[2023-06-19 00:40:25,898] [INFO] DFAST_QC pipeline started.
[2023-06-19 00:40:25,904] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 00:40:25,905] [INFO] DQC Reference Directory: /var/lib/cwl/stg67cb8bd8-9bec-4d24-9eca-c2814e643f33/dqc_reference
[2023-06-19 00:40:27,215] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 00:40:27,216] [INFO] Task started: Prodigal
[2023-06-19 00:40:27,216] [INFO] Running command: gunzip -c /var/lib/cwl/stg7c9f8d09-cb92-4bf7-b7b4-74f6e7a7bcff/GCA_018702955.1_ASM1870295v1_genomic.fna.gz | prodigal -d GCA_018702955.1_ASM1870295v1_genomic.fna/cds.fna -a GCA_018702955.1_ASM1870295v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 00:40:37,017] [INFO] Task succeeded: Prodigal
[2023-06-19 00:40:37,017] [INFO] Task started: HMMsearch
[2023-06-19 00:40:37,018] [INFO] Running command: hmmsearch --tblout GCA_018702955.1_ASM1870295v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67cb8bd8-9bec-4d24-9eca-c2814e643f33/dqc_reference/reference_markers.hmm GCA_018702955.1_ASM1870295v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 00:40:37,258] [INFO] Task succeeded: HMMsearch
[2023-06-19 00:40:37,260] [INFO] Found 6/6 markers.
[2023-06-19 00:40:37,300] [INFO] Query marker FASTA was written to GCA_018702955.1_ASM1870295v1_genomic.fna/markers.fasta
[2023-06-19 00:40:37,300] [INFO] Task started: Blastn
[2023-06-19 00:40:37,300] [INFO] Running command: blastn -query GCA_018702955.1_ASM1870295v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67cb8bd8-9bec-4d24-9eca-c2814e643f33/dqc_reference/reference_markers.fasta -out GCA_018702955.1_ASM1870295v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:40:38,079] [INFO] Task succeeded: Blastn
[2023-06-19 00:40:38,084] [INFO] Selected 33 target genomes.
[2023-06-19 00:40:38,085] [INFO] Target genome list was writen to GCA_018702955.1_ASM1870295v1_genomic.fna/target_genomes.txt
[2023-06-19 00:40:38,126] [INFO] Task started: fastANI
[2023-06-19 00:40:38,126] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c9f8d09-cb92-4bf7-b7b4-74f6e7a7bcff/GCA_018702955.1_ASM1870295v1_genomic.fna.gz --refList GCA_018702955.1_ASM1870295v1_genomic.fna/target_genomes.txt --output GCA_018702955.1_ASM1870295v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 00:41:06,504] [INFO] Task succeeded: fastANI
[2023-06-19 00:41:06,505] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67cb8bd8-9bec-4d24-9eca-c2814e643f33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 00:41:06,506] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67cb8bd8-9bec-4d24-9eca-c2814e643f33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 00:41:06,538] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 00:41:06,538] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 00:41:06,539] [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
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.4646	104	1047	95	below_threshold
Reyranella massiliensis	strain=521	GCA_000312425.1	445220	445220	type	True	76.3851	109	1047	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.3653	126	1047	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.349	118	1047	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	76.1832	104	1047	95	below_threshold
Pelagibius litoralis	strain=DSM 21314	GCA_011683915.1	374515	374515	type	True	76.1626	105	1047	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.1597	92	1047	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.1402	147	1047	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	76.0293	77	1047	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.0136	147	1047	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	75.9576	71	1047	95	below_threshold
Pacificispira spongiicola	strain=KN72	GCA_012926505.1	2729598	2729598	type	True	75.8927	82	1047	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.8922	74	1047	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	75.8854	131	1047	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	75.8555	71	1047	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	75.8548	64	1047	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	75.8107	97	1047	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	75.8104	134	1047	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	75.7738	86	1047	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	75.7554	90	1047	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	75.7408	77	1047	95	below_threshold
Mesorhizobium sophorae	strain=ICMP 19535	GCA_002270415.1	1300294	1300294	type	True	75.7018	91	1047	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	75.6587	82	1047	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.6558	136	1047	95	below_threshold
Bosea thiooxidans	strain=DSM 9653	GCA_900168195.1	53254	53254	type	True	75.6247	94	1047	95	below_threshold
Methylobacterium durans	strain=17SD2-17	GCA_003173715.1	2202825	2202825	type	True	75.6152	76	1047	95	below_threshold
Aureimonas endophytica	strain=CGMCC 1.15367	GCA_014642635.1	2027858	2027858	type	True	75.6053	84	1047	95	below_threshold
Aminobacter ciceronei	strain=DSM 15910	GCA_014138625.1	150723	150723	type	True	75.5962	99	1047	95	below_threshold
Aminobacter ciceronei	strain=DSM 17455	GCA_014138635.1	150723	150723	type	True	75.5962	99	1047	95	below_threshold
Mesorhizobium loti	strain=DSM 2626	GCA_003148495.1	381	381	suspected-type	True	75.5877	91	1047	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 00:41:06,540] [INFO] DFAST Taxonomy check result was written to GCA_018702955.1_ASM1870295v1_genomic.fna/tc_result.tsv
[2023-06-19 00:41:06,543] [INFO] ===== Taxonomy check completed =====
[2023-06-19 00:41:06,544] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 00:41:06,544] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67cb8bd8-9bec-4d24-9eca-c2814e643f33/dqc_reference/checkm_data
[2023-06-19 00:41:06,545] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 00:41:06,584] [INFO] Task started: CheckM
[2023-06-19 00:41:06,584] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018702955.1_ASM1870295v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018702955.1_ASM1870295v1_genomic.fna/checkm_input GCA_018702955.1_ASM1870295v1_genomic.fna/checkm_result
[2023-06-19 00:41:39,343] [INFO] Task succeeded: CheckM
[2023-06-19 00:41:39,345] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.58%
Contamintation: 4.55%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 00:41:39,385] [INFO] ===== Completeness check finished =====
[2023-06-19 00:41:39,385] [INFO] ===== Start GTDB Search =====
[2023-06-19 00:41:39,386] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018702955.1_ASM1870295v1_genomic.fna/markers.fasta)
[2023-06-19 00:41:39,386] [INFO] Task started: Blastn
[2023-06-19 00:41:39,386] [INFO] Running command: blastn -query GCA_018702955.1_ASM1870295v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67cb8bd8-9bec-4d24-9eca-c2814e643f33/dqc_reference/reference_markers_gtdb.fasta -out GCA_018702955.1_ASM1870295v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:41:40,757] [INFO] Task succeeded: Blastn
[2023-06-19 00:41:40,762] [INFO] Selected 11 target genomes.
[2023-06-19 00:41:40,762] [INFO] Target genome list was writen to GCA_018702955.1_ASM1870295v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 00:41:40,773] [INFO] Task started: fastANI
[2023-06-19 00:41:40,773] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c9f8d09-cb92-4bf7-b7b4-74f6e7a7bcff/GCA_018702955.1_ASM1870295v1_genomic.fna.gz --refList GCA_018702955.1_ASM1870295v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018702955.1_ASM1870295v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 00:41:48,880] [INFO] Task succeeded: fastANI
[2023-06-19 00:41:48,893] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 00:41:48,893] [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_018702955.1	s__UBA8079 sp018702955	100.0	1038	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	99.54	99.39	0.93	0.91	5	conclusive
GCA_018667335.1	s__UBA8079 sp018667335	85.5731	899	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	99.89	99.79	0.96	0.96	6	-
GCA_002724635.1	s__UBA8079 sp002724635	79.3234	467	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002727315.1	s__UBA8079 sp002727315	79.3182	432	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643325.1	s__JABJAG01 sp017643325	78.5253	370	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABJAG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722515.1	s__UBA8079 sp002722515	77.7183	253	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018666195.1	s__JABJAG01 sp018666195	77.498	278	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABJAG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011087645.1	s__JABDJY01 sp011087645	76.9202	278	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABDJY01	95.0	99.97	99.97	0.97	0.97	2	-
GCF_000442515.1	s__Phaeospirillum fulvum_B	75.8194	64	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173715.1	s__Methylobacterium durans	75.5961	77	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 00:41:48,895] [INFO] GTDB search result was written to GCA_018702955.1_ASM1870295v1_genomic.fna/result_gtdb.tsv
[2023-06-19 00:41:48,895] [INFO] ===== GTDB Search completed =====
[2023-06-19 00:41:48,902] [INFO] DFAST_QC result json was written to GCA_018702955.1_ASM1870295v1_genomic.fna/dqc_result.json
[2023-06-19 00:41:48,903] [INFO] DFAST_QC completed!
[2023-06-19 00:41:48,903] [INFO] Total running time: 0h1m23s