[2023-06-27 20:39:31,013] [INFO] DFAST_QC pipeline started.
[2023-06-27 20:39:31,016] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 20:39:31,016] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1bee638-4f43-405b-a7b3-3fb340dc75d7/dqc_reference
[2023-06-27 20:39:34,753] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 20:39:34,754] [INFO] Task started: Prodigal
[2023-06-27 20:39:34,755] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb087cc5-40ad-4de6-a42d-cd8794464b8e/GCA_026710105.1_ASM2671010v1_genomic.fna.gz | prodigal -d GCA_026710105.1_ASM2671010v1_genomic.fna/cds.fna -a GCA_026710105.1_ASM2671010v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 20:39:43,840] [INFO] Task succeeded: Prodigal
[2023-06-27 20:39:43,841] [INFO] Task started: HMMsearch
[2023-06-27 20:39:43,841] [INFO] Running command: hmmsearch --tblout GCA_026710105.1_ASM2671010v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1bee638-4f43-405b-a7b3-3fb340dc75d7/dqc_reference/reference_markers.hmm GCA_026710105.1_ASM2671010v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 20:39:44,155] [INFO] Task succeeded: HMMsearch
[2023-06-27 20:39:44,157] [INFO] Found 6/6 markers.
[2023-06-27 20:39:44,197] [INFO] Query marker FASTA was written to GCA_026710105.1_ASM2671010v1_genomic.fna/markers.fasta
[2023-06-27 20:39:44,198] [INFO] Task started: Blastn
[2023-06-27 20:39:44,198] [INFO] Running command: blastn -query GCA_026710105.1_ASM2671010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1bee638-4f43-405b-a7b3-3fb340dc75d7/dqc_reference/reference_markers.fasta -out GCA_026710105.1_ASM2671010v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 20:39:47,939] [INFO] Task succeeded: Blastn
[2023-06-27 20:39:47,945] [INFO] Selected 31 target genomes.
[2023-06-27 20:39:47,946] [INFO] Target genome list was writen to GCA_026710105.1_ASM2671010v1_genomic.fna/target_genomes.txt
[2023-06-27 20:39:47,955] [INFO] Task started: fastANI
[2023-06-27 20:39:47,955] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb087cc5-40ad-4de6-a42d-cd8794464b8e/GCA_026710105.1_ASM2671010v1_genomic.fna.gz --refList GCA_026710105.1_ASM2671010v1_genomic.fna/target_genomes.txt --output GCA_026710105.1_ASM2671010v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 20:40:09,086] [INFO] Task succeeded: fastANI
[2023-06-27 20:40:09,086] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1bee638-4f43-405b-a7b3-3fb340dc75d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 20:40:09,087] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1bee638-4f43-405b-a7b3-3fb340dc75d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 20:40:09,107] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 20:40:09,108] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 20:40:09,108] [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
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	75.9412	86	979	95	below_threshold
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	75.7918	54	979	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	75.7692	77	979	95	below_threshold
Acidibrevibacterium fodinaquatile	strain=G45-3	GCA_003352165.1	1969806	1969806	type	True	75.7373	53	979	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	75.678	100	979	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	75.648	62	979	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	75.6473	66	979	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	75.6205	108	979	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	75.6205	108	979	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	75.5476	102	979	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	75.5341	106	979	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	75.502	84	979	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	75.4997	97	979	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	75.4822	90	979	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	75.4561	57	979	95	below_threshold
Bradyrhizobium diversitatis	strain=CNPSo 4019	GCA_016031635.1	2755406	2755406	type	True	75.4322	78	979	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	75.4315	64	979	95	below_threshold
Zavarzinia compransoris	strain=DSM 1231	GCA_004362995.1	1264899	1264899	type	True	75.4066	83	979	95	below_threshold
Zavarzinia compransoris	strain=DSM 1231	GCA_003173055.1	1264899	1264899	type	True	75.3989	84	979	95	below_threshold
Roseomonas hellenica	strain=LMG 31523	GCA_018129085.1	2687306	2687306	type	True	75.3935	100	979	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	75.3372	57	979	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 20:40:09,110] [INFO] DFAST Taxonomy check result was written to GCA_026710105.1_ASM2671010v1_genomic.fna/tc_result.tsv
[2023-06-27 20:40:09,110] [INFO] ===== Taxonomy check completed =====
[2023-06-27 20:40:09,111] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 20:40:09,111] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1bee638-4f43-405b-a7b3-3fb340dc75d7/dqc_reference/checkm_data
[2023-06-27 20:40:09,112] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 20:40:09,149] [INFO] Task started: CheckM
[2023-06-27 20:40:09,150] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026710105.1_ASM2671010v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026710105.1_ASM2671010v1_genomic.fna/checkm_input GCA_026710105.1_ASM2671010v1_genomic.fna/checkm_result
[2023-06-27 20:40:39,568] [INFO] Task succeeded: CheckM
[2023-06-27 20:40:39,571] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 20:40:39,593] [INFO] ===== Completeness check finished =====
[2023-06-27 20:40:39,594] [INFO] ===== Start GTDB Search =====
[2023-06-27 20:40:39,594] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026710105.1_ASM2671010v1_genomic.fna/markers.fasta)
[2023-06-27 20:40:39,594] [INFO] Task started: Blastn
[2023-06-27 20:40:39,595] [INFO] Running command: blastn -query GCA_026710105.1_ASM2671010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1bee638-4f43-405b-a7b3-3fb340dc75d7/dqc_reference/reference_markers_gtdb.fasta -out GCA_026710105.1_ASM2671010v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 20:40:41,085] [INFO] Task succeeded: Blastn
[2023-06-27 20:40:41,091] [INFO] Selected 29 target genomes.
[2023-06-27 20:40:41,091] [INFO] Target genome list was writen to GCA_026710105.1_ASM2671010v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 20:40:41,141] [INFO] Task started: fastANI
[2023-06-27 20:40:41,142] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb087cc5-40ad-4de6-a42d-cd8794464b8e/GCA_026710105.1_ASM2671010v1_genomic.fna.gz --refList GCA_026710105.1_ASM2671010v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026710105.1_ASM2671010v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 20:41:00,829] [INFO] Task succeeded: fastANI
[2023-06-27 20:41:00,847] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 20:41:00,848] [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_002238885.1	s__Bin95 sp002238885	80.9072	410	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Bin95;f__Bin95;g__Bin95	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001618175.1	s__Oceanibaculum pacificum	75.9412	86	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001657395.1	s__Pelagibius sp001657395	75.8726	72	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__Pelagibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	75.809	105	979	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_006738865.1	s__Stella sp006738865	75.7631	92	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_018240745.1	s__Reyranella sp018240745	75.6889	78	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_900177295.1	s__Tistlia consotensis	75.6405	106	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_016869975.1	s__JAFAZJ01 sp016869975	75.5927	90	979	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	75.5915	70	979	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_000164635.1	s__Roseomonas cervicalis	75.577	88	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640745.1	s__Nisaea sp017640745	75.5567	83	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006738645.1	s__Stella humosa	75.5448	105	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016869645.1	s__SHVW01 sp016869645	75.5443	88	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVW01;f__SHVW01;g__SHVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014925385.1	s__WHTV01 sp014925385	75.505	88	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124535.1	s__RI-112 sp016124535	75.4145	57	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__RI-112	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129085.1	s__Roseomonas_C hellenica	75.3935	100	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_C	95.0	97.71	97.71	0.92	0.92	2	-
GCA_004296815.1	s__Reyranella sp004296815	75.3673	71	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_002220095.1	s__Bosea sp002220095	75.3605	85	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173035.1	s__Zavarzinia aquatilis	75.3467	67	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Zavarziniales;f__Zavarziniaceae;g__Zavarzinia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016195115.1	s__JACQAI01 sp016195115	75.2698	67	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Elsterales;f__Elsteraceae;g__JACQAI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793965.1	s__JAEULF01 sp016793965	75.2635	65	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__JAEULF01;f__JAEULF01;g__JAEULF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197855.1	s__Rhodospira marina	75.2114	52	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	100.00	99.99	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2023-06-27 20:41:00,850] [INFO] GTDB search result was written to GCA_026710105.1_ASM2671010v1_genomic.fna/result_gtdb.tsv
[2023-06-27 20:41:00,850] [INFO] ===== GTDB Search completed =====
[2023-06-27 20:41:00,855] [INFO] DFAST_QC result json was written to GCA_026710105.1_ASM2671010v1_genomic.fna/dqc_result.json
[2023-06-27 20:41:00,855] [INFO] DFAST_QC completed!
[2023-06-27 20:41:00,855] [INFO] Total running time: 0h1m30s