[2024-01-24 13:45:41,562] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:41,564] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:41,564] [INFO] DQC Reference Directory: /var/lib/cwl/stg8bf8014d-26e4-4eca-a639-b45dfc8e0792/dqc_reference
[2024-01-24 13:45:42,772] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:42,773] [INFO] Task started: Prodigal
[2024-01-24 13:45:42,773] [INFO] Running command: gunzip -c /var/lib/cwl/stg0e06f4d0-7e55-4061-b01f-8ada7422aac0/GCF_008973825.1_ASM897382v1_genomic.fna.gz | prodigal -d GCF_008973825.1_ASM897382v1_genomic.fna/cds.fna -a GCF_008973825.1_ASM897382v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:45:56,485] [INFO] Task succeeded: Prodigal
[2024-01-24 13:45:56,485] [INFO] Task started: HMMsearch
[2024-01-24 13:45:56,485] [INFO] Running command: hmmsearch --tblout GCF_008973825.1_ASM897382v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8bf8014d-26e4-4eca-a639-b45dfc8e0792/dqc_reference/reference_markers.hmm GCF_008973825.1_ASM897382v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:45:56,788] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:45:56,792] [INFO] Found 6/6 markers.
[2024-01-24 13:45:56,835] [INFO] Query marker FASTA was written to GCF_008973825.1_ASM897382v1_genomic.fna/markers.fasta
[2024-01-24 13:45:56,836] [INFO] Task started: Blastn
[2024-01-24 13:45:56,836] [INFO] Running command: blastn -query GCF_008973825.1_ASM897382v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8bf8014d-26e4-4eca-a639-b45dfc8e0792/dqc_reference/reference_markers.fasta -out GCF_008973825.1_ASM897382v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:45:57,717] [INFO] Task succeeded: Blastn
[2024-01-24 13:45:57,722] [INFO] Selected 15 target genomes.
[2024-01-24 13:45:57,723] [INFO] Target genome list was writen to GCF_008973825.1_ASM897382v1_genomic.fna/target_genomes.txt
[2024-01-24 13:45:57,745] [INFO] Task started: fastANI
[2024-01-24 13:45:57,745] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e06f4d0-7e55-4061-b01f-8ada7422aac0/GCF_008973825.1_ASM897382v1_genomic.fna.gz --refList GCF_008973825.1_ASM897382v1_genomic.fna/target_genomes.txt --output GCF_008973825.1_ASM897382v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:10,682] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:10,682] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8bf8014d-26e4-4eca-a639-b45dfc8e0792/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:10,683] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8bf8014d-26e4-4eca-a639-b45dfc8e0792/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:10,695] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:10,695] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:10,695] [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 serpentinus	strain=HB-1	GCA_008973825.1	2652247	2652247	type	True	100.0	1390	1390	95	conclusive
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	83.4546	858	1390	95	below_threshold
Gemmobacter lutimaris	strain=YJ-T1-11	GCA_003570715.1	2306023	2306023	type	True	81.343	764	1390	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	81.1535	790	1390	95	below_threshold
Gemmobacter lanyuensis	strain=KCTC 23714	GCA_014652355.1	1054497	1054497	type	True	81.1208	698	1390	95	below_threshold
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	81.1124	756	1390	95	below_threshold
Gemmobacter caeni	strain=DSM 21823	GCA_003054195.1	589035	589035	type	True	81.0544	753	1390	95	below_threshold
Gemmobacter caeni	strain=CGMCC 1.7745	GCA_007830625.1	589035	589035	type	True	81.0074	768	1390	95	below_threshold
Gemmobacter aquaticus	strain=CGMCC 1.7029	GCA_014645295.1	490185	490185	type	True	80.3366	624	1390	95	below_threshold
Gemmobacter aquaticus	strain=A1-9	GCA_007859075.1	490185	490185	type	True	80.3004	631	1390	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	79.2815	524	1390	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	79.2459	528	1390	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	79.1438	570	1390	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	79.0581	517	1390	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	78.6309	500	1390	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:10,696] [INFO] DFAST Taxonomy check result was written to GCF_008973825.1_ASM897382v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:10,697] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:10,697] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:10,697] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8bf8014d-26e4-4eca-a639-b45dfc8e0792/dqc_reference/checkm_data
[2024-01-24 13:46:10,698] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:10,739] [INFO] Task started: CheckM
[2024-01-24 13:46:10,739] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008973825.1_ASM897382v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008973825.1_ASM897382v1_genomic.fna/checkm_input GCF_008973825.1_ASM897382v1_genomic.fna/checkm_result
[2024-01-24 13:47:05,439] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:05,440] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:05,459] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:05,459] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:05,460] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008973825.1_ASM897382v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:05,460] [INFO] Task started: Blastn
[2024-01-24 13:47:05,460] [INFO] Running command: blastn -query GCF_008973825.1_ASM897382v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8bf8014d-26e4-4eca-a639-b45dfc8e0792/dqc_reference/reference_markers_gtdb.fasta -out GCF_008973825.1_ASM897382v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:07,133] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:07,137] [INFO] Selected 8 target genomes.
[2024-01-24 13:47:07,138] [INFO] Target genome list was writen to GCF_008973825.1_ASM897382v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:07,153] [INFO] Task started: fastANI
[2024-01-24 13:47:07,153] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e06f4d0-7e55-4061-b01f-8ada7422aac0/GCF_008973825.1_ASM897382v1_genomic.fna.gz --refList GCF_008973825.1_ASM897382v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008973825.1_ASM897382v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:16,062] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:16,071] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:16,071] [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_008973825.1	s__Gemmobacter serpentinus	100.0	1390	1390	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008271655.1	s__Gemmobacter caeruleus	83.4544	858	1390	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792925.1	s__Gemmobacter sp016792925	82.894	644	1390	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003570715.1	s__Gemmobacter lutimaris	81.3428	763	1390	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	81.1518	750	1390	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652355.1	s__Gemmobacter lanyuensis	81.1324	696	1390	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054195.1	s__Gemmobacter caeni	81.0216	756	1390	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	98.77	98.23	0.88	0.79	5	-
GCF_007859075.1	s__Gemmobacter aquaticus	80.3248	628	1390	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:16,072] [INFO] GTDB search result was written to GCF_008973825.1_ASM897382v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:16,073] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:16,079] [INFO] DFAST_QC result json was written to GCF_008973825.1_ASM897382v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:16,080] [INFO] DFAST_QC completed!
[2024-01-24 13:47:16,080] [INFO] Total running time: 0h1m35s