[2023-06-28 23:45:30,795] [INFO] DFAST_QC pipeline started.
[2023-06-28 23:45:30,797] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 23:45:30,797] [INFO] DQC Reference Directory: /var/lib/cwl/stg9aa8253e-e700-482a-9c8b-8cd6035d801c/dqc_reference
[2023-06-28 23:45:32,022] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 23:45:32,023] [INFO] Task started: Prodigal
[2023-06-28 23:45:32,023] [INFO] Running command: gunzip -c /var/lib/cwl/stgb7819188-8f79-49aa-a82b-110005e30664/GCA_020849715.1_ASM2084971v1_genomic.fna.gz | prodigal -d GCA_020849715.1_ASM2084971v1_genomic.fna/cds.fna -a GCA_020849715.1_ASM2084971v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 23:45:43,394] [INFO] Task succeeded: Prodigal
[2023-06-28 23:45:43,394] [INFO] Task started: HMMsearch
[2023-06-28 23:45:43,395] [INFO] Running command: hmmsearch --tblout GCA_020849715.1_ASM2084971v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9aa8253e-e700-482a-9c8b-8cd6035d801c/dqc_reference/reference_markers.hmm GCA_020849715.1_ASM2084971v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 23:45:43,651] [INFO] Task succeeded: HMMsearch
[2023-06-28 23:45:43,652] [INFO] Found 6/6 markers.
[2023-06-28 23:45:43,686] [INFO] Query marker FASTA was written to GCA_020849715.1_ASM2084971v1_genomic.fna/markers.fasta
[2023-06-28 23:45:43,686] [INFO] Task started: Blastn
[2023-06-28 23:45:43,686] [INFO] Running command: blastn -query GCA_020849715.1_ASM2084971v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9aa8253e-e700-482a-9c8b-8cd6035d801c/dqc_reference/reference_markers.fasta -out GCA_020849715.1_ASM2084971v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:45:44,621] [INFO] Task succeeded: Blastn
[2023-06-28 23:45:44,626] [INFO] Selected 31 target genomes.
[2023-06-28 23:45:44,626] [INFO] Target genome list was writen to GCA_020849715.1_ASM2084971v1_genomic.fna/target_genomes.txt
[2023-06-28 23:45:44,655] [INFO] Task started: fastANI
[2023-06-28 23:45:44,655] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7819188-8f79-49aa-a82b-110005e30664/GCA_020849715.1_ASM2084971v1_genomic.fna.gz --refList GCA_020849715.1_ASM2084971v1_genomic.fna/target_genomes.txt --output GCA_020849715.1_ASM2084971v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 23:46:11,223] [INFO] Task succeeded: fastANI
[2023-06-28 23:46:11,224] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9aa8253e-e700-482a-9c8b-8cd6035d801c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 23:46:11,224] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9aa8253e-e700-482a-9c8b-8cd6035d801c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 23:46:11,248] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 23:46:11,249] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 23:46:11,249] [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	77.2069	145	1161	95	below_threshold
Steroidobacter agaridevorans	strain=SA29-B	GCA_009932555.1	2695856	2695856	type	True	76.9797	176	1161	95	below_threshold
Steroidobacter agariperforans	strain=KA5-B	GCA_004138335.1	268404	268404	type	True	76.9629	170	1161	95	below_threshold
Steroidobacter gossypii	strain=S1-65	GCA_016801985.1	2805490	2805490	type	True	76.8683	177	1161	95	below_threshold
Steroidobacter denitrificans	strain=DSM 18526	GCA_001579945.1	465721	465721	type	True	76.8636	91	1161	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	76.7678	143	1161	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	76.7592	201	1161	95	below_threshold
Steroidobacter cummioxidans	strain=35Y	GCA_003104955.1	1803913	1803913	type	True	76.7421	177	1161	95	below_threshold
Steroidobacter soli	strain=JW-3	GCA_004138485.1	2497877	2497877	type	True	76.742	184	1161	95	below_threshold
Lysobacter defluvii	strain=IMMIB APB-9	GCA_000769985.1	391738	391738	type	True	76.6642	108	1161	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	76.6608	107	1161	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	76.659	215	1161	95	below_threshold
Lysobacter defluvii	strain=DSM 18482	GCA_000423325.1	391738	391738	type	True	76.5809	122	1161	95	below_threshold
Rhodanobacter thiooxydans	strain=LCS2	GCA_000264375.1	416169	416169	type	True	76.495	149	1161	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	76.4888	164	1161	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	76.2952	103	1161	95	below_threshold
Guyparkeria hydrothermalis	strain=R3	GCA_023555375.1	923	923	type	True	76.2943	60	1161	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.16	205	1161	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	76.1537	167	1161	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.1147	124	1161	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	76.0676	235	1161	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	75.9428	255	1161	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	75.9198	244	1161	95	below_threshold
Fluviicoccus keumensis	strain=DSM 105135	GCA_004217445.1	1435465	1435465	type	True	75.8769	62	1161	95	below_threshold
Ramlibacter monticola	strain=KACC 19175	GCA_016722785.1	1926872	1926872	type	True	75.8502	183	1161	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	75.836	168	1161	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	75.7686	114	1161	95	below_threshold
Myxococcus fulvus	strain=DSM 16525	GCA_900111765.1	33	33	type	True	74.9274	114	1161	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	74.9115	116	1161	95	below_threshold
Corallococcus aberystwythensis	strain=AB050A	GCA_003612165.1	2316722	2316722	type	True	74.8626	120	1161	95	below_threshold
Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis	strain=AM401	GCA_006636215.1	2590453	2590453	type	True	74.7898	100	1161	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 23:46:11,251] [INFO] DFAST Taxonomy check result was written to GCA_020849715.1_ASM2084971v1_genomic.fna/tc_result.tsv
[2023-06-28 23:46:11,252] [INFO] ===== Taxonomy check completed =====
[2023-06-28 23:46:11,252] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 23:46:11,252] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9aa8253e-e700-482a-9c8b-8cd6035d801c/dqc_reference/checkm_data
[2023-06-28 23:46:11,253] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 23:46:11,294] [INFO] Task started: CheckM
[2023-06-28 23:46:11,294] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020849715.1_ASM2084971v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020849715.1_ASM2084971v1_genomic.fna/checkm_input GCA_020849715.1_ASM2084971v1_genomic.fna/checkm_result
[2023-06-28 23:46:53,409] [INFO] Task succeeded: CheckM
[2023-06-28 23:46:53,411] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 23:46:53,432] [INFO] ===== Completeness check finished =====
[2023-06-28 23:46:53,433] [INFO] ===== Start GTDB Search =====
[2023-06-28 23:46:53,433] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020849715.1_ASM2084971v1_genomic.fna/markers.fasta)
[2023-06-28 23:46:53,433] [INFO] Task started: Blastn
[2023-06-28 23:46:53,433] [INFO] Running command: blastn -query GCA_020849715.1_ASM2084971v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9aa8253e-e700-482a-9c8b-8cd6035d801c/dqc_reference/reference_markers_gtdb.fasta -out GCA_020849715.1_ASM2084971v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:46:55,258] [INFO] Task succeeded: Blastn
[2023-06-28 23:46:55,263] [INFO] Selected 21 target genomes.
[2023-06-28 23:46:55,263] [INFO] Target genome list was writen to GCA_020849715.1_ASM2084971v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 23:46:55,277] [INFO] Task started: fastANI
[2023-06-28 23:46:55,278] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7819188-8f79-49aa-a82b-110005e30664/GCA_020849715.1_ASM2084971v1_genomic.fna.gz --refList GCA_020849715.1_ASM2084971v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020849715.1_ASM2084971v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 23:47:09,020] [INFO] Task succeeded: fastANI
[2023-06-28 23:47:09,045] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 23:47:09,045] [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_016720075.1	s__ZC4RG30 sp016720075	98.0241	1036	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__ZC4RG30	95.0	98.74	98.64	0.92	0.90	3	conclusive
GCA_003242275.1	s__ZC4RG30 sp003242275	80.6073	488	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__ZC4RG30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655465.1	s__ZC4RG30 sp015655465	79.6196	398	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__ZC4RG30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903868595.1	s__ZC4RG30 sp903868595	79.2788	360	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__ZC4RG30	95.0	99.92	99.90	0.97	0.96	3	-
GCA_009923475.1	s__UBA964 sp009923475	78.0852	139	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241455.1	s__FEN-1191 sp018241455	78.067	174	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__FEN-1191	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240525.1	s__13-2-20CM-66-19 sp018240525	78.0499	250	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019187495.1	s__CADEFQ01 sp019187495	77.9589	198	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CADEFQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826635.1	s__CADEFQ01 sp902826635	77.5639	222	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CADEFQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903938365.1	s__UBA964 sp903938365	77.5227	233	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	99.27	99.13	0.88	0.87	4	-
GCA_902826225.1	s__CADEED01 sp902826225	77.506	194	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CADEED01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903908825.1	s__ZC4RG30 sp903908825	77.5013	233	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__ZC4RG30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016707425.1	s__JADJHU01 sp016707425	77.3916	179	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__JADJHU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826575.1	s__CADEFQ01 sp902826575	77.3902	206	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CADEFQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003132025.1	s__FEN-1191 sp003132025	77.3193	199	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__FEN-1191	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012026925.1	s__RPQJ01 sp012026925	76.9214	119	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__RPQJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359565.1	s__Immundisolibacter sp014359565	76.1952	143	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Immundisolibacterales;f__Immundisolibacteraceae;g__Immundisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006386545.1	s__Pseudorivibacter rhizosphaerae	76.1506	173	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudorivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014873965.1	s__VBDL01 sp014873965	76.0867	209	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__VBDL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003265685.1	s__Piscinibacter caeni	76.0756	243	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011805.1	s__Piscinibacter defluvii	75.9144	247	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 23:47:09,047] [INFO] GTDB search result was written to GCA_020849715.1_ASM2084971v1_genomic.fna/result_gtdb.tsv
[2023-06-28 23:47:09,048] [INFO] ===== GTDB Search completed =====
[2023-06-28 23:47:09,053] [INFO] DFAST_QC result json was written to GCA_020849715.1_ASM2084971v1_genomic.fna/dqc_result.json
[2023-06-28 23:47:09,053] [INFO] DFAST_QC completed!
[2023-06-28 23:47:09,053] [INFO] Total running time: 0h1m38s