[2024-01-24 12:06:23,837] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:23,840] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:23,840] [INFO] DQC Reference Directory: /var/lib/cwl/stg05856dd5-5ac2-4c05-b5f5-0758afbb230d/dqc_reference
[2024-01-24 12:06:25,265] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:25,266] [INFO] Task started: Prodigal
[2024-01-24 12:06:25,266] [INFO] Running command: gunzip -c /var/lib/cwl/stg80547c1a-a1df-4f42-9162-a3aae87b2c01/GCF_004015795.1_ASM401579v1_genomic.fna.gz | prodigal -d GCF_004015795.1_ASM401579v1_genomic.fna/cds.fna -a GCF_004015795.1_ASM401579v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:35,309] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:35,309] [INFO] Task started: HMMsearch
[2024-01-24 12:06:35,310] [INFO] Running command: hmmsearch --tblout GCF_004015795.1_ASM401579v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05856dd5-5ac2-4c05-b5f5-0758afbb230d/dqc_reference/reference_markers.hmm GCF_004015795.1_ASM401579v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:35,559] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:35,561] [INFO] Found 6/6 markers.
[2024-01-24 12:06:35,590] [INFO] Query marker FASTA was written to GCF_004015795.1_ASM401579v1_genomic.fna/markers.fasta
[2024-01-24 12:06:35,591] [INFO] Task started: Blastn
[2024-01-24 12:06:35,591] [INFO] Running command: blastn -query GCF_004015795.1_ASM401579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05856dd5-5ac2-4c05-b5f5-0758afbb230d/dqc_reference/reference_markers.fasta -out GCF_004015795.1_ASM401579v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:36,582] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:36,587] [INFO] Selected 30 target genomes.
[2024-01-24 12:06:36,587] [INFO] Target genome list was writen to GCF_004015795.1_ASM401579v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:36,607] [INFO] Task started: fastANI
[2024-01-24 12:06:36,607] [INFO] Running command: fastANI --query /var/lib/cwl/stg80547c1a-a1df-4f42-9162-a3aae87b2c01/GCF_004015795.1_ASM401579v1_genomic.fna.gz --refList GCF_004015795.1_ASM401579v1_genomic.fna/target_genomes.txt --output GCF_004015795.1_ASM401579v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:57,649] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:57,650] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05856dd5-5ac2-4c05-b5f5-0758afbb230d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:57,650] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05856dd5-5ac2-4c05-b5f5-0758afbb230d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:57,672] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:06:57,672] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:06:57,672] [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	78.9244	363	991	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	78.8536	386	991	95	below_threshold
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	78.7219	339	991	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	78.658	336	991	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	78.6516	337	991	95	below_threshold
Frigidibacter albus	strain=CGMCC 1.13995	GCA_014640395.1	1465486	1465486	type	True	78.6135	341	991	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_010993795.1	1465486	1465486	type	True	78.5813	338	991	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009908165.1	1465486	1465486	type	True	78.5703	335	991	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009881095.1	1465486	1465486	type	True	78.5592	340	991	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	78.5474	356	991	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.5359	333	991	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	78.467	350	991	95	below_threshold
Gemmobacter lanyuensis	strain=KCTC 23714	GCA_014652355.1	1054497	1054497	type	True	78.4062	336	991	95	below_threshold
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	78.3772	320	991	95	below_threshold
Gemmobacter serpentinus	strain=HB-1	GCA_008973825.1	2652247	2652247	type	True	78.3594	301	991	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	78.3456	355	991	95	below_threshold
Paracoccus lichenicola	strain=YIM 132242	GCA_009708075.1	2665644	2665644	type	True	78.333	312	991	95	below_threshold
Paracoccus liaowanqingii	strain=2251	GCA_004683865.2	2560053	2560053	type	True	78.3301	340	991	95	below_threshold
Gemmobacter nectariphilus	strain=DSM 15620	GCA_000429765.1	220343	220343	type	True	78.3153	322	991	95	below_threshold
[Luteovulum] sphaeroides subsp. megalophilum	strain=DSM 18937	GCA_900188265.1	418630	1063	type	True	78.3131	335	991	95	below_threshold
Paracoccus aestuarii	strain=DSM 19484	GCA_003594815.1	453842	453842	type	True	78.249	288	991	95	below_threshold
Paracoccus zhejiangensis	strain=J6	GCA_002847445.1	1077935	1077935	type	True	78.2228	290	991	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	78.1773	284	991	95	below_threshold
Paracoccus gahaiensis	strain=KCTC 42687	GCA_005048225.1	1706839	1706839	type	True	78.1593	320	991	95	below_threshold
Paracoccus salipaludis	strain=WN007	GCA_002287065.1	2032623	2032623	type	True	78.1005	293	991	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	78.0194	304	991	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	77.9367	220	991	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	77.768	256	991	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	77.7197	248	991	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	77.7149	293	991	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:57,674] [INFO] DFAST Taxonomy check result was written to GCF_004015795.1_ASM401579v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:57,674] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:57,675] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:57,675] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05856dd5-5ac2-4c05-b5f5-0758afbb230d/dqc_reference/checkm_data
[2024-01-24 12:06:57,676] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:57,706] [INFO] Task started: CheckM
[2024-01-24 12:06:57,707] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004015795.1_ASM401579v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004015795.1_ASM401579v1_genomic.fna/checkm_input GCF_004015795.1_ASM401579v1_genomic.fna/checkm_result
[2024-01-24 12:07:33,221] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:33,222] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:33,239] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:33,239] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:33,240] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004015795.1_ASM401579v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:33,240] [INFO] Task started: Blastn
[2024-01-24 12:07:33,240] [INFO] Running command: blastn -query GCF_004015795.1_ASM401579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05856dd5-5ac2-4c05-b5f5-0758afbb230d/dqc_reference/reference_markers_gtdb.fasta -out GCF_004015795.1_ASM401579v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:35,105] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:35,108] [INFO] Selected 16 target genomes.
[2024-01-24 12:07:35,109] [INFO] Target genome list was writen to GCF_004015795.1_ASM401579v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:35,122] [INFO] Task started: fastANI
[2024-01-24 12:07:35,122] [INFO] Running command: fastANI --query /var/lib/cwl/stg80547c1a-a1df-4f42-9162-a3aae87b2c01/GCF_004015795.1_ASM401579v1_genomic.fna.gz --refList GCF_004015795.1_ASM401579v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004015795.1_ASM401579v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:45,741] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:45,754] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:45,755] [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_004015795.1	s__Falsirhodobacter deserti	100.0	990	991	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Falsirhodobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018279165.1	s__Falsirhodobacter sp018279165	82.3303	533	991	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Falsirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004959935.1	s__Falsirhodobacter xinxiangensis	81.0433	540	991	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Falsirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739715.2	s__Falsirhodobacter sp000739715	79.3517	397	991	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Falsirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034985.1	s__Cereibacter changlensis	78.9365	362	991	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter	95.0	98.07	96.18	0.89	0.78	3	-
GCF_004799285.1	s__Gemmobacter_D aestuarii	78.759	361	991	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_009908265.2	s__Gemmobacter_B sp009908265	78.6455	337	991	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_009908165.1	s__Frigidibacter albus	78.5589	336	991	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	100.00	100.00	1.00	0.99	4	-
GCA_017599285.1	s__Cereibacter_A azotoformans	78.4788	331	991	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.0	98.54	95.54	0.92	0.86	6	-
GCF_014652355.1	s__Gemmobacter lanyuensis	78.4064	336	991	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009708075.1	s__Paracoccus lichenicola	78.3372	313	991	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429765.1	s__Wagnerdoeblera nectariphila	78.3153	322	991	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wagnerdoeblera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005048225.1	s__Paracoccus gahaiensis	78.1721	319	991	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002855575.1	s__Gemmobacter_B sp002855575	78.0407	330	991	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_011174775.1	s__Tabrizicola sp011174775	77.9965	306	991	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649175.1	s__Rhodovulum strictum	77.755	257	991	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:45,756] [INFO] GTDB search result was written to GCF_004015795.1_ASM401579v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:45,757] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:45,761] [INFO] DFAST_QC result json was written to GCF_004015795.1_ASM401579v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:45,762] [INFO] DFAST_QC completed!
[2024-01-24 12:07:45,762] [INFO] Total running time: 0h1m22s