[2023-06-08 08:35:21,341] [INFO] DFAST_QC pipeline started.
[2023-06-08 08:35:21,347] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 08:35:21,348] [INFO] DQC Reference Directory: /var/lib/cwl/stg83e09d84-a345-40a5-9165-66e1070714ef/dqc_reference
[2023-06-08 08:35:23,620] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 08:35:23,621] [INFO] Task started: Prodigal
[2023-06-08 08:35:23,621] [INFO] Running command: gunzip -c /var/lib/cwl/stga85a85b7-fc75-4c72-b582-59a1f148d288/GCA_945889015.1_MH-09jul19-70_genomic.fna.gz | prodigal -d GCA_945889015.1_MH-09jul19-70_genomic.fna/cds.fna -a GCA_945889015.1_MH-09jul19-70_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 08:35:36,423] [INFO] Task succeeded: Prodigal
[2023-06-08 08:35:36,423] [INFO] Task started: HMMsearch
[2023-06-08 08:35:36,423] [INFO] Running command: hmmsearch --tblout GCA_945889015.1_MH-09jul19-70_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83e09d84-a345-40a5-9165-66e1070714ef/dqc_reference/reference_markers.hmm GCA_945889015.1_MH-09jul19-70_genomic.fna/protein.faa > /dev/null
[2023-06-08 08:35:36,751] [INFO] Task succeeded: HMMsearch
[2023-06-08 08:35:36,753] [INFO] Found 6/6 markers.
[2023-06-08 08:35:36,822] [INFO] Query marker FASTA was written to GCA_945889015.1_MH-09jul19-70_genomic.fna/markers.fasta
[2023-06-08 08:35:36,822] [INFO] Task started: Blastn
[2023-06-08 08:35:36,823] [INFO] Running command: blastn -query GCA_945889015.1_MH-09jul19-70_genomic.fna/markers.fasta -db /var/lib/cwl/stg83e09d84-a345-40a5-9165-66e1070714ef/dqc_reference/reference_markers.fasta -out GCA_945889015.1_MH-09jul19-70_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 08:35:38,107] [INFO] Task succeeded: Blastn
[2023-06-08 08:35:38,113] [INFO] Selected 18 target genomes.
[2023-06-08 08:35:38,114] [INFO] Target genome list was writen to GCA_945889015.1_MH-09jul19-70_genomic.fna/target_genomes.txt
[2023-06-08 08:35:38,146] [INFO] Task started: fastANI
[2023-06-08 08:35:38,147] [INFO] Running command: fastANI --query /var/lib/cwl/stga85a85b7-fc75-4c72-b582-59a1f148d288/GCA_945889015.1_MH-09jul19-70_genomic.fna.gz --refList GCA_945889015.1_MH-09jul19-70_genomic.fna/target_genomes.txt --output GCA_945889015.1_MH-09jul19-70_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 08:35:54,803] [INFO] Task succeeded: fastANI
[2023-06-08 08:35:54,804] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83e09d84-a345-40a5-9165-66e1070714ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 08:35:54,804] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83e09d84-a345-40a5-9165-66e1070714ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 08:35:54,819] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 08:35:54,820] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 08:35:54,820] [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
Hyphomicrobium album	strain=XQ2	GCA_009708035.1	2665159	2665159	type	True	78.0316	326	1433	95	below_threshold
Hyphomicrobium zavarzinii	strain=ZV-622	GCA_000383415.1	48292	48292	type	True	77.8586	294	1433	95	below_threshold
Hyphomicrobium nitrativorans	strain=NL23	GCA_000503895.1	1427356	1427356	type	True	77.548	228	1433	95	below_threshold
Hyphomicrobium sulfonivorans	strain=S1	GCA_013306565.1	121290	121290	type	True	77.3753	189	1433	95	below_threshold
Hyphomicrobium sulfonivorans	strain=S1	GCA_016125985.1	121290	121290	type	True	77.3116	196	1433	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	77.1522	307	1433	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	77.1176	343	1433	95	below_threshold
Rhodoplanes piscinae	strain=DSM 19946	GCA_003258855.1	444923	444923	type	True	77.0884	278	1433	95	below_threshold
Phreatobacter cathodiphilus	strain=S-12	GCA_003008515.1	1868589	1868589	type	True	77.0872	290	1433	95	below_threshold
Bradyrhizobium oligotrophicum	strain=S58	GCA_000344805.1	44255	44255	type	True	76.9776	322	1433	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	76.9518	276	1433	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	76.9399	260	1433	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	76.6147	161	1433	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	76.5068	191	1433	95	below_threshold
Lichenibacterium ramalinae	strain=RmlP001	GCA_004137085.1	2316527	2316527	type	True	76.4629	226	1433	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	76.3271	252	1433	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.1939	275	1433	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	76.1841	201	1433	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 08:35:54,822] [INFO] DFAST Taxonomy check result was written to GCA_945889015.1_MH-09jul19-70_genomic.fna/tc_result.tsv
[2023-06-08 08:35:54,823] [INFO] ===== Taxonomy check completed =====
[2023-06-08 08:35:54,823] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 08:35:54,823] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83e09d84-a345-40a5-9165-66e1070714ef/dqc_reference/checkm_data
[2023-06-08 08:35:54,825] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 08:35:54,885] [INFO] Task started: CheckM
[2023-06-08 08:35:54,885] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945889015.1_MH-09jul19-70_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945889015.1_MH-09jul19-70_genomic.fna/checkm_input GCA_945889015.1_MH-09jul19-70_genomic.fna/checkm_result
[2023-06-08 08:36:34,664] [INFO] Task succeeded: CheckM
[2023-06-08 08:36:34,666] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 08:36:34,689] [INFO] ===== Completeness check finished =====
[2023-06-08 08:36:34,689] [INFO] ===== Start GTDB Search =====
[2023-06-08 08:36:34,690] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945889015.1_MH-09jul19-70_genomic.fna/markers.fasta)
[2023-06-08 08:36:34,690] [INFO] Task started: Blastn
[2023-06-08 08:36:34,690] [INFO] Running command: blastn -query GCA_945889015.1_MH-09jul19-70_genomic.fna/markers.fasta -db /var/lib/cwl/stg83e09d84-a345-40a5-9165-66e1070714ef/dqc_reference/reference_markers_gtdb.fasta -out GCA_945889015.1_MH-09jul19-70_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 08:36:36,636] [INFO] Task succeeded: Blastn
[2023-06-08 08:36:36,640] [INFO] Selected 23 target genomes.
[2023-06-08 08:36:36,640] [INFO] Target genome list was writen to GCA_945889015.1_MH-09jul19-70_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 08:36:36,682] [INFO] Task started: fastANI
[2023-06-08 08:36:36,683] [INFO] Running command: fastANI --query /var/lib/cwl/stga85a85b7-fc75-4c72-b582-59a1f148d288/GCA_945889015.1_MH-09jul19-70_genomic.fna.gz --refList GCA_945889015.1_MH-09jul19-70_genomic.fna/target_genomes_gtdb.txt --output GCA_945889015.1_MH-09jul19-70_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 08:36:53,577] [INFO] Task succeeded: fastANI
[2023-06-08 08:36:53,606] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 08:36:53,607] [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_009708035.1	s__Hyphomicrobium_A sp009708035	78.0458	324	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009026145.1	s__Hyphomicrobium_A sp009026145	77.9997	332	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383415.1	s__Hyphomicrobium zavarzinii	77.877	294	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	98.69	98.69	0.95	0.95	2	-
GCF_900117415.1	s__Ga0077555 sp900117415	77.8502	331	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Ga0077555	95.0	97.09	97.07	0.95	0.91	3	-
GCA_019137195.1	s__Hyphomicrobium sp019137195	77.7617	283	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793635.1	s__JAEUMD01 sp016793635	77.7534	317	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__JAEUMD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304275.1	s__Hyphomicrobium sp017304275	77.7075	247	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963125.1	s__AWTP1-13 sp003963125	77.7043	377	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__AWTP1-13	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900117455.1	s__Hyphomicrobium sp900117455	77.6465	288	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826555.1	s__Hyphomicrobium sp902826555	77.5702	250	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008933705.1	s__AWTP1-13 sp008933705	77.5685	376	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__AWTP1-13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464655.1	s__Ga0077555 sp001464655	77.5163	272	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Ga0077555	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716745.1	s__GCA-013693735 sp016716745	77.4466	292	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__GCA-013693735	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464855.1	s__Ga0077555 sp001464855	77.3589	215	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Ga0077555	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011330955.1	s__DSSY01 sp011330955	77.3159	290	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__DSSY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009720755.1	s__Rhodoplanes serenus	77.1967	306	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	97.72	97.48	0.91	0.88	4	-
GCA_016793445.1	s__Hyphomicrobium sp016793445	77.1806	192	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013377085.1	s__Rhodoplanes sp013377085	77.0083	316	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423225.1	s__Kaistia adipata	76.9599	259	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000253295.1	s__Hyphomicrobium sp000253295	76.8807	179	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	99.46	99.46	0.96	0.96	2	-
GCA_901457705.2	s__RH-AL1 sp901457705	76.8051	247	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__RH-AL1	95.0	99.94	99.94	0.99	0.99	3	-
GCF_013626205.1	s__Hyphomicrobium methylovorum	76.7646	119	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464285.1	s__Hyphomicrobium sp001464285	76.6199	155	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 08:36:53,609] [INFO] GTDB search result was written to GCA_945889015.1_MH-09jul19-70_genomic.fna/result_gtdb.tsv
[2023-06-08 08:36:53,610] [INFO] ===== GTDB Search completed =====
[2023-06-08 08:36:53,615] [INFO] DFAST_QC result json was written to GCA_945889015.1_MH-09jul19-70_genomic.fna/dqc_result.json
[2023-06-08 08:36:53,615] [INFO] DFAST_QC completed!
[2023-06-08 08:36:53,615] [INFO] Total running time: 0h1m32s