[2023-06-30 15:07:22,626] [INFO] DFAST_QC pipeline started.
[2023-06-30 15:07:22,633] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 15:07:22,633] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a6a0982-7731-493c-b4d0-11a885153671/dqc_reference
[2023-06-30 15:07:24,897] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 15:07:24,898] [INFO] Task started: Prodigal
[2023-06-30 15:07:24,899] [INFO] Running command: gunzip -c /var/lib/cwl/stgdcce198d-2706-4b02-a89b-c6c2d5103a10/GCA_016869145.1_JGI_2017-08-21_genomic.fna.gz | prodigal -d GCA_016869145.1_JGI_2017-08-21_genomic.fna/cds.fna -a GCA_016869145.1_JGI_2017-08-21_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 15:07:34,351] [INFO] Task succeeded: Prodigal
[2023-06-30 15:07:34,352] [INFO] Task started: HMMsearch
[2023-06-30 15:07:34,352] [INFO] Running command: hmmsearch --tblout GCA_016869145.1_JGI_2017-08-21_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a6a0982-7731-493c-b4d0-11a885153671/dqc_reference/reference_markers.hmm GCA_016869145.1_JGI_2017-08-21_genomic.fna/protein.faa > /dev/null
[2023-06-30 15:07:34,590] [INFO] Task succeeded: HMMsearch
[2023-06-30 15:07:34,591] [INFO] Found 6/6 markers.
[2023-06-30 15:07:34,633] [INFO] Query marker FASTA was written to GCA_016869145.1_JGI_2017-08-21_genomic.fna/markers.fasta
[2023-06-30 15:07:34,634] [INFO] Task started: Blastn
[2023-06-30 15:07:34,634] [INFO] Running command: blastn -query GCA_016869145.1_JGI_2017-08-21_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a6a0982-7731-493c-b4d0-11a885153671/dqc_reference/reference_markers.fasta -out GCA_016869145.1_JGI_2017-08-21_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:07:35,566] [INFO] Task succeeded: Blastn
[2023-06-30 15:07:35,573] [INFO] Selected 32 target genomes.
[2023-06-30 15:07:35,574] [INFO] Target genome list was writen to GCA_016869145.1_JGI_2017-08-21_genomic.fna/target_genomes.txt
[2023-06-30 15:07:35,578] [INFO] Task started: fastANI
[2023-06-30 15:07:35,578] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcce198d-2706-4b02-a89b-c6c2d5103a10/GCA_016869145.1_JGI_2017-08-21_genomic.fna.gz --refList GCA_016869145.1_JGI_2017-08-21_genomic.fna/target_genomes.txt --output GCA_016869145.1_JGI_2017-08-21_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 15:08:06,282] [INFO] Task succeeded: fastANI
[2023-06-30 15:08:06,283] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a6a0982-7731-493c-b4d0-11a885153671/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 15:08:06,283] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a6a0982-7731-493c-b4d0-11a885153671/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 15:08:06,316] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 15:08:06,316] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 15:08:06,317] [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	77.1461	327	1181	95	below_threshold
Hypericibacter terrae	strain=R5913	GCA_008728855.1	2602015	2602015	type	True	76.9371	280	1181	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.8586	181	1181	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.7067	344	1181	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	76.7021	254	1181	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.7008	307	1181	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.6824	219	1181	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	76.6752	312	1181	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	76.6379	256	1181	95	below_threshold
Skermanella rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	76.5967	293	1181	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.5961	254	1181	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.5423	348	1181	95	below_threshold
Azospirillum lipoferum	strain=59b	GCA_008364955.1	193	193	type	True	76.5326	274	1181	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.5264	178	1181	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	76.4323	288	1181	95	below_threshold
Lutibaculum baratangense	strain=AMV1	GCA_000496075.1	1358440	1358440	type	True	76.4091	256	1181	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	76.3889	284	1181	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	76.3762	345	1181	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	76.3618	332	1181	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	76.3601	315	1181	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	76.3476	289	1181	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	76.3371	300	1181	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	76.2955	302	1181	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	76.1894	376	1181	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	76.0355	223	1181	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.9763	212	1181	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.953	242	1181	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	75.8859	135	1181	95	below_threshold
Rhizocola hellebori	strain=NBRC 109834	GCA_016862955.1	1392758	1392758	type	True	74.8257	131	1181	95	below_threshold
Jongsikchunia kroppenstedtii	strain=NP8-5	GCA_000380485.1	1121721	1121721	type	True	74.7675	97	1181	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 15:08:06,319] [INFO] DFAST Taxonomy check result was written to GCA_016869145.1_JGI_2017-08-21_genomic.fna/tc_result.tsv
[2023-06-30 15:08:06,319] [INFO] ===== Taxonomy check completed =====
[2023-06-30 15:08:06,320] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 15:08:06,320] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a6a0982-7731-493c-b4d0-11a885153671/dqc_reference/checkm_data
[2023-06-30 15:08:06,321] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 15:08:06,365] [INFO] Task started: CheckM
[2023-06-30 15:08:06,365] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016869145.1_JGI_2017-08-21_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016869145.1_JGI_2017-08-21_genomic.fna/checkm_input GCA_016869145.1_JGI_2017-08-21_genomic.fna/checkm_result
[2023-06-30 15:08:50,380] [INFO] Task succeeded: CheckM
[2023-06-30 15:08:50,381] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 15:08:50,404] [INFO] ===== Completeness check finished =====
[2023-06-30 15:08:50,404] [INFO] ===== Start GTDB Search =====
[2023-06-30 15:08:50,405] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016869145.1_JGI_2017-08-21_genomic.fna/markers.fasta)
[2023-06-30 15:08:50,405] [INFO] Task started: Blastn
[2023-06-30 15:08:50,405] [INFO] Running command: blastn -query GCA_016869145.1_JGI_2017-08-21_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a6a0982-7731-493c-b4d0-11a885153671/dqc_reference/reference_markers_gtdb.fasta -out GCA_016869145.1_JGI_2017-08-21_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:08:52,369] [INFO] Task succeeded: Blastn
[2023-06-30 15:08:52,374] [INFO] Selected 26 target genomes.
[2023-06-30 15:08:52,375] [INFO] Target genome list was writen to GCA_016869145.1_JGI_2017-08-21_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 15:08:52,391] [INFO] Task started: fastANI
[2023-06-30 15:08:52,391] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcce198d-2706-4b02-a89b-c6c2d5103a10/GCA_016869145.1_JGI_2017-08-21_genomic.fna.gz --refList GCA_016869145.1_JGI_2017-08-21_genomic.fna/target_genomes_gtdb.txt --output GCA_016869145.1_JGI_2017-08-21_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 15:09:13,502] [INFO] Task succeeded: fastANI
[2023-06-30 15:09:13,524] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 15:09:13,524] [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_016869145.1	s__VGEU01 sp016869145	100.0	1175	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__VGEU01;g__VGEU01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002239065.1	s__MPNO01 sp002239065	77.5625	444	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__MPNO01;g__MPNO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576685.1	s__SYSU-D60014 sp003576685	77.4122	242	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377375.1	s__WHUE01 sp009377375	77.1686	361	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WHUE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728835.1	s__Hypericibacter adhaerens	77.1639	325	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Hypericibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869285.1	s__SHVZ01 sp016869285	77.0791	276	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVZ01;f__SHVZ01;g__SHVZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015232485.1	s__JADFZP01 sp015232485	77.0177	188	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	96.70	95.97	0.70	0.69	3	-
GCA_000518365.1	s__URHD0088 sp000518365	76.955	383	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__URHD0088	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006739055.1	s__Stella vacuolata	76.9259	332	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240745.1	s__Reyranella sp018240745	76.7822	308	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006738865.1	s__Stella sp006738865	76.6748	365	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004296815.1	s__Reyranella sp004296815	76.6712	220	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869915.1	s__CAIOSQ01 sp016869915	76.6438	290	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__CAIOSQ01	95.0	97.96	97.96	0.75	0.75	2	-
GCA_018432935.1	s__JAHDSF01 sp018432935	76.6413	238	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JAHDSF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401495.1	s__Thalassobaculum_A sp018401495	76.6373	312	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900110395.1	s__Reyranella sp900110395	76.5861	325	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005888425.1	s__AP-15 sp005888425	76.496	151	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__AP-15	95.0	97.44	97.38	0.68	0.66	3	-
GCA_016793165.1	s__CAIOSQ01 sp016793165	76.4895	433	1181	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	-
GCA_016212565.1	s__JACRFY01 sp016212565	76.4414	198	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JACRFY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000496075.1	s__Lutibaculum baratangense	76.4173	255	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Tepidamorphaceae;g__Lutibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016653355.1	s__Rhodoplanes elegans	76.3754	345	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	99.89	99.89	0.96	0.96	2	-
GCF_006980715.1	s__Oleiliquidispirillum nitrogeniifigens	76.3156	177	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Oleiliquidispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009694135.1	s__SHVS01 sp009694135	76.2108	121	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__SHVS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019240125.1	s__AP-15 sp019240125	76.2092	164	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__AP-15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240635.1	s__JAFEFJ01 sp018240635	76.0694	216	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFEFJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911975.1	s__Aquabacter sp013911975	76.0607	147	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Aquabacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 15:09:13,528] [INFO] GTDB search result was written to GCA_016869145.1_JGI_2017-08-21_genomic.fna/result_gtdb.tsv
[2023-06-30 15:09:13,528] [INFO] ===== GTDB Search completed =====
[2023-06-30 15:09:13,539] [INFO] DFAST_QC result json was written to GCA_016869145.1_JGI_2017-08-21_genomic.fna/dqc_result.json
[2023-06-30 15:09:13,539] [INFO] DFAST_QC completed!
[2023-06-30 15:09:13,539] [INFO] Total running time: 0h1m51s