[2023-06-17 00:46:07,550] [INFO] DFAST_QC pipeline started.
[2023-06-17 00:46:07,553] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 00:46:07,553] [INFO] DQC Reference Directory: /var/lib/cwl/stg5dfe987a-45b6-47e7-bffb-e4808e02794f/dqc_reference
[2023-06-17 00:46:08,825] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 00:46:08,826] [INFO] Task started: Prodigal
[2023-06-17 00:46:08,826] [INFO] Running command: gunzip -c /var/lib/cwl/stg68fc5ab1-c5c3-4429-a68c-4fef49bd659f/GCA_028871455.1_ASM2887145v1_genomic.fna.gz | prodigal -d GCA_028871455.1_ASM2887145v1_genomic.fna/cds.fna -a GCA_028871455.1_ASM2887145v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 00:46:17,799] [INFO] Task succeeded: Prodigal
[2023-06-17 00:46:17,800] [INFO] Task started: HMMsearch
[2023-06-17 00:46:17,800] [INFO] Running command: hmmsearch --tblout GCA_028871455.1_ASM2887145v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5dfe987a-45b6-47e7-bffb-e4808e02794f/dqc_reference/reference_markers.hmm GCA_028871455.1_ASM2887145v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 00:46:18,084] [INFO] Task succeeded: HMMsearch
[2023-06-17 00:46:18,085] [INFO] Found 6/6 markers.
[2023-06-17 00:46:18,116] [INFO] Query marker FASTA was written to GCA_028871455.1_ASM2887145v1_genomic.fna/markers.fasta
[2023-06-17 00:46:18,116] [INFO] Task started: Blastn
[2023-06-17 00:46:18,116] [INFO] Running command: blastn -query GCA_028871455.1_ASM2887145v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5dfe987a-45b6-47e7-bffb-e4808e02794f/dqc_reference/reference_markers.fasta -out GCA_028871455.1_ASM2887145v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 00:46:19,084] [INFO] Task succeeded: Blastn
[2023-06-17 00:46:19,088] [INFO] Selected 32 target genomes.
[2023-06-17 00:46:19,088] [INFO] Target genome list was writen to GCA_028871455.1_ASM2887145v1_genomic.fna/target_genomes.txt
[2023-06-17 00:46:19,095] [INFO] Task started: fastANI
[2023-06-17 00:46:19,095] [INFO] Running command: fastANI --query /var/lib/cwl/stg68fc5ab1-c5c3-4429-a68c-4fef49bd659f/GCA_028871455.1_ASM2887145v1_genomic.fna.gz --refList GCA_028871455.1_ASM2887145v1_genomic.fna/target_genomes.txt --output GCA_028871455.1_ASM2887145v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 00:46:51,916] [INFO] Task succeeded: fastANI
[2023-06-17 00:46:51,917] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5dfe987a-45b6-47e7-bffb-e4808e02794f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 00:46:51,918] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5dfe987a-45b6-47e7-bffb-e4808e02794f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 00:46:51,948] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 00:46:51,948] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 00:46:51,948] [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
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	77.2144	231	979	95	below_threshold
Aliidongia dinghuensis	strain=CGMCC 1.15725	GCA_014643535.1	1867774	1867774	type	True	77.1848	254	979	95	below_threshold
Hypericibacter terrae	strain=R5913	GCA_008728855.1	2602015	2602015	type	True	77.0448	229	979	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	77.0074	173	979	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.9818	281	979	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.9331	282	979	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	76.8148	216	979	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	76.8048	211	979	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.778	218	979	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	76.7655	170	979	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	76.7342	215	979	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	76.7124	220	979	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	76.6882	235	979	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.6833	195	979	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.6577	109	979	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.6124	239	979	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.5823	174	979	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	76.5051	191	979	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	76.4936	173	979	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	76.4903	249	979	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	76.4683	149	979	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	76.4497	204	979	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	76.3548	224	979	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	76.3516	165	979	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.3115	174	979	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	76.2408	75	979	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	76.1464	137	979	95	below_threshold
Methylobacterium soli	strain=KCTC 22810	GCA_022179555.1	553447	553447	type	True	75.8245	108	979	95	below_threshold
Croceicoccus pelagius	strain=Ery9	GCA_001661915.1	1703341	1703341	type	True	75.793	52	979	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	75.7907	156	979	95	below_threshold
Sphingopyxis panaciterrulae	strain=DSM 27163	GCA_014199295.1	462372	462372	type	True	75.6957	136	979	95	below_threshold
Novosphingobium guangzhouense	strain=SA925	GCA_002896965.1	1850347	1850347	type	True	75.3936	78	979	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 00:46:51,950] [INFO] DFAST Taxonomy check result was written to GCA_028871455.1_ASM2887145v1_genomic.fna/tc_result.tsv
[2023-06-17 00:46:51,951] [INFO] ===== Taxonomy check completed =====
[2023-06-17 00:46:51,951] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 00:46:51,951] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5dfe987a-45b6-47e7-bffb-e4808e02794f/dqc_reference/checkm_data
[2023-06-17 00:46:51,953] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 00:46:51,984] [INFO] Task started: CheckM
[2023-06-17 00:46:51,984] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028871455.1_ASM2887145v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028871455.1_ASM2887145v1_genomic.fna/checkm_input GCA_028871455.1_ASM2887145v1_genomic.fna/checkm_result
[2023-06-17 00:47:21,306] [INFO] Task succeeded: CheckM
[2023-06-17 00:47:21,307] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 00:47:21,329] [INFO] ===== Completeness check finished =====
[2023-06-17 00:47:21,330] [INFO] ===== Start GTDB Search =====
[2023-06-17 00:47:21,330] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028871455.1_ASM2887145v1_genomic.fna/markers.fasta)
[2023-06-17 00:47:21,331] [INFO] Task started: Blastn
[2023-06-17 00:47:21,331] [INFO] Running command: blastn -query GCA_028871455.1_ASM2887145v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5dfe987a-45b6-47e7-bffb-e4808e02794f/dqc_reference/reference_markers_gtdb.fasta -out GCA_028871455.1_ASM2887145v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 00:47:23,204] [INFO] Task succeeded: Blastn
[2023-06-17 00:47:23,209] [INFO] Selected 25 target genomes.
[2023-06-17 00:47:23,209] [INFO] Target genome list was writen to GCA_028871455.1_ASM2887145v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 00:47:23,228] [INFO] Task started: fastANI
[2023-06-17 00:47:23,229] [INFO] Running command: fastANI --query /var/lib/cwl/stg68fc5ab1-c5c3-4429-a68c-4fef49bd659f/GCA_028871455.1_ASM2887145v1_genomic.fna.gz --refList GCA_028871455.1_ASM2887145v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028871455.1_ASM2887145v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 00:47:42,900] [INFO] Task succeeded: fastANI
[2023-06-17 00:47:42,920] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 00:47:42,920] [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_018971215.1	s__REEB95 sp018971215	83.0178	482	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__REEB95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000518365.1	s__URHD0088 sp000518365	78.0379	334	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__URHD0088	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903828515.1	s__CAIKMD01 sp903828515	77.6324	295	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__CAIKMD01	95.0	99.99	99.96	1.00	0.99	5	-
GCA_006739055.1	s__Stella vacuolata	77.3713	233	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869375.1	s__SHVZ01 sp016869375	77.2227	197	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVZ01;f__SHVZ01;g__SHVZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643535.1	s__Aliidongia dinghuensis	77.173	255	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Aliidongia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654725.1	s__JAATGI01 sp015654725	77.0806	147	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__JAATGI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869645.1	s__SHVW01 sp016869645	77.0669	227	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVW01;f__SHVW01;g__SHVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903822185.1	s__CAIKMD01 sp903822185	77.063	219	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__CAIKMD01	95.0	99.70	99.51	0.99	0.98	4	-
GCA_016869145.1	s__VGEU01 sp016869145	77.0497	206	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__VGEU01;g__VGEU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793045.1	s__JAEUKZ01 sp016793045	77.0468	235	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__JAEUKZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	76.9667	278	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCA_016869285.1	s__SHVZ01 sp016869285	76.9591	186	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVZ01;f__SHVZ01;g__SHVZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006738865.1	s__Stella sp006738865	76.899	220	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197805.1	s__Rhodospirillum_A centenum	76.8179	157	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Rhodospirillum_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_019241915.1	s__AP-15 sp019241915	76.768	171	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__AP-15	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992495.1	s__Reyranella soli	76.7559	213	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966715.1	s__Blastochloris tepida	76.7529	170	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Blastochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876115.1	s__Azospirillum picis	76.7128	220	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016861165.1	s__BOKV01 sp016861165	76.6984	149	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__BOKV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793165.1	s__CAIOSQ01 sp016793165	76.5124	251	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__CAIOSQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630065.1	s__Blastochloris sulfoviridis	76.4936	173	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Blastochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124525.1	s__Oceanicella actignis	76.4544	150	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicella	95.0	98.87	98.87	0.96	0.96	3	-
GCA_016793965.1	s__JAEULF01 sp016793965	76.3895	170	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__JAEULF01;f__JAEULF01;g__JAEULF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019240125.1	s__AP-15 sp019240125	76.2236	166	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__AP-15	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 00:47:42,922] [INFO] GTDB search result was written to GCA_028871455.1_ASM2887145v1_genomic.fna/result_gtdb.tsv
[2023-06-17 00:47:42,923] [INFO] ===== GTDB Search completed =====
[2023-06-17 00:47:42,928] [INFO] DFAST_QC result json was written to GCA_028871455.1_ASM2887145v1_genomic.fna/dqc_result.json
[2023-06-17 00:47:42,928] [INFO] DFAST_QC completed!
[2023-06-17 00:47:42,928] [INFO] Total running time: 0h1m35s