[2023-06-27 11:26:27,620] [INFO] DFAST_QC pipeline started.
[2023-06-27 11:26:27,623] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 11:26:27,623] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e4468ef-ecfc-46bf-8956-04a81b52e212/dqc_reference
[2023-06-27 11:26:28,953] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 11:26:28,954] [INFO] Task started: Prodigal
[2023-06-27 11:26:28,955] [INFO] Running command: gunzip -c /var/lib/cwl/stgc275c3b4-fa3e-4e1b-b8be-eedbc4b073ab/GCA_026461475.1_ASM2646147v1_genomic.fna.gz | prodigal -d GCA_026461475.1_ASM2646147v1_genomic.fna/cds.fna -a GCA_026461475.1_ASM2646147v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 11:26:34,823] [INFO] Task succeeded: Prodigal
[2023-06-27 11:26:34,824] [INFO] Task started: HMMsearch
[2023-06-27 11:26:34,824] [INFO] Running command: hmmsearch --tblout GCA_026461475.1_ASM2646147v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e4468ef-ecfc-46bf-8956-04a81b52e212/dqc_reference/reference_markers.hmm GCA_026461475.1_ASM2646147v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 11:26:35,031] [INFO] Task succeeded: HMMsearch
[2023-06-27 11:26:35,032] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc275c3b4-fa3e-4e1b-b8be-eedbc4b073ab/GCA_026461475.1_ASM2646147v1_genomic.fna.gz]
[2023-06-27 11:26:35,065] [INFO] Query marker FASTA was written to GCA_026461475.1_ASM2646147v1_genomic.fna/markers.fasta
[2023-06-27 11:26:35,065] [INFO] Task started: Blastn
[2023-06-27 11:26:35,066] [INFO] Running command: blastn -query GCA_026461475.1_ASM2646147v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e4468ef-ecfc-46bf-8956-04a81b52e212/dqc_reference/reference_markers.fasta -out GCA_026461475.1_ASM2646147v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:26:35,737] [INFO] Task succeeded: Blastn
[2023-06-27 11:26:35,740] [INFO] Selected 24 target genomes.
[2023-06-27 11:26:35,741] [INFO] Target genome list was writen to GCA_026461475.1_ASM2646147v1_genomic.fna/target_genomes.txt
[2023-06-27 11:26:35,763] [INFO] Task started: fastANI
[2023-06-27 11:26:35,764] [INFO] Running command: fastANI --query /var/lib/cwl/stgc275c3b4-fa3e-4e1b-b8be-eedbc4b073ab/GCA_026461475.1_ASM2646147v1_genomic.fna.gz --refList GCA_026461475.1_ASM2646147v1_genomic.fna/target_genomes.txt --output GCA_026461475.1_ASM2646147v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 11:26:50,331] [INFO] Task succeeded: fastANI
[2023-06-27 11:26:50,332] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e4468ef-ecfc-46bf-8956-04a81b52e212/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 11:26:50,333] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e4468ef-ecfc-46bf-8956-04a81b52e212/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 11:26:50,354] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 11:26:50,354] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 11:26:50,355] [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
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	78.9314	79	226	95	below_threshold
Paracoccus limosus	strain=JCM 17370	GCA_009711185.1	913252	913252	type	True	78.2807	57	226	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	78.2359	79	226	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	78.2293	80	226	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.2262	51	226	95	below_threshold
Cereibacter changlensis	strain=JA139	GCA_003034985.1	402884	402884	type	True	78.03	77	226	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009881095.1	1465486	1465486	type	True	77.9668	81	226	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009908165.1	1465486	1465486	type	True	77.9547	82	226	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_003034995.1	33049	33049	type	True	77.9292	78	226	95	below_threshold
Paracoccus lutimaris	strain=CECT 8525	GCA_003337565.1	1490030	1490030	type	True	77.9288	61	226	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	77.7862	88	226	95	below_threshold
Gemmobacter lutimaris	strain=YJ-T1-11	GCA_003570715.1	2306023	2306023	type	True	77.7513	86	226	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	77.5207	53	226	95	below_threshold
Gemmobacter nectariphilus	strain=DSM 15620	GCA_000429765.1	220343	220343	type	True	77.3374	73	226	95	below_threshold
Paracoccus aminovorans	strain=DSM 8537	GCA_900113565.1	34004	34004	type	True	77.3276	56	226	95	below_threshold
Paracoccus aminovorans		GCA_900005615.1	34004	34004	type	True	77.3276	56	226	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.2214	65	226	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	77.1652	67	226	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	77.034	67	226	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	77.0002	64	226	95	below_threshold
Pseudogemmobacter hezensis	strain=D13-10-4-6	GCA_013155295.1	2737662	2737662	type	True	76.8863	68	226	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 11:26:50,357] [INFO] DFAST Taxonomy check result was written to GCA_026461475.1_ASM2646147v1_genomic.fna/tc_result.tsv
[2023-06-27 11:26:50,358] [INFO] ===== Taxonomy check completed =====
[2023-06-27 11:26:50,358] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 11:26:50,359] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e4468ef-ecfc-46bf-8956-04a81b52e212/dqc_reference/checkm_data
[2023-06-27 11:26:50,360] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 11:26:50,391] [INFO] Task started: CheckM
[2023-06-27 11:26:50,392] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026461475.1_ASM2646147v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026461475.1_ASM2646147v1_genomic.fna/checkm_input GCA_026461475.1_ASM2646147v1_genomic.fna/checkm_result
[2023-06-27 11:27:14,726] [INFO] Task succeeded: CheckM
[2023-06-27 11:27:14,728] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.55%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-27 11:27:14,762] [INFO] ===== Completeness check finished =====
[2023-06-27 11:27:14,763] [INFO] ===== Start GTDB Search =====
[2023-06-27 11:27:14,763] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026461475.1_ASM2646147v1_genomic.fna/markers.fasta)
[2023-06-27 11:27:14,763] [INFO] Task started: Blastn
[2023-06-27 11:27:14,764] [INFO] Running command: blastn -query GCA_026461475.1_ASM2646147v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e4468ef-ecfc-46bf-8956-04a81b52e212/dqc_reference/reference_markers_gtdb.fasta -out GCA_026461475.1_ASM2646147v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:27:15,649] [INFO] Task succeeded: Blastn
[2023-06-27 11:27:15,654] [INFO] Selected 21 target genomes.
[2023-06-27 11:27:15,655] [INFO] Target genome list was writen to GCA_026461475.1_ASM2646147v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 11:27:15,690] [INFO] Task started: fastANI
[2023-06-27 11:27:15,690] [INFO] Running command: fastANI --query /var/lib/cwl/stgc275c3b4-fa3e-4e1b-b8be-eedbc4b073ab/GCA_026461475.1_ASM2646147v1_genomic.fna.gz --refList GCA_026461475.1_ASM2646147v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026461475.1_ASM2646147v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 11:27:28,981] [INFO] Task succeeded: fastANI
[2023-06-27 11:27:29,005] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 11:27:29,006] [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_018240425.1	s__TMP-24 sp018240425	79.4204	132	226	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_008271655.1	s__Gemmobacter caeruleus	78.9314	79	226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011008935.1	s__KMS-5 sp011008935	78.7147	89	226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__KMS-5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280515.1	s__Albidovulum sp002280515	78.3378	91	226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110025.1	s__Gemmobacter aquatilis	78.3062	91	226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869835.1	s__KMS-5 sp016869835	78.2907	75	226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__KMS-5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765795.1	s__UBA1943 sp016765795	78.174	77	226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124615.1	s__Solirhodobacter sp016124615	78.1501	82	226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Solirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176015.1	s__Pseudorhodobacter_B sp000176015	78.0393	79	226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034985.1	s__Cereibacter changlensis	78.03	77	226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter	95.0	98.07	96.18	0.89	0.78	3	-
GCA_002841115.1	s__Albidovulum sp002841115	77.9536	101	226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011620265.1	s__Albidovulum sp011620265	77.9482	87	226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337565.1	s__Paracoccus lutimaris	77.9288	61	226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003993775.1	s__Frigidibacter sp003993775	77.9115	67	226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001620265.1	s__Frigidibacter mobilis	77.8238	87	226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196965.1	s__Actibacterium_A naphthalenivorans	77.4527	62	226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium_A	95.0	98.28	97.38	0.93	0.89	4	-
GCF_003594815.1	s__Paracoccus aestuarii	77.4333	60	226	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	77.3374	73	226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wagnerdoeblera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900005615.1	s__Paracoccus aminovorans	77.3276	56	226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_001546115.1	s__Paracoccus aminovorans_B	76.9739	56	226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	95.35	95.35	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-06-27 11:27:29,008] [INFO] GTDB search result was written to GCA_026461475.1_ASM2646147v1_genomic.fna/result_gtdb.tsv
[2023-06-27 11:27:29,009] [INFO] ===== GTDB Search completed =====
[2023-06-27 11:27:29,014] [INFO] DFAST_QC result json was written to GCA_026461475.1_ASM2646147v1_genomic.fna/dqc_result.json
[2023-06-27 11:27:29,014] [INFO] DFAST_QC completed!
[2023-06-27 11:27:29,014] [INFO] Total running time: 0h1m1s