[2023-06-29 19:34:24,579] [INFO] DFAST_QC pipeline started.
[2023-06-29 19:34:24,582] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 19:34:24,582] [INFO] DQC Reference Directory: /var/lib/cwl/stgeec3b401-a1a2-4199-aa32-e39e4adae534/dqc_reference
[2023-06-29 19:34:26,002] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 19:34:26,002] [INFO] Task started: Prodigal
[2023-06-29 19:34:26,003] [INFO] Running command: gunzip -c /var/lib/cwl/stg5eeb66b3-9599-41f3-82c6-c0e9234e4238/GCA_023418035.1_ASM2341803v1_genomic.fna.gz | prodigal -d GCA_023418035.1_ASM2341803v1_genomic.fna/cds.fna -a GCA_023418035.1_ASM2341803v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 19:34:42,393] [INFO] Task succeeded: Prodigal
[2023-06-29 19:34:42,393] [INFO] Task started: HMMsearch
[2023-06-29 19:34:42,394] [INFO] Running command: hmmsearch --tblout GCA_023418035.1_ASM2341803v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeec3b401-a1a2-4199-aa32-e39e4adae534/dqc_reference/reference_markers.hmm GCA_023418035.1_ASM2341803v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 19:34:42,730] [INFO] Task succeeded: HMMsearch
[2023-06-29 19:34:42,732] [INFO] Found 6/6 markers.
[2023-06-29 19:34:42,784] [INFO] Query marker FASTA was written to GCA_023418035.1_ASM2341803v1_genomic.fna/markers.fasta
[2023-06-29 19:34:42,784] [INFO] Task started: Blastn
[2023-06-29 19:34:42,785] [INFO] Running command: blastn -query GCA_023418035.1_ASM2341803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeec3b401-a1a2-4199-aa32-e39e4adae534/dqc_reference/reference_markers.fasta -out GCA_023418035.1_ASM2341803v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:34:43,614] [INFO] Task succeeded: Blastn
[2023-06-29 19:34:43,619] [INFO] Selected 19 target genomes.
[2023-06-29 19:34:43,620] [INFO] Target genome list was writen to GCA_023418035.1_ASM2341803v1_genomic.fna/target_genomes.txt
[2023-06-29 19:34:43,622] [INFO] Task started: fastANI
[2023-06-29 19:34:43,623] [INFO] Running command: fastANI --query /var/lib/cwl/stg5eeb66b3-9599-41f3-82c6-c0e9234e4238/GCA_023418035.1_ASM2341803v1_genomic.fna.gz --refList GCA_023418035.1_ASM2341803v1_genomic.fna/target_genomes.txt --output GCA_023418035.1_ASM2341803v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 19:34:58,538] [INFO] Task succeeded: fastANI
[2023-06-29 19:34:58,538] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeec3b401-a1a2-4199-aa32-e39e4adae534/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 19:34:58,539] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeec3b401-a1a2-4199-aa32-e39e4adae534/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 19:34:58,553] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 19:34:58,553] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 19:34:58,553] [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
Povalibacter uvarum	strain=DSM 26723	GCA_014202975.1	732238	732238	type	True	78.7255	557	1747	95	below_threshold
Steroidobacter soli	strain=JW-3	GCA_004138485.1	2497877	2497877	type	True	78.0396	414	1747	95	below_threshold
Steroidobacter agaridevorans	strain=SA29-B	GCA_009932555.1	2695856	2695856	type	True	78.0284	428	1747	95	below_threshold
Steroidobacter agariperforans	strain=KA5-B	GCA_004138335.1	268404	268404	type	True	77.8403	410	1747	95	below_threshold
Steroidobacter gossypii	strain=S1-65	GCA_016801985.1	2805490	2805490	type	True	77.7624	380	1747	95	below_threshold
Steroidobacter cummioxidans	strain=35Y	GCA_003104955.1	1803913	1803913	type	True	77.5756	415	1747	95	below_threshold
Steroidobacter denitrificans	strain=DSM 18526	GCA_001579945.1	465721	465721	type	True	76.9785	157	1747	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	76.0858	75	1747	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	76.0062	57	1747	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	75.9787	58	1747	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	75.7456	63	1747	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	75.728	50	1747	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	75.5918	70	1747	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	75.5531	68	1747	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	75.5323	70	1747	95	below_threshold
Dokdonella immobilis	strain=CGMCC 1.7659	GCA_900115085.1	578942	578942	type	True	75.4524	81	1747	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	75.147	60	1747	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 19:34:58,555] [INFO] DFAST Taxonomy check result was written to GCA_023418035.1_ASM2341803v1_genomic.fna/tc_result.tsv
[2023-06-29 19:34:58,556] [INFO] ===== Taxonomy check completed =====
[2023-06-29 19:34:58,556] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 19:34:58,556] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeec3b401-a1a2-4199-aa32-e39e4adae534/dqc_reference/checkm_data
[2023-06-29 19:34:58,558] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 19:34:58,614] [INFO] Task started: CheckM
[2023-06-29 19:34:58,615] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023418035.1_ASM2341803v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023418035.1_ASM2341803v1_genomic.fna/checkm_input GCA_023418035.1_ASM2341803v1_genomic.fna/checkm_result
[2023-06-29 19:35:48,557] [INFO] Task succeeded: CheckM
[2023-06-29 19:35:48,558] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.94%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 19:35:48,584] [INFO] ===== Completeness check finished =====
[2023-06-29 19:35:48,584] [INFO] ===== Start GTDB Search =====
[2023-06-29 19:35:48,585] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023418035.1_ASM2341803v1_genomic.fna/markers.fasta)
[2023-06-29 19:35:48,585] [INFO] Task started: Blastn
[2023-06-29 19:35:48,585] [INFO] Running command: blastn -query GCA_023418035.1_ASM2341803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeec3b401-a1a2-4199-aa32-e39e4adae534/dqc_reference/reference_markers_gtdb.fasta -out GCA_023418035.1_ASM2341803v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:35:50,009] [INFO] Task succeeded: Blastn
[2023-06-29 19:35:50,014] [INFO] Selected 17 target genomes.
[2023-06-29 19:35:50,015] [INFO] Target genome list was writen to GCA_023418035.1_ASM2341803v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 19:35:50,022] [INFO] Task started: fastANI
[2023-06-29 19:35:50,022] [INFO] Running command: fastANI --query /var/lib/cwl/stg5eeb66b3-9599-41f3-82c6-c0e9234e4238/GCA_023418035.1_ASM2341803v1_genomic.fna.gz --refList GCA_023418035.1_ASM2341803v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023418035.1_ASM2341803v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 19:36:03,840] [INFO] Task succeeded: fastANI
[2023-06-29 19:36:03,857] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 19:36:03,857] [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_014202975.1	s__Povalibacter uvarum	78.7418	555	1747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Povalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004138485.1	s__Steroidobacter_A soli	78.0276	416	1747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009932555.1	s__Steroidobacter_A agaridevorans	78.0152	429	1747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter_A	95.0	99.33	99.33	0.96	0.96	2	-
GCF_004138335.1	s__Steroidobacter_A agariperforans	77.8476	411	1747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016801985.1	s__Steroidobacter_A sp016801985	77.7597	381	1747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790065.1	s__Steroidobacter_A sp016790065	77.4265	311	1747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017577615.1	s__JAAYXG01 sp017577615	77.2447	213	1747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__JAAYXG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903884105.1	s__CAIUGU01 sp903884105	77.1501	142	1747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CAIUGU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012516015.1	s__JAAYXG01 sp012516015	77.1407	168	1747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__JAAYXG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242495.1	s__ZC4RG39 sp003242495	77.115	230	1747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__ZC4RG39	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001579945.1	s__Steroidobacter denitrificans	76.9785	157	1747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016704655.1	s__RPQJ01 sp016704655	76.8801	154	1747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__RPQJ01	95.0	98.97	98.97	0.93	0.93	2	-
GCF_011064545.1	s__XN24 sp011064545	76.6569	74	1747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__XN24;f__XN24;g__XN24	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720075.1	s__ZC4RG30 sp016720075	76.645	104	1747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__ZC4RG30	95.0	98.74	98.64	0.92	0.90	3	-
GCA_007127715.1	s__PWYM01 sp007127715	76.1174	57	1747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PWYM01;f__PWYM01;g__PWYM01	95.0	99.45	99.43	0.90	0.89	3	-
GCA_016927175.1	s__ZC4RG20 sp016927175	76.049	82	1747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA6522;f__UBA6522;g__ZC4RG20	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 19:36:03,860] [INFO] GTDB search result was written to GCA_023418035.1_ASM2341803v1_genomic.fna/result_gtdb.tsv
[2023-06-29 19:36:03,860] [INFO] ===== GTDB Search completed =====
[2023-06-29 19:36:03,864] [INFO] DFAST_QC result json was written to GCA_023418035.1_ASM2341803v1_genomic.fna/dqc_result.json
[2023-06-29 19:36:03,865] [INFO] DFAST_QC completed!
[2023-06-29 19:36:03,865] [INFO] Total running time: 0h1m39s