[2024-01-24 11:34:43,082] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:43,083] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:43,084] [INFO] DQC Reference Directory: /var/lib/cwl/stgb6b77caa-3166-4a18-820c-9835136b1968/dqc_reference
[2024-01-24 11:34:44,452] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:44,454] [INFO] Task started: Prodigal
[2024-01-24 11:34:44,454] [INFO] Running command: gunzip -c /var/lib/cwl/stg58e7a865-a0ab-4d09-a758-5d41a415d3ea/GCF_020179405.1_ASM2017940v1_genomic.fna.gz | prodigal -d GCF_020179405.1_ASM2017940v1_genomic.fna/cds.fna -a GCF_020179405.1_ASM2017940v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:56,685] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:56,685] [INFO] Task started: HMMsearch
[2024-01-24 11:34:56,685] [INFO] Running command: hmmsearch --tblout GCF_020179405.1_ASM2017940v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb6b77caa-3166-4a18-820c-9835136b1968/dqc_reference/reference_markers.hmm GCF_020179405.1_ASM2017940v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:56,994] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:56,995] [INFO] Found 6/6 markers.
[2024-01-24 11:34:57,048] [INFO] Query marker FASTA was written to GCF_020179405.1_ASM2017940v1_genomic.fna/markers.fasta
[2024-01-24 11:34:57,048] [INFO] Task started: Blastn
[2024-01-24 11:34:57,049] [INFO] Running command: blastn -query GCF_020179405.1_ASM2017940v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6b77caa-3166-4a18-820c-9835136b1968/dqc_reference/reference_markers.fasta -out GCF_020179405.1_ASM2017940v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:58,100] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:58,104] [INFO] Selected 16 target genomes.
[2024-01-24 11:34:58,104] [INFO] Target genome list was writen to GCF_020179405.1_ASM2017940v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:58,111] [INFO] Task started: fastANI
[2024-01-24 11:34:58,111] [INFO] Running command: fastANI --query /var/lib/cwl/stg58e7a865-a0ab-4d09-a758-5d41a415d3ea/GCF_020179405.1_ASM2017940v1_genomic.fna.gz --refList GCF_020179405.1_ASM2017940v1_genomic.fna/target_genomes.txt --output GCF_020179405.1_ASM2017940v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:12,066] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:12,066] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb6b77caa-3166-4a18-820c-9835136b1968/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:12,067] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb6b77caa-3166-4a18-820c-9835136b1968/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:12,080] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:35:12,081] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:35:12,081] [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	80.6609	668	1385	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	80.5086	684	1385	95	below_threshold
Rhodobacter flagellatus	strain=SYSU G03088	GCA_008271465.1	2593021	2593021	type	True	80.389	648	1385	95	below_threshold
Gemmobacter caeni	strain=DSM 21823	GCA_003054195.1	589035	589035	type	True	80.1174	649	1385	95	below_threshold
Gemmobacter caeni	strain=CGMCC 1.7745	GCA_007830625.1	589035	589035	type	True	80.0808	636	1385	95	below_threshold
Rhodobacter thermarum	strain=YIM 73036	GCA_003574395.1	2670345	2670345	type	True	80.0455	661	1385	95	below_threshold
Gemmobacter lutimaris	strain=YJ-T1-11	GCA_003570715.1	2306023	2306023	type	True	79.9694	644	1385	95	below_threshold
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	79.877	672	1385	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	79.8335	613	1385	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	79.8061	616	1385	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	79.7083	671	1385	95	below_threshold
Pseudogemmobacter bohemicus	strain=Cd-10	GCA_003290025.1	2250708	2250708	type	True	79.4968	631	1385	95	below_threshold
Pseudogemmobacter hezensis	strain=D13-10-4-6	GCA_013155295.1	2737662	2737662	type	True	79.3653	564	1385	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	79.2465	584	1385	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	79.2451	624	1385	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	79.1346	551	1385	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:12,083] [INFO] DFAST Taxonomy check result was written to GCF_020179405.1_ASM2017940v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:12,083] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:12,083] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:12,084] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb6b77caa-3166-4a18-820c-9835136b1968/dqc_reference/checkm_data
[2024-01-24 11:35:12,085] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:12,130] [INFO] Task started: CheckM
[2024-01-24 11:35:12,131] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020179405.1_ASM2017940v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020179405.1_ASM2017940v1_genomic.fna/checkm_input GCF_020179405.1_ASM2017940v1_genomic.fna/checkm_result
[2024-01-24 11:35:56,072] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:56,073] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:56,088] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:56,089] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:56,089] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020179405.1_ASM2017940v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:56,090] [INFO] Task started: Blastn
[2024-01-24 11:35:56,090] [INFO] Running command: blastn -query GCF_020179405.1_ASM2017940v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6b77caa-3166-4a18-820c-9835136b1968/dqc_reference/reference_markers_gtdb.fasta -out GCF_020179405.1_ASM2017940v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:57,947] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:57,950] [INFO] Selected 18 target genomes.
[2024-01-24 11:35:57,950] [INFO] Target genome list was writen to GCF_020179405.1_ASM2017940v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:58,007] [INFO] Task started: fastANI
[2024-01-24 11:35:58,008] [INFO] Running command: fastANI --query /var/lib/cwl/stg58e7a865-a0ab-4d09-a758-5d41a415d3ea/GCF_020179405.1_ASM2017940v1_genomic.fna.gz --refList GCF_020179405.1_ASM2017940v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020179405.1_ASM2017940v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:13,446] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:13,473] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:36:13,474] [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_011043545.1	s__JAAKGP01 sp011043545	82.036	801	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAKGP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034965.1	s__Fuscovulum blasticum	81.8829	774	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fuscovulum	95.0	97.58	97.58	0.96	0.96	2	-
GCA_018058035.1	s__JAAKGP01 sp018058035	81.7091	649	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAKGP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016704435.1	s__JAAKGP01 sp016704435	81.4197	762	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAKGP01	95.0	99.06	99.06	0.93	0.93	2	-
GCF_900609055.1	s__Pseudogemmobacter humi	81.1262	684	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859945.1	s__UBA1943 sp014859945	81.0057	608	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879735.1	s__Pseudogemmobacter sp014879735	80.8563	674	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015999335.1	s__Tabrizicola soli	80.69	708	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011008935.1	s__KMS-5 sp011008935	80.5388	633	1385	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_002900975.1	s__Tabrizicola aquatica	80.2577	676	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110025.1	s__Gemmobacter aquatilis	79.8644	674	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003993775.1	s__Frigidibacter sp003993775	79.817	600	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908265.2	s__Gemmobacter_B sp009908265	79.8116	616	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016792925.1	s__Gemmobacter sp016792925	79.6615	534	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000500915.1	s__Gemmobacter_B sp000500915	79.4306	545	1385	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_002900965.1	s__ETT8 sp002900965	79.3843	559	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010915705.1	s__ETT8 sp010915705	79.2423	585	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009380135.2	s__Fertoeibacter niger	79.0948	636	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fertoeibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:13,475] [INFO] GTDB search result was written to GCF_020179405.1_ASM2017940v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:13,475] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:13,483] [INFO] DFAST_QC result json was written to GCF_020179405.1_ASM2017940v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:13,484] [INFO] DFAST_QC completed!
[2024-01-24 11:36:13,484] [INFO] Total running time: 0h1m30s