[2023-06-27 03:10:12,804] [INFO] DFAST_QC pipeline started.
[2023-06-27 03:10:12,812] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 03:10:12,814] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0c213c7-6f46-4a38-ae36-8260a1c516b7/dqc_reference
[2023-06-27 03:10:14,393] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 03:10:14,395] [INFO] Task started: Prodigal
[2023-06-27 03:10:14,395] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5a1a916-b0fc-4e04-9cc0-0bf93f982e7c/GCA_026398775.1_ASM2639877v1_genomic.fna.gz | prodigal -d GCA_026398775.1_ASM2639877v1_genomic.fna/cds.fna -a GCA_026398775.1_ASM2639877v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 03:10:23,866] [INFO] Task succeeded: Prodigal
[2023-06-27 03:10:23,867] [INFO] Task started: HMMsearch
[2023-06-27 03:10:23,867] [INFO] Running command: hmmsearch --tblout GCA_026398775.1_ASM2639877v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0c213c7-6f46-4a38-ae36-8260a1c516b7/dqc_reference/reference_markers.hmm GCA_026398775.1_ASM2639877v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 03:10:24,283] [INFO] Task succeeded: HMMsearch
[2023-06-27 03:10:24,285] [INFO] Found 6/6 markers.
[2023-06-27 03:10:24,325] [INFO] Query marker FASTA was written to GCA_026398775.1_ASM2639877v1_genomic.fna/markers.fasta
[2023-06-27 03:10:24,325] [INFO] Task started: Blastn
[2023-06-27 03:10:24,325] [INFO] Running command: blastn -query GCA_026398775.1_ASM2639877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0c213c7-6f46-4a38-ae36-8260a1c516b7/dqc_reference/reference_markers.fasta -out GCA_026398775.1_ASM2639877v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 03:10:25,775] [INFO] Task succeeded: Blastn
[2023-06-27 03:10:25,787] [INFO] Selected 36 target genomes.
[2023-06-27 03:10:25,788] [INFO] Target genome list was writen to GCA_026398775.1_ASM2639877v1_genomic.fna/target_genomes.txt
[2023-06-27 03:10:25,794] [INFO] Task started: fastANI
[2023-06-27 03:10:25,794] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5a1a916-b0fc-4e04-9cc0-0bf93f982e7c/GCA_026398775.1_ASM2639877v1_genomic.fna.gz --refList GCA_026398775.1_ASM2639877v1_genomic.fna/target_genomes.txt --output GCA_026398775.1_ASM2639877v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 03:10:54,562] [INFO] Task succeeded: fastANI
[2023-06-27 03:10:54,563] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0c213c7-6f46-4a38-ae36-8260a1c516b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 03:10:54,563] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0c213c7-6f46-4a38-ae36-8260a1c516b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 03:10:54,590] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 03:10:54,590] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 03:10:54,590] [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	76.9936	85	849	95	below_threshold
Steroidobacter cummioxidans	strain=35Y	GCA_003104955.1	1803913	1803913	type	True	76.8612	97	849	95	below_threshold
Lysobacter defluvii	strain=IMMIB APB-9	GCA_000769985.1	391738	391738	type	True	76.7791	54	849	95	below_threshold
Lysobacter defluvii	strain=DSM 18482	GCA_000423325.1	391738	391738	type	True	76.7641	60	849	95	below_threshold
Lysobacter terrigena	strain=17J7-1	GCA_004361065.1	2488749	2488749	type	True	76.7273	69	849	95	below_threshold
Steroidobacter gossypii	strain=S1-65	GCA_016801985.1	2805490	2805490	type	True	76.6429	91	849	95	below_threshold
Steroidobacter agariperforans	strain=KA5-B	GCA_004138335.1	268404	268404	type	True	76.5372	98	849	95	below_threshold
Steroidobacter agaridevorans	strain=SA29-B	GCA_009932555.1	2695856	2695856	type	True	76.4618	106	849	95	below_threshold
Steroidobacter soli	strain=JW-3	GCA_004138485.1	2497877	2497877	type	True	76.4525	111	849	95	below_threshold
Rhodanobacter thiooxydans	strain=LCS2	GCA_000264375.1	416169	416169	type	True	76.4229	72	849	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.3447	118	849	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	76.329	71	849	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	76.3226	56	849	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	76.3081	76	849	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	76.2806	86	849	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.0794	55	849	95	below_threshold
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	76.0749	62	849	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	76.0697	56	849	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	76.0094	68	849	95	below_threshold
Solimonas flava	strain=DSM 18980	GCA_000426685.1	415849	415849	type	True	75.8483	95	849	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	75.7937	55	849	95	below_threshold
Tepidimonas sediminis	strain=YIM 72259	GCA_007556605.1	2588941	2588941	type	True	75.7372	73	849	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	75.6625	67	849	95	below_threshold
Pseudomonas delhiensis	strain=RLD-1	GCA_900187975.1	366289	366289	type	True	75.6365	84	849	95	below_threshold
Stutzerimonas azotifigens	strain=DSM 17556	GCA_000425625.1	291995	291995	type	True	75.6319	69	849	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	75.6131	84	849	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	75.1783	61	849	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	75.1374	50	849	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 03:10:54,593] [INFO] DFAST Taxonomy check result was written to GCA_026398775.1_ASM2639877v1_genomic.fna/tc_result.tsv
[2023-06-27 03:10:54,593] [INFO] ===== Taxonomy check completed =====
[2023-06-27 03:10:54,594] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 03:10:54,594] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0c213c7-6f46-4a38-ae36-8260a1c516b7/dqc_reference/checkm_data
[2023-06-27 03:10:54,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 03:10:54,637] [INFO] Task started: CheckM
[2023-06-27 03:10:54,637] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026398775.1_ASM2639877v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026398775.1_ASM2639877v1_genomic.fna/checkm_input GCA_026398775.1_ASM2639877v1_genomic.fna/checkm_result
[2023-06-27 03:11:27,635] [INFO] Task succeeded: CheckM
[2023-06-27 03:11:27,636] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.73%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 03:11:27,661] [INFO] ===== Completeness check finished =====
[2023-06-27 03:11:27,661] [INFO] ===== Start GTDB Search =====
[2023-06-27 03:11:27,661] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026398775.1_ASM2639877v1_genomic.fna/markers.fasta)
[2023-06-27 03:11:27,662] [INFO] Task started: Blastn
[2023-06-27 03:11:27,662] [INFO] Running command: blastn -query GCA_026398775.1_ASM2639877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0c213c7-6f46-4a38-ae36-8260a1c516b7/dqc_reference/reference_markers_gtdb.fasta -out GCA_026398775.1_ASM2639877v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 03:11:29,512] [INFO] Task succeeded: Blastn
[2023-06-27 03:11:29,539] [INFO] Selected 20 target genomes.
[2023-06-27 03:11:29,540] [INFO] Target genome list was writen to GCA_026398775.1_ASM2639877v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 03:11:29,577] [INFO] Task started: fastANI
[2023-06-27 03:11:29,580] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5a1a916-b0fc-4e04-9cc0-0bf93f982e7c/GCA_026398775.1_ASM2639877v1_genomic.fna.gz --refList GCA_026398775.1_ASM2639877v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026398775.1_ASM2639877v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 03:11:44,039] [INFO] Task succeeded: fastANI
[2023-06-27 03:11:44,056] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 03:11:44,057] [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_903927005.1	s__CAIYLH01 sp903927005	99.285	734	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CAIYLH01	95.0	99.60	99.60	0.92	0.92	2	conclusive
GCA_903884235.1	s__CAIYLH01 sp903884235	80.342	457	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CAIYLH01	95.0	99.42	99.08	0.95	0.88	22	-
GCA_018241525.1	s__SZAS-83 sp018241525	79.4601	344	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__SZAS-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241545.1	s__SZAS-83 sp018241545	78.9078	229	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__SZAS-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903890265.1	s__CAIKMS01 sp903890265	77.8156	123	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CAIKMS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016705325.1	s__RPQJ01 sp016705325	77.7706	114	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__RPQJ01	95.0	98.86	98.83	0.87	0.85	3	-
GCA_903908265.1	s__CAIYLH01 sp903908265	77.6526	112	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CAIYLH01	95.0	99.59	99.26	0.90	0.86	35	-
GCA_019187495.1	s__CADEFQ01 sp019187495	77.3706	117	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CADEFQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903839465.1	s__CAIKMS01 sp903839465	77.2312	173	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CAIKMS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202975.1	s__Povalibacter uvarum	76.9936	85	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Povalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011391405.1	s__RPQJ01 sp011391405	76.8641	102	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__RPQJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018261655.1	s__SG8-30 sp018261655	76.7567	103	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__SG8-30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242275.1	s__ZC4RG30 sp003242275	76.6838	91	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__ZC4RG30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903879335.1	s__CAIYLH01 sp903879335	76.6528	78	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CAIYLH01	95.0	99.91	99.87	0.98	0.96	13	-
GCF_000264375.1	s__Rhodanobacter thiooxydans	76.3971	73	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	99.24	99.24	0.91	0.91	2	-
GCA_018240265.1	s__TMP-86 sp018240265	76.3575	83	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__TMP-86	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 03:11:44,059] [INFO] GTDB search result was written to GCA_026398775.1_ASM2639877v1_genomic.fna/result_gtdb.tsv
[2023-06-27 03:11:44,059] [INFO] ===== GTDB Search completed =====
[2023-06-27 03:11:44,068] [INFO] DFAST_QC result json was written to GCA_026398775.1_ASM2639877v1_genomic.fna/dqc_result.json
[2023-06-27 03:11:44,068] [INFO] DFAST_QC completed!
[2023-06-27 03:11:44,068] [INFO] Total running time: 0h1m31s