[2024-01-24 13:21:10,871] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:10,873] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:10,873] [INFO] DQC Reference Directory: /var/lib/cwl/stg9baf10fa-997a-4dc0-a5a2-5d085411bdc7/dqc_reference
[2024-01-24 13:21:12,346] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:12,349] [INFO] Task started: Prodigal
[2024-01-24 13:21:12,350] [INFO] Running command: gunzip -c /var/lib/cwl/stgec7c498e-a7b7-4aaa-b0b6-7d63ad286e04/GCF_021491355.1_26_genomic.fna.gz | prodigal -d GCF_021491355.1_26_genomic.fna/cds.fna -a GCF_021491355.1_26_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:21:25,322] [INFO] Task succeeded: Prodigal
[2024-01-24 13:21:25,322] [INFO] Task started: HMMsearch
[2024-01-24 13:21:25,322] [INFO] Running command: hmmsearch --tblout GCF_021491355.1_26_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9baf10fa-997a-4dc0-a5a2-5d085411bdc7/dqc_reference/reference_markers.hmm GCF_021491355.1_26_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:21:25,632] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:21:25,633] [INFO] Found 6/6 markers.
[2024-01-24 13:21:25,683] [INFO] Query marker FASTA was written to GCF_021491355.1_26_genomic.fna/markers.fasta
[2024-01-24 13:21:25,683] [INFO] Task started: Blastn
[2024-01-24 13:21:25,683] [INFO] Running command: blastn -query GCF_021491355.1_26_genomic.fna/markers.fasta -db /var/lib/cwl/stg9baf10fa-997a-4dc0-a5a2-5d085411bdc7/dqc_reference/reference_markers.fasta -out GCF_021491355.1_26_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:26,721] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:26,726] [INFO] Selected 21 target genomes.
[2024-01-24 13:21:26,726] [INFO] Target genome list was writen to GCF_021491355.1_26_genomic.fna/target_genomes.txt
[2024-01-24 13:21:26,739] [INFO] Task started: fastANI
[2024-01-24 13:21:26,740] [INFO] Running command: fastANI --query /var/lib/cwl/stgec7c498e-a7b7-4aaa-b0b6-7d63ad286e04/GCF_021491355.1_26_genomic.fna.gz --refList GCF_021491355.1_26_genomic.fna/target_genomes.txt --output GCF_021491355.1_26_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:21:43,867] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:43,867] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9baf10fa-997a-4dc0-a5a2-5d085411bdc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:21:43,868] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9baf10fa-997a-4dc0-a5a2-5d085411bdc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:21:43,930] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:21:43,930] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:21:43,930] [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
Cereibacter changlensis	strain=JA139	GCA_003034985.1	402884	402884	type	True	79.9775	561	1393	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	79.9073	586	1393	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	79.7811	511	1393	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	79.6552	482	1393	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	79.6439	500	1393	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	79.5699	541	1393	95	below_threshold
Cereibacter sphaeroides	strain=NBRC 12203	GCA_007991035.1	1063	1063	type	True	79.5542	489	1393	95	below_threshold
Cereibacter sphaeroides	strain=2.4.1	GCA_003324715.1	1063	1063	type	True	79.5377	495	1393	95	below_threshold
Rhodobacter thermarum	strain=YIM 73036	GCA_003574395.1	2670345	2670345	type	True	79.5311	547	1393	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	79.5229	544	1393	95	below_threshold
Cereibacter sphaeroides	strain=2.4.1	GCA_000273405.1	1063	1063	type	True	79.5217	497	1393	95	below_threshold
Rhodobacter flagellatus	strain=SYSU G03088	GCA_008271465.1	2593021	2593021	type	True	79.3987	568	1393	95	below_threshold
Gemmobacter nectariphilus	strain=DSM 15620	GCA_000429765.1	220343	220343	type	True	79.3225	429	1393	95	below_threshold
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	79.2266	506	1393	95	below_threshold
Gemmobacter aquaticus	strain=CGMCC 1.7029	GCA_014645295.1	490185	490185	type	True	79.1373	448	1393	95	below_threshold
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	79.0833	545	1393	95	below_threshold
Gemmobacter lanyuensis	strain=KCTC 23714	GCA_014652355.1	1054497	1054497	type	True	79.0563	447	1393	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	79.0259	533	1393	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	78.9447	441	1393	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.5553	394	1393	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	78.4832	458	1393	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:21:43,932] [INFO] DFAST Taxonomy check result was written to GCF_021491355.1_26_genomic.fna/tc_result.tsv
[2024-01-24 13:21:43,933] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:21:43,933] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:21:43,934] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9baf10fa-997a-4dc0-a5a2-5d085411bdc7/dqc_reference/checkm_data
[2024-01-24 13:21:43,935] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:21:43,982] [INFO] Task started: CheckM
[2024-01-24 13:21:43,982] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021491355.1_26_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021491355.1_26_genomic.fna/checkm_input GCF_021491355.1_26_genomic.fna/checkm_result
[2024-01-24 13:22:25,434] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:25,437] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:25,476] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:25,477] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:25,477] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021491355.1_26_genomic.fna/markers.fasta)
[2024-01-24 13:22:25,478] [INFO] Task started: Blastn
[2024-01-24 13:22:25,478] [INFO] Running command: blastn -query GCF_021491355.1_26_genomic.fna/markers.fasta -db /var/lib/cwl/stg9baf10fa-997a-4dc0-a5a2-5d085411bdc7/dqc_reference/reference_markers_gtdb.fasta -out GCF_021491355.1_26_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:27,732] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:27,736] [INFO] Selected 28 target genomes.
[2024-01-24 13:22:27,736] [INFO] Target genome list was writen to GCF_021491355.1_26_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:27,776] [INFO] Task started: fastANI
[2024-01-24 13:22:27,777] [INFO] Running command: fastANI --query /var/lib/cwl/stgec7c498e-a7b7-4aaa-b0b6-7d63ad286e04/GCF_021491355.1_26_genomic.fna.gz --refList GCF_021491355.1_26_genomic.fna/target_genomes_gtdb.txt --output GCF_021491355.1_26_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:49,370] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:49,397] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:22:49,397] [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
GCF_003034985.1	s__Cereibacter changlensis	79.9679	562	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter	95.0	98.07	96.18	0.89	0.78	3	-
GCF_015999335.1	s__Tabrizicola soli	79.9427	576	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017599285.1	s__Cereibacter_A azotoformans	79.7743	460	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.0	98.54	95.54	0.92	0.86	6	-
GCA_003243455.1	s__Rhodobacter_F sphaeroides_A	79.7622	598	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011043545.1	s__JAAKGP01 sp011043545	79.7207	560	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAKGP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908265.2	s__Gemmobacter_B sp009908265	79.56	540	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000012905.2	s__Cereibacter_A sphaeroides	79.5316	496	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.1736	98.82	96.57	0.94	0.87	24	-
GCF_003993775.1	s__Frigidibacter sp003993775	79.5311	495	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859945.1	s__UBA1943 sp014859945	79.5214	462	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763725.1	s__JACXUX01 sp014763725	79.4639	417	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JACXUX01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008271465.1	s__Tabrizicola flagellata	79.3986	570	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240425.1	s__TMP-24 sp018240425	79.3523	466	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__TMP-24	95.0	99.95	99.95	0.97	0.97	2	-
GCF_004799285.1	s__Gemmobacter_D aestuarii	79.3043	569	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000500915.1	s__Gemmobacter_B sp000500915	79.2998	464	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008271655.1	s__Gemmobacter caeruleus	79.2359	505	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018058035.1	s__JAAKGP01 sp018058035	79.1407	493	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAKGP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859075.1	s__Gemmobacter aquaticus	79.1359	440	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002855575.1	s__Gemmobacter_B sp002855575	79.0953	576	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002900975.1	s__Tabrizicola aquatica	79.0748	524	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303485.1	s__Tabrizicola sp017303485	79.0681	504	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652355.1	s__Gemmobacter lanyuensis	79.0462	447	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013297695.1	s__Rhodobacter_F sp013297695	79.0357	497	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280515.1	s__Albidovulum sp002280515	78.8127	466	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900609055.1	s__Pseudogemmobacter humi	78.7866	441	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014654775.1	s__Gemmobacter_B sp014654775	78.6166	511	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018798885.1	s__Gemmobacter sp018798885	78.4921	457	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002196855.1	s__Haematobacter sp002196855	78.2883	273	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Haematobacter	95.0	98.61	98.61	0.86	0.86	2	-
GCF_016765775.1	s__Pseudorhodobacter sp016765775	78.047	412	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:22:49,399] [INFO] GTDB search result was written to GCF_021491355.1_26_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:49,399] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:49,404] [INFO] DFAST_QC result json was written to GCF_021491355.1_26_genomic.fna/dqc_result.json
[2024-01-24 13:22:49,405] [INFO] DFAST_QC completed!
[2024-01-24 13:22:49,405] [INFO] Total running time: 0h1m39s