[2023-06-14 01:47:41,591] [INFO] DFAST_QC pipeline started.
[2023-06-14 01:47:41,594] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 01:47:41,595] [INFO] DQC Reference Directory: /var/lib/cwl/stg0397d708-d366-462d-bb62-febe1c96d3d2/dqc_reference
[2023-06-14 01:47:42,974] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 01:47:42,975] [INFO] Task started: Prodigal
[2023-06-14 01:47:42,976] [INFO] Running command: gunzip -c /var/lib/cwl/stga1e97a3e-0da6-4b53-be6a-f922b49bc3e8/GCA_022739055.1_ASM2273905v1_genomic.fna.gz | prodigal -d GCA_022739055.1_ASM2273905v1_genomic.fna/cds.fna -a GCA_022739055.1_ASM2273905v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 01:47:47,441] [INFO] Task succeeded: Prodigal
[2023-06-14 01:47:47,442] [INFO] Task started: HMMsearch
[2023-06-14 01:47:47,442] [INFO] Running command: hmmsearch --tblout GCA_022739055.1_ASM2273905v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0397d708-d366-462d-bb62-febe1c96d3d2/dqc_reference/reference_markers.hmm GCA_022739055.1_ASM2273905v1_genomic.fna/protein.faa > /dev/null
[2023-06-14 01:47:47,651] [INFO] Task succeeded: HMMsearch
[2023-06-14 01:47:47,652] [INFO] Found 6/6 markers.
[2023-06-14 01:47:47,680] [INFO] Query marker FASTA was written to GCA_022739055.1_ASM2273905v1_genomic.fna/markers.fasta
[2023-06-14 01:47:47,680] [INFO] Task started: Blastn
[2023-06-14 01:47:47,680] [INFO] Running command: blastn -query GCA_022739055.1_ASM2273905v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0397d708-d366-462d-bb62-febe1c96d3d2/dqc_reference/reference_markers.fasta -out GCA_022739055.1_ASM2273905v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:47:48,343] [INFO] Task succeeded: Blastn
[2023-06-14 01:47:48,347] [INFO] Selected 17 target genomes.
[2023-06-14 01:47:48,348] [INFO] Target genome list was writen to GCA_022739055.1_ASM2273905v1_genomic.fna/target_genomes.txt
[2023-06-14 01:47:48,354] [INFO] Task started: fastANI
[2023-06-14 01:47:48,354] [INFO] Running command: fastANI --query /var/lib/cwl/stga1e97a3e-0da6-4b53-be6a-f922b49bc3e8/GCA_022739055.1_ASM2273905v1_genomic.fna.gz --refList GCA_022739055.1_ASM2273905v1_genomic.fna/target_genomes.txt --output GCA_022739055.1_ASM2273905v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 01:47:58,357] [INFO] Task succeeded: fastANI
[2023-06-14 01:47:58,357] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0397d708-d366-462d-bb62-febe1c96d3d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 01:47:58,358] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0397d708-d366-462d-bb62-febe1c96d3d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 01:47:58,359] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-14 01:47:58,359] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-14 01:47:58,360] [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
--------------------------------------------------------------------------------
[2023-06-14 01:47:58,361] [INFO] DFAST Taxonomy check result was written to GCA_022739055.1_ASM2273905v1_genomic.fna/tc_result.tsv
[2023-06-14 01:47:58,362] [INFO] ===== Taxonomy check completed =====
[2023-06-14 01:47:58,362] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 01:47:58,362] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0397d708-d366-462d-bb62-febe1c96d3d2/dqc_reference/checkm_data
[2023-06-14 01:47:58,365] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 01:47:58,390] [INFO] Task started: CheckM
[2023-06-14 01:47:58,390] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022739055.1_ASM2273905v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022739055.1_ASM2273905v1_genomic.fna/checkm_input GCA_022739055.1_ASM2273905v1_genomic.fna/checkm_result
[2023-06-14 01:48:19,727] [INFO] Task succeeded: CheckM
[2023-06-14 01:48:19,728] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-14 01:48:19,749] [INFO] ===== Completeness check finished =====
[2023-06-14 01:48:19,750] [INFO] ===== Start GTDB Search =====
[2023-06-14 01:48:19,750] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022739055.1_ASM2273905v1_genomic.fna/markers.fasta)
[2023-06-14 01:48:19,751] [INFO] Task started: Blastn
[2023-06-14 01:48:19,751] [INFO] Running command: blastn -query GCA_022739055.1_ASM2273905v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0397d708-d366-462d-bb62-febe1c96d3d2/dqc_reference/reference_markers_gtdb.fasta -out GCA_022739055.1_ASM2273905v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:48:20,836] [INFO] Task succeeded: Blastn
[2023-06-14 01:48:20,840] [INFO] Selected 20 target genomes.
[2023-06-14 01:48:20,840] [INFO] Target genome list was writen to GCA_022739055.1_ASM2273905v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 01:48:20,852] [INFO] Task started: fastANI
[2023-06-14 01:48:20,853] [INFO] Running command: fastANI --query /var/lib/cwl/stga1e97a3e-0da6-4b53-be6a-f922b49bc3e8/GCA_022739055.1_ASM2273905v1_genomic.fna.gz --refList GCA_022739055.1_ASM2273905v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022739055.1_ASM2273905v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 01:48:27,777] [INFO] Task succeeded: fastANI
[2023-06-14 01:48:27,797] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-14 01:48:27,798] [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_000432435.1	s__Fimenecus sp000432435	98.329	558	621	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Fimenecus	95.0	98.55	98.08	0.94	0.85	30	conclusive
GCA_002437245.1	s__Fimenecus sp002437245	89.6801	519	621	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Fimenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004556705.1	s__Fimenecus sp004556705	79.2848	141	621	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Fimenecus	95.0	96.73	95.72	0.84	0.76	9	-
GCA_017438845.1	s__Fimenecus sp017438845	77.1271	90	621	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Fimenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315985.1	s__Fimenecus sp900315985	77.115	94	621	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Fimenecus	95.0	97.95	96.57	0.90	0.84	11	-
GCA_018712805.1	s__Fimenecus excrementavium	77.0843	68	621	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Fimenecus	95.0	98.06	98.06	0.85	0.85	2	-
GCA_002361875.1	s__Fimenecus sp002361875	77.0248	67	621	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Fimenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002490525.1	s__Fimenecus sp002490525	76.943	52	621	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Fimenecus	95.0	99.95	99.94	0.93	0.88	4	-
GCA_015066635.1	s__Fimenecus sp015066635	76.8579	83	621	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Fimenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540295.1	s__Fimenecus sp900540295	76.8165	74	621	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Fimenecus	95.0	98.52	98.30	0.90	0.86	3	-
GCA_015066565.1	s__SIG554 sp015066565	76.7165	75	621	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__SIG554	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017613735.1	s__SIG554 sp017613735	76.4929	67	621	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__SIG554	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-14 01:48:27,801] [INFO] GTDB search result was written to GCA_022739055.1_ASM2273905v1_genomic.fna/result_gtdb.tsv
[2023-06-14 01:48:27,801] [INFO] ===== GTDB Search completed =====
[2023-06-14 01:48:27,806] [INFO] DFAST_QC result json was written to GCA_022739055.1_ASM2273905v1_genomic.fna/dqc_result.json
[2023-06-14 01:48:27,807] [INFO] DFAST_QC completed!
[2023-06-14 01:48:27,807] [INFO] Total running time: 0h0m46s