_C sp002412775	84.0656	511	758	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Acidaminobacteraceae;g__Fusibacter_C	95.0	99.85	99.85	0.95	0.95	2	-
GCF_001748365.1	s__Fusibacter_A sp001748365	77.7198	67	758	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Acidaminobacteraceae;g__Fusibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908355.1	s__Fusibacter_C tunisiensis	77.4635	73	758	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Acidaminobacteraceae;g__Fusibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003482695.1	s__Fusibacter_C sp003482695	76.5228	57	758	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Acidaminobacteraceae;g__Fusibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 06:52:03,656] [INFO] GTDB search result was written to GCA_024636005.1_ASM2463600v1_genomic.fna/result_gtdb.tsv
[2023-07-01 06:52:03,656] [INFO] ===== GTDB Search completed =====
[2023-07-01 06:52:03,659] [INFO] DFAST_QC result json was written to GCA_024636005.1_ASM2463600v1_genomic.fna/dqc_result.json
[2023-07-01 06:52:03,660] [INFO] DFAST_QC completed!
[2023-07-01 06:52:03,660] [INFO] Total running time: 0h0m58s