[2023-06-19 08:45:49,152] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:45:49,154] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:45:49,154] [INFO] DQC Reference Directory: /var/lib/cwl/stg2708c7ef-808f-4fab-a0cc-8828f0385f8f/dqc_reference
[2023-06-19 08:45:50,431] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:45:50,432] [INFO] Task started: Prodigal
[2023-06-19 08:45:50,432] [INFO] Running command: gunzip -c /var/lib/cwl/stg5fc36028-433e-4e14-b320-b93a41137485/GCA_013414705.1_ASM1341470v1_genomic.fna.gz | prodigal -d GCA_013414705.1_ASM1341470v1_genomic.fna/cds.fna -a GCA_013414705.1_ASM1341470v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:46:03,941] [INFO] Task succeeded: Prodigal
[2023-06-19 08:46:03,941] [INFO] Task started: HMMsearch
[2023-06-19 08:46:03,941] [INFO] Running command: hmmsearch --tblout GCA_013414705.1_ASM1341470v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2708c7ef-808f-4fab-a0cc-8828f0385f8f/dqc_reference/reference_markers.hmm GCA_013414705.1_ASM1341470v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:46:04,223] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:46:04,224] [INFO] Found 6/6 markers.
[2023-06-19 08:46:04,274] [INFO] Query marker FASTA was written to GCA_013414705.1_ASM1341470v1_genomic.fna/markers.fasta
[2023-06-19 08:46:04,275] [INFO] Task started: Blastn
[2023-06-19 08:46:04,275] [INFO] Running command: blastn -query GCA_013414705.1_ASM1341470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2708c7ef-808f-4fab-a0cc-8828f0385f8f/dqc_reference/reference_markers.fasta -out GCA_013414705.1_ASM1341470v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:46:05,122] [INFO] Task succeeded: Blastn
[2023-06-19 08:46:05,128] [INFO] Selected 32 target genomes.
[2023-06-19 08:46:05,129] [INFO] Target genome list was writen to GCA_013414705.1_ASM1341470v1_genomic.fna/target_genomes.txt
[2023-06-19 08:46:05,137] [INFO] Task started: fastANI
[2023-06-19 08:46:05,137] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fc36028-433e-4e14-b320-b93a41137485/GCA_013414705.1_ASM1341470v1_genomic.fna.gz --refList GCA_013414705.1_ASM1341470v1_genomic.fna/target_genomes.txt --output GCA_013414705.1_ASM1341470v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:46:29,450] [INFO] Task succeeded: fastANI
[2023-06-19 08:46:29,451] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2708c7ef-808f-4fab-a0cc-8828f0385f8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:46:29,452] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2708c7ef-808f-4fab-a0cc-8828f0385f8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:46:29,477] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:46:29,477] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 08:46:29,477] [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
Defluviicoccus vanus	strain=Ben 114	GCA_014672695.1	111831	111831	type	True	78.5104	295	1450	95	below_threshold
Magnetospirillum magnetotacticum	strain=MS-1	GCA_000829825.1	188	188	type	True	76.9138	111	1450	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	76.8452	148	1450	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.801	157	1450	95	below_threshold
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	76.7299	136	1450	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	76.6698	151	1450	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.5957	142	1450	95	below_threshold
Dongia mobilis	strain=CGMCC 1.7660	GCA_004363235.1	578943	578943	type	True	76.5446	104	1450	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.5021	224	1450	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.4987	166	1450	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	76.4888	117	1450	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_008630015.1	140057	140057	type	True	76.4754	115	1450	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.4723	227	1450	95	below_threshold
Sphingomicrobium astaxanthinifaciens	strain=JCM 18551	GCA_022865105.1	1227949	1227949	type	True	76.4642	52	1450	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.4583	138	1450	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.4143	107	1450	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	76.4114	135	1450	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_014203135.1	140057	140057	type	True	76.3419	113	1450	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	76.31	202	1450	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_014197855.1	140057	140057	type	True	76.3097	115	1450	95	below_threshold
Roseiarcus fermentans	strain=DSM 24875	GCA_003315135.1	1473586	1473586	type	True	76.3025	138	1450	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	76.3014	173	1450	95	below_threshold
Rhodopseudomonas pentothenatexigens	strain=JA575	GCA_900218015.1	999699	999699	type	True	76.286	142	1450	95	below_threshold
Hankyongella ginsenosidimutans	strain=W1-2-3	GCA_005144965.1	1763828	1763828	type	True	76.1794	82	1450	95	below_threshold
Rhodospirillum rubrum	strain=ATCC 11170	GCA_000013085.1	1085	1085	type	True	76.1723	109	1450	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	76.1699	163	1450	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.1697	172	1450	95	below_threshold
Rhodospirillum rubrum	strain=DSM 467	GCA_019134555.1	1085	1085	type	True	76.1532	109	1450	95	below_threshold
Methylobrevis pamukkalensis	strain=PK2	GCA_001720135.1	1439726	1439726	type	True	76.1164	109	1450	95	below_threshold
Skermanella aerolata	strain=5416T-32	GCA_000936425.1	393310	393310	type	True	76.1037	149	1450	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	76.1033	95	1450	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 08:46:29,480] [INFO] DFAST Taxonomy check result was written to GCA_013414705.1_ASM1341470v1_genomic.fna/tc_result.tsv
[2023-06-19 08:46:29,480] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:46:29,480] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:46:29,481] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2708c7ef-808f-4fab-a0cc-8828f0385f8f/dqc_reference/checkm_data
[2023-06-19 08:46:29,482] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:46:29,531] [INFO] Task started: CheckM
[2023-06-19 08:46:29,532] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013414705.1_ASM1341470v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013414705.1_ASM1341470v1_genomic.fna/checkm_input GCA_013414705.1_ASM1341470v1_genomic.fna/checkm_result
[2023-06-19 08:47:12,299] [INFO] Task succeeded: CheckM
[2023-06-19 08:47:12,301] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:47:12,329] [INFO] ===== Completeness check finished =====
[2023-06-19 08:47:12,329] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:47:12,330] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013414705.1_ASM1341470v1_genomic.fna/markers.fasta)
[2023-06-19 08:47:12,330] [INFO] Task started: Blastn
[2023-06-19 08:47:12,330] [INFO] Running command: blastn -query GCA_013414705.1_ASM1341470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2708c7ef-808f-4fab-a0cc-8828f0385f8f/dqc_reference/reference_markers_gtdb.fasta -out GCA_013414705.1_ASM1341470v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:47:13,861] [INFO] Task succeeded: Blastn
[2023-06-19 08:47:13,866] [INFO] Selected 20 target genomes.
[2023-06-19 08:47:13,866] [INFO] Target genome list was writen to GCA_013414705.1_ASM1341470v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:47:13,905] [INFO] Task started: fastANI
[2023-06-19 08:47:13,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fc36028-433e-4e14-b320-b93a41137485/GCA_013414705.1_ASM1341470v1_genomic.fna.gz --refList GCA_013414705.1_ASM1341470v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013414705.1_ASM1341470v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:47:30,374] [INFO] Task succeeded: fastANI
[2023-06-19 08:47:30,397] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:47:30,397] [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_013414705.1	s__SSA4 sp013414705	100.0	1450	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__SSA4	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016712595.1	s__SSA4 sp016712595	78.6756	402	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__SSA4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793875.1	s__SSA4 sp016793875	78.5831	395	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__SSA4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712375.1	s__SSA4 sp016712375	78.4801	391	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__SSA4	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014672695.1	s__Defluviicoccus vanus	78.4521	296	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__Defluviicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793925.1	s__JAEULH01 sp016793925	77.4722	211	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__JAEULH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900609035.2	s__Defluviicoccus_A seviourii	77.4546	231	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__Defluviicoccus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016710335.1	s__JADJXQ01 sp016710335	77.2939	211	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__JADJXQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000342045.1	s__Phaeospirillum caucaseum	76.8023	158	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007695045.1	s__REEP01 sp007695045	76.7738	167	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__REEP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100455.1	s__Roseospirillum parvum	76.7299	136	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Roseospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016212565.1	s__JACRFY01 sp016212565	76.7075	154	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JACRFY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002239065.1	s__MPNO01 sp002239065	76.4715	100	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__MPNO01;g__MPNO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008365375.1	s__Azospirillum sp008365375	76.4429	169	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377375.1	s__WHUE01 sp009377375	76.35	144	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WHUE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315795.1	s__Caenispirillum salinarum	76.1699	163	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Caenispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018648445.1	s__JABGRG01 sp018648445	76.1502	55	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JABGRG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019239835.1	s__JAFAZJ01 sp019239835	76.1481	85	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__JAFAZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576685.1	s__SYSU-D60014 sp003576685	76.0967	158	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60014	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016775475.1	s__Belnapia sp016775475	75.9343	135	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 08:47:30,399] [INFO] GTDB search result was written to GCA_013414705.1_ASM1341470v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:47:30,400] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:47:30,409] [INFO] DFAST_QC result json was written to GCA_013414705.1_ASM1341470v1_genomic.fna/dqc_result.json
[2023-06-19 08:47:30,409] [INFO] DFAST_QC completed!
[2023-06-19 08:47:30,409] [INFO] Total running time: 0h1m41s