[2023-06-29 14:21:59,741] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:21:59,743] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:21:59,744] [INFO] DQC Reference Directory: /var/lib/cwl/stg28c0b1e4-9199-4dae-b0c1-d5f936575831/dqc_reference
[2023-06-29 14:22:01,010] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:22:01,011] [INFO] Task started: Prodigal
[2023-06-29 14:22:01,011] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb6620cf-67a7-450f-8aa6-6eaf9ef1458f/GCA_021604925.1_ASM2160492v1_genomic.fna.gz | prodigal -d GCA_021604925.1_ASM2160492v1_genomic.fna/cds.fna -a GCA_021604925.1_ASM2160492v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:22:09,689] [INFO] Task succeeded: Prodigal
[2023-06-29 14:22:09,689] [INFO] Task started: HMMsearch
[2023-06-29 14:22:09,689] [INFO] Running command: hmmsearch --tblout GCA_021604925.1_ASM2160492v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28c0b1e4-9199-4dae-b0c1-d5f936575831/dqc_reference/reference_markers.hmm GCA_021604925.1_ASM2160492v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:22:09,969] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:22:09,970] [INFO] Found 6/6 markers.
[2023-06-29 14:22:10,001] [INFO] Query marker FASTA was written to GCA_021604925.1_ASM2160492v1_genomic.fna/markers.fasta
[2023-06-29 14:22:10,002] [INFO] Task started: Blastn
[2023-06-29 14:22:10,002] [INFO] Running command: blastn -query GCA_021604925.1_ASM2160492v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28c0b1e4-9199-4dae-b0c1-d5f936575831/dqc_reference/reference_markers.fasta -out GCA_021604925.1_ASM2160492v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:22:10,668] [INFO] Task succeeded: Blastn
[2023-06-29 14:22:10,680] [INFO] Selected 32 target genomes.
[2023-06-29 14:22:10,681] [INFO] Target genome list was writen to GCA_021604925.1_ASM2160492v1_genomic.fna/target_genomes.txt
[2023-06-29 14:22:10,685] [INFO] Task started: fastANI
[2023-06-29 14:22:10,685] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb6620cf-67a7-450f-8aa6-6eaf9ef1458f/GCA_021604925.1_ASM2160492v1_genomic.fna.gz --refList GCA_021604925.1_ASM2160492v1_genomic.fna/target_genomes.txt --output GCA_021604925.1_ASM2160492v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:22:38,007] [INFO] Task succeeded: fastANI
[2023-06-29 14:22:38,008] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28c0b1e4-9199-4dae-b0c1-d5f936575831/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:22:38,008] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28c0b1e4-9199-4dae-b0c1-d5f936575831/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:22:38,020] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:22:38,021] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 14:22:38,021] [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
Longimicrobium terrae	strain=CECT 8660	GCA_014198875.1	1639882	1639882	type	True	75.2399	50	863	95	below_threshold
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	75.2399	50	863	95	below_threshold
Longimicrobium terrae	strain=DSM 29007	GCA_014202995.1	1639882	1639882	type	True	75.2399	50	863	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.0533	60	863	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	74.9953	64	863	95	below_threshold
Myxococcus stipitatus	strain=DSM 14675	GCA_000331735.1	83455	83455	neotype	True	74.9606	70	863	95	below_threshold
Corallococcus coralloides	strain=DSM 2259	GCA_000255295.1	184914	184914	type	True	74.9453	83	863	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	74.8868	82	863	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:22:38,023] [INFO] DFAST Taxonomy check result was written to GCA_021604925.1_ASM2160492v1_genomic.fna/tc_result.tsv
[2023-06-29 14:22:38,024] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:22:38,024] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:22:38,024] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28c0b1e4-9199-4dae-b0c1-d5f936575831/dqc_reference/checkm_data
[2023-06-29 14:22:38,025] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:22:38,061] [INFO] Task started: CheckM
[2023-06-29 14:22:38,061] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021604925.1_ASM2160492v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021604925.1_ASM2160492v1_genomic.fna/checkm_input GCA_021604925.1_ASM2160492v1_genomic.fna/checkm_result
[2023-06-29 14:23:07,626] [INFO] Task succeeded: CheckM
[2023-06-29 14:23:07,627] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:23:07,652] [INFO] ===== Completeness check finished =====
[2023-06-29 14:23:07,652] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:23:07,653] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021604925.1_ASM2160492v1_genomic.fna/markers.fasta)
[2023-06-29 14:23:07,653] [INFO] Task started: Blastn
[2023-06-29 14:23:07,653] [INFO] Running command: blastn -query GCA_021604925.1_ASM2160492v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28c0b1e4-9199-4dae-b0c1-d5f936575831/dqc_reference/reference_markers_gtdb.fasta -out GCA_021604925.1_ASM2160492v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:23:08,653] [INFO] Task succeeded: Blastn
[2023-06-29 14:23:08,659] [INFO] Selected 38 target genomes.
[2023-06-29 14:23:08,659] [INFO] Target genome list was writen to GCA_021604925.1_ASM2160492v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:23:08,673] [INFO] Task started: fastANI
[2023-06-29 14:23:08,673] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb6620cf-67a7-450f-8aa6-6eaf9ef1458f/GCA_021604925.1_ASM2160492v1_genomic.fna.gz --refList GCA_021604925.1_ASM2160492v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021604925.1_ASM2160492v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:23:36,861] [INFO] Task succeeded: fastANI
[2023-06-29 14:23:36,871] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 14:23:36,871] [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_016235265.1	s__JACRLI01 sp016235265	75.6012	50	863	d__Bacteria;p__Eisenbacteria;c__RBG-16-71-46;o__RBG-16-71-46;f__JACRLI01;g__JACRLI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016215625.1	s__CAIXRL01 sp016215625	75.2034	52	863	d__Bacteria;p__Eisenbacteria;c__RBG-16-71-46;o__RBG-16-71-46;f__RBG-16-71-46;g__CAIXRL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011357805.1	s__DSQF01 sp011357805	75.2032	53	863	d__Bacteria;p__Eisenbacteria;c__RBG-16-71-46;o__RBG-16-71-46;f__RBG-16-71-46;g__DSQF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717005.1	s__UBA2376 sp016717005	74.6879	85	863	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 14:23:36,873] [INFO] GTDB search result was written to GCA_021604925.1_ASM2160492v1_genomic.fna/result_gtdb.tsv
[2023-06-29 14:23:36,874] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:23:36,877] [INFO] DFAST_QC result json was written to GCA_021604925.1_ASM2160492v1_genomic.fna/dqc_result.json
[2023-06-29 14:23:36,877] [INFO] DFAST_QC completed!
[2023-06-29 14:23:36,877] [INFO] Total running time: 0h1m37s