[2023-06-27 02:40:42,564] [INFO] DFAST_QC pipeline started.
[2023-06-27 02:40:42,567] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 02:40:42,567] [INFO] DQC Reference Directory: /var/lib/cwl/stg99fa6d8d-5397-40c0-8441-ded3ff5855b8/dqc_reference
[2023-06-27 02:40:43,854] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 02:40:43,855] [INFO] Task started: Prodigal
[2023-06-27 02:40:43,855] [INFO] Running command: gunzip -c /var/lib/cwl/stg2c6ac234-9fbb-4733-83c3-7e2ab3af21b1/GCA_026126115.1_ASM2612611v1_genomic.fna.gz | prodigal -d GCA_026126115.1_ASM2612611v1_genomic.fna/cds.fna -a GCA_026126115.1_ASM2612611v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 02:41:02,068] [INFO] Task succeeded: Prodigal
[2023-06-27 02:41:02,068] [INFO] Task started: HMMsearch
[2023-06-27 02:41:02,068] [INFO] Running command: hmmsearch --tblout GCA_026126115.1_ASM2612611v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99fa6d8d-5397-40c0-8441-ded3ff5855b8/dqc_reference/reference_markers.hmm GCA_026126115.1_ASM2612611v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 02:41:02,456] [INFO] Task succeeded: HMMsearch
[2023-06-27 02:41:02,457] [INFO] Found 6/6 markers.
[2023-06-27 02:41:02,529] [INFO] Query marker FASTA was written to GCA_026126115.1_ASM2612611v1_genomic.fna/markers.fasta
[2023-06-27 02:41:02,530] [INFO] Task started: Blastn
[2023-06-27 02:41:02,530] [INFO] Running command: blastn -query GCA_026126115.1_ASM2612611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99fa6d8d-5397-40c0-8441-ded3ff5855b8/dqc_reference/reference_markers.fasta -out GCA_026126115.1_ASM2612611v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 02:41:03,629] [INFO] Task succeeded: Blastn
[2023-06-27 02:41:03,659] [INFO] Selected 25 target genomes.
[2023-06-27 02:41:03,660] [INFO] Target genome list was writen to GCA_026126115.1_ASM2612611v1_genomic.fna/target_genomes.txt
[2023-06-27 02:41:03,663] [INFO] Task started: fastANI
[2023-06-27 02:41:03,664] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c6ac234-9fbb-4733-83c3-7e2ab3af21b1/GCA_026126115.1_ASM2612611v1_genomic.fna.gz --refList GCA_026126115.1_ASM2612611v1_genomic.fna/target_genomes.txt --output GCA_026126115.1_ASM2612611v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 02:41:31,487] [INFO] Task succeeded: fastANI
[2023-06-27 02:41:31,488] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99fa6d8d-5397-40c0-8441-ded3ff5855b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 02:41:31,489] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99fa6d8d-5397-40c0-8441-ded3ff5855b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 02:41:31,511] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 02:41:31,511] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 02:41:31,511] [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
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	80.7625	1149	2067	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	80.0206	1054	2067	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	79.3695	865	2067	95	below_threshold
Reyranella massiliensis	strain=521	GCA_000312425.1	445220	445220	type	True	79.0922	787	2067	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	77.1924	570	2067	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.9638	445	2067	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.9447	349	2067	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.9322	477	2067	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.8748	292	2067	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	76.8101	625	2067	95	below_threshold
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	76.7682	285	2067	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.5004	439	2067	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	76.4734	343	2067	95	below_threshold
Methylobacterium mesophilicum	strain=NBRC 15688	GCA_022179445.1	39956	39956	type	True	76.4129	329	2067	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	76.4096	338	2067	95	below_threshold
Methylobacterium brachiatum	strain=B0021	GCA_020523825.1	269660	269660	type	True	76.3925	387	2067	95	below_threshold
Zavarzinia compransoris	strain=DSM 1231	GCA_003173055.1	1264899	1264899	type	True	76.3588	352	2067	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	76.345	467	2067	95	below_threshold
Roseiarcus fermentans	strain=DSM 24875	GCA_003315135.1	1473586	1473586	type	True	76.3079	416	2067	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	76.2756	290	2067	95	below_threshold
Pararhodospirillum oryzae	strain=NBRC 107573	GCA_007992075.1	478448	478448	type	True	76.2681	165	2067	95	below_threshold
Parvularcula dongshanensis	strain=DSM 102850	GCA_014199615.1	1173995	1173995	type	True	76.1721	165	2067	95	below_threshold
Acuticoccus kandeliae	strain=J103	GCA_003073115.1	2073160	2073160	type	True	76.1091	365	2067	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	75.9399	327	2067	95	below_threshold
Rhizobium tumorigenes	strain=1078	GCA_003240565.1	2041385	2041385	type	True	75.7801	159	2067	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 02:41:31,533] [INFO] DFAST Taxonomy check result was written to GCA_026126115.1_ASM2612611v1_genomic.fna/tc_result.tsv
[2023-06-27 02:41:31,534] [INFO] ===== Taxonomy check completed =====
[2023-06-27 02:41:31,534] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 02:41:31,534] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99fa6d8d-5397-40c0-8441-ded3ff5855b8/dqc_reference/checkm_data
[2023-06-27 02:41:31,537] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 02:41:31,615] [INFO] Task started: CheckM
[2023-06-27 02:41:31,615] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026126115.1_ASM2612611v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026126115.1_ASM2612611v1_genomic.fna/checkm_input GCA_026126115.1_ASM2612611v1_genomic.fna/checkm_result
[2023-06-27 02:42:28,404] [INFO] Task succeeded: CheckM
[2023-06-27 02:42:28,406] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 02:42:28,431] [INFO] ===== Completeness check finished =====
[2023-06-27 02:42:28,431] [INFO] ===== Start GTDB Search =====
[2023-06-27 02:42:28,432] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026126115.1_ASM2612611v1_genomic.fna/markers.fasta)
[2023-06-27 02:42:28,432] [INFO] Task started: Blastn
[2023-06-27 02:42:28,432] [INFO] Running command: blastn -query GCA_026126115.1_ASM2612611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99fa6d8d-5397-40c0-8441-ded3ff5855b8/dqc_reference/reference_markers_gtdb.fasta -out GCA_026126115.1_ASM2612611v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 02:42:30,153] [INFO] Task succeeded: Blastn
[2023-06-27 02:42:30,158] [INFO] Selected 16 target genomes.
[2023-06-27 02:42:30,159] [INFO] Target genome list was writen to GCA_026126115.1_ASM2612611v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 02:42:30,195] [INFO] Task started: fastANI
[2023-06-27 02:42:30,195] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c6ac234-9fbb-4733-83c3-7e2ab3af21b1/GCA_026126115.1_ASM2612611v1_genomic.fna.gz --refList GCA_026126115.1_ASM2612611v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026126115.1_ASM2612611v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 02:42:49,491] [INFO] Task succeeded: fastANI
[2023-06-27 02:42:49,506] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 02:42:49,506] [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_016869975.1	s__JAFAZJ01 sp016869975	88.3575	1389	2067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__JAFAZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019239835.1	s__JAFAZJ01 sp019239835	87.1374	852	2067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__JAFAZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016699855.1	s__GCA-016699855 sp016699855	81.6345	1100	2067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__GCA-016699855	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008039615.1	s__SYSU-D60007 sp008039615	80.588	1184	2067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__SYSU-D60007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305915.1	s__Reyranella sp017305915	80.3448	1049	2067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240745.1	s__Reyranella sp018240745	80.0639	905	2067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003574685.1	s__SYSU-D60007 sp003574685	79.8591	887	2067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__SYSU-D60007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004296815.1	s__Reyranella sp004296815	79.8453	715	2067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859315.1	s__SYSU-D60007 sp007859315	79.7163	1104	2067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__SYSU-D60007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016212565.1	s__JACRFY01 sp016212565	76.9904	313	2067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JACRFY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230255.1	s__Caenispirillum bisanense	76.5672	474	2067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Caenispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315135.1	s__Roseiarcus fermentans	76.2697	431	2067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Roseiarcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018819265.1	s__Filomicrobium sp018819265	76.2593	145	2067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Filomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199615.1	s__Parvularcula dongshanensis	76.152	167	2067	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 02:42:49,525] [INFO] GTDB search result was written to GCA_026126115.1_ASM2612611v1_genomic.fna/result_gtdb.tsv
[2023-06-27 02:42:49,526] [INFO] ===== GTDB Search completed =====
[2023-06-27 02:42:49,541] [INFO] DFAST_QC result json was written to GCA_026126115.1_ASM2612611v1_genomic.fna/dqc_result.json
[2023-06-27 02:42:49,542] [INFO] DFAST_QC completed!
[2023-06-27 02:42:49,542] [INFO] Total running time: 0h2m7s