[2024-01-24 11:26:12,609] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:12,614] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:12,615] [INFO] DQC Reference Directory: /var/lib/cwl/stgc96915e1-cb9b-4e6d-b497-62608e041d26/dqc_reference
[2024-01-24 11:26:14,043] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:14,044] [INFO] Task started: Prodigal
[2024-01-24 11:26:14,045] [INFO] Running command: gunzip -c /var/lib/cwl/stg850e026b-91cc-4805-a9fa-d976eb64b1ed/GCF_004799285.1_ASM479928v1_genomic.fna.gz | prodigal -d GCF_004799285.1_ASM479928v1_genomic.fna/cds.fna -a GCF_004799285.1_ASM479928v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:25,629] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:25,630] [INFO] Task started: HMMsearch
[2024-01-24 11:26:25,630] [INFO] Running command: hmmsearch --tblout GCF_004799285.1_ASM479928v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc96915e1-cb9b-4e6d-b497-62608e041d26/dqc_reference/reference_markers.hmm GCF_004799285.1_ASM479928v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:25,957] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:25,958] [INFO] Found 6/6 markers.
[2024-01-24 11:26:26,001] [INFO] Query marker FASTA was written to GCF_004799285.1_ASM479928v1_genomic.fna/markers.fasta
[2024-01-24 11:26:26,001] [INFO] Task started: Blastn
[2024-01-24 11:26:26,001] [INFO] Running command: blastn -query GCF_004799285.1_ASM479928v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc96915e1-cb9b-4e6d-b497-62608e041d26/dqc_reference/reference_markers.fasta -out GCF_004799285.1_ASM479928v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:27,164] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:27,167] [INFO] Selected 25 target genomes.
[2024-01-24 11:26:27,167] [INFO] Target genome list was writen to GCF_004799285.1_ASM479928v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:27,176] [INFO] Task started: fastANI
[2024-01-24 11:26:27,176] [INFO] Running command: fastANI --query /var/lib/cwl/stg850e026b-91cc-4805-a9fa-d976eb64b1ed/GCF_004799285.1_ASM479928v1_genomic.fna.gz --refList GCF_004799285.1_ASM479928v1_genomic.fna/target_genomes.txt --output GCF_004799285.1_ASM479928v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:48,981] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:48,982] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc96915e1-cb9b-4e6d-b497-62608e041d26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:48,982] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc96915e1-cb9b-4e6d-b497-62608e041d26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:49,015] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:26:49,015] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:26:49,016] [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	80.4752	681	1247	95	below_threshold
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	80.2213	674	1247	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	80.1972	681	1247	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	80.189	683	1247	95	below_threshold
Gemmobacter lutimaris	strain=YJ-T1-11	GCA_003570715.1	2306023	2306023	type	True	80.1523	688	1247	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	80.1168	626	1247	95	below_threshold
Gemmobacter caeni	strain=DSM 21823	GCA_003054195.1	589035	589035	type	True	80.0996	661	1247	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	80.0656	645	1247	95	below_threshold
Gemmobacter caeni	strain=CGMCC 1.7745	GCA_007830625.1	589035	589035	type	True	80.0513	670	1247	95	below_threshold
Gemmobacter lanyuensis	strain=KCTC 23714	GCA_014652355.1	1054497	1054497	type	True	80.0477	597	1247	95	below_threshold
Rhodobacter flagellatus	strain=SYSU G03088	GCA_008271465.1	2593021	2593021	type	True	79.9977	664	1247	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	79.9611	653	1247	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	79.8578	580	1247	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	79.6698	535	1247	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	79.6422	540	1247	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	79.5629	659	1247	95	below_threshold
Gemmobacter aquaticus	strain=A1-9	GCA_007859075.1	490185	490185	type	True	79.5606	528	1247	95	below_threshold
Gemmobacter aquaticus	strain=CGMCC 1.7029	GCA_014645295.1	490185	490185	type	True	79.5305	530	1247	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	79.4611	581	1247	95	below_threshold
Allgaiera indica	strain=CGMCC 1.10859	GCA_014653075.1	765699	765699	type	True	79.0797	515	1247	95	below_threshold
Allgaiera indica	strain=DSM 24802	GCA_900106675.1	765699	765699	type	True	79.0486	520	1247	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	79.0315	502	1247	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	78.9303	500	1247	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.8948	502	1247	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	78.887	503	1247	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:49,025] [INFO] DFAST Taxonomy check result was written to GCF_004799285.1_ASM479928v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:49,026] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:49,026] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:49,027] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc96915e1-cb9b-4e6d-b497-62608e041d26/dqc_reference/checkm_data
[2024-01-24 11:26:49,028] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:49,069] [INFO] Task started: CheckM
[2024-01-24 11:26:49,069] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004799285.1_ASM479928v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004799285.1_ASM479928v1_genomic.fna/checkm_input GCF_004799285.1_ASM479928v1_genomic.fna/checkm_result
[2024-01-24 11:27:31,872] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:31,873] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:31,896] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:31,897] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:31,897] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004799285.1_ASM479928v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:31,898] [INFO] Task started: Blastn
[2024-01-24 11:27:31,898] [INFO] Running command: blastn -query GCF_004799285.1_ASM479928v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc96915e1-cb9b-4e6d-b497-62608e041d26/dqc_reference/reference_markers_gtdb.fasta -out GCF_004799285.1_ASM479928v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:33,896] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:33,900] [INFO] Selected 26 target genomes.
[2024-01-24 11:27:33,900] [INFO] Target genome list was writen to GCF_004799285.1_ASM479928v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:33,928] [INFO] Task started: fastANI
[2024-01-24 11:27:33,929] [INFO] Running command: fastANI --query /var/lib/cwl/stg850e026b-91cc-4805-a9fa-d976eb64b1ed/GCF_004799285.1_ASM479928v1_genomic.fna.gz --refList GCF_004799285.1_ASM479928v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004799285.1_ASM479928v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:54,902] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:54,933] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:54,934] [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_004799285.1	s__Gemmobacter_D aestuarii	100.0	1246	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014763725.1	s__JACXUX01 sp014763725	80.7143	524	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JACXUX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859945.1	s__UBA1943 sp014859945	80.5398	532	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008271655.1	s__Gemmobacter caeruleus	80.4918	681	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110025.1	s__Gemmobacter aquatilis	80.2047	677	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011043545.1	s__JAAKGP01 sp011043545	80.1816	634	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAKGP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003570715.1	s__Gemmobacter lutimaris	80.1553	688	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908265.2	s__Gemmobacter_B sp009908265	80.1397	689	1247	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_003054195.1	s__Gemmobacter caeni	80.0837	664	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	98.77	98.23	0.88	0.79	5	-
GCA_013693875.1	s__SSD5 sp013693875	80.0784	637	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SSD5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008271465.1	s__Tabrizicola flagellata	80.0432	658	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003993775.1	s__Frigidibacter sp003993775	80.0287	576	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652355.1	s__Gemmobacter lanyuensis	80.0111	601	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002407205.1	s__Cereibacter_A sp002407205	79.8728	580	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011008935.1	s__KMS-5 sp011008935	79.768	655	1247	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_014243445.1	s__Gemmobacter_B straminiformis	79.7502	627	1247	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_007859075.1	s__Gemmobacter aquaticus	79.5766	527	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_014654775.1	s__Gemmobacter_B sp014654775	79.4943	612	1247	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_010915705.1	s__ETT8 sp010915705	79.464	580	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900609055.1	s__Pseudogemmobacter humi	79.3554	530	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002423245.1	s__Frigidibacter sp002423245	79.2637	464	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	98.55	98.55	0.85	0.85	2	-
GCA_016869835.1	s__KMS-5 sp016869835	79.2518	476	1247	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_018139985.1	s__JAGSOU01 sp018139985	79.1878	513	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106675.1	s__Acidimangrovimonas indica	79.0399	520	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Acidimangrovimonas	95.0	99.99	99.99	1.00	0.99	3	-
GCF_014196965.1	s__Actibacterium_A naphthalenivorans	78.8045	444	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium_A	95.0	98.28	97.38	0.93	0.89	4	-
GCA_001828855.1	s__Cypionkella sp001828855	78.7391	545	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cypionkella	95.0	99.95	99.91	0.99	0.97	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:54,936] [INFO] GTDB search result was written to GCF_004799285.1_ASM479928v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:54,937] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:54,941] [INFO] DFAST_QC result json was written to GCF_004799285.1_ASM479928v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:54,942] [INFO] DFAST_QC completed!
[2024-01-24 11:27:54,942] [INFO] Total running time: 0h1m42s