[2024-01-25 17:48:05,622] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:48:05,625] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:48:05,625] [INFO] DQC Reference Directory: /var/lib/cwl/stg765c51f7-a659-4b85-aa55-a14e6d95deb8/dqc_reference
[2024-01-25 17:48:06,779] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:48:06,780] [INFO] Task started: Prodigal
[2024-01-25 17:48:06,780] [INFO] Running command: gunzip -c /var/lib/cwl/stg1179872e-8d6b-4b23-b1dd-3e7e2ca93dbf/GCF_022899245.1_ASM2289924v1_genomic.fna.gz | prodigal -d GCF_022899245.1_ASM2289924v1_genomic.fna/cds.fna -a GCF_022899245.1_ASM2289924v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:48:15,498] [INFO] Task succeeded: Prodigal
[2024-01-25 17:48:15,498] [INFO] Task started: HMMsearch
[2024-01-25 17:48:15,499] [INFO] Running command: hmmsearch --tblout GCF_022899245.1_ASM2289924v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg765c51f7-a659-4b85-aa55-a14e6d95deb8/dqc_reference/reference_markers.hmm GCF_022899245.1_ASM2289924v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:48:15,694] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:48:15,695] [INFO] Found 6/6 markers.
[2024-01-25 17:48:15,721] [INFO] Query marker FASTA was written to GCF_022899245.1_ASM2289924v1_genomic.fna/markers.fasta
[2024-01-25 17:48:15,721] [INFO] Task started: Blastn
[2024-01-25 17:48:15,721] [INFO] Running command: blastn -query GCF_022899245.1_ASM2289924v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg765c51f7-a659-4b85-aa55-a14e6d95deb8/dqc_reference/reference_markers.fasta -out GCF_022899245.1_ASM2289924v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:48:16,646] [INFO] Task succeeded: Blastn
[2024-01-25 17:48:16,649] [INFO] Selected 25 target genomes.
[2024-01-25 17:48:16,649] [INFO] Target genome list was writen to GCF_022899245.1_ASM2289924v1_genomic.fna/target_genomes.txt
[2024-01-25 17:48:16,660] [INFO] Task started: fastANI
[2024-01-25 17:48:16,660] [INFO] Running command: fastANI --query /var/lib/cwl/stg1179872e-8d6b-4b23-b1dd-3e7e2ca93dbf/GCF_022899245.1_ASM2289924v1_genomic.fna.gz --refList GCF_022899245.1_ASM2289924v1_genomic.fna/target_genomes.txt --output GCF_022899245.1_ASM2289924v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:48:34,726] [INFO] Task succeeded: fastANI
[2024-01-25 17:48:34,726] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg765c51f7-a659-4b85-aa55-a14e6d95deb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:48:34,726] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg765c51f7-a659-4b85-aa55-a14e6d95deb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:48:34,741] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:48:34,741] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:48:34,741] [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 ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	79.2593	378	1023	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	79.2183	452	1023	95	below_threshold
Cereibacter changlensis	strain=JA139	GCA_003034985.1	402884	402884	type	True	79.2143	434	1023	95	below_threshold
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	78.9423	383	1023	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	78.8612	371	1023	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.801	355	1023	95	below_threshold
Cereibacter johrii	strain=JA192	GCA_001720585.1	445629	445629	type	True	78.7559	373	1023	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	78.5891	394	1023	95	below_threshold
Cereibacter johrii	strain=JA192	GCA_003046325.1	445629	445629	type	True	78.5845	399	1023	95	below_threshold
Gemmobacter lutimaris	strain=YJ-T1-11	GCA_003570715.1	2306023	2306023	type	True	78.5824	373	1023	95	below_threshold
Gemmobacter lanyuensis	strain=KCTC 23714	GCA_014652355.1	1054497	1054497	type	True	78.5463	355	1023	95	below_threshold
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	78.4571	355	1023	95	below_threshold
Paracoccus aestuarii	strain=DSM 19484	GCA_003594815.1	453842	453842	type	True	78.4568	356	1023	95	below_threshold
Gemmobacter serpentinus	strain=HB-1	GCA_008973825.1	2652247	2652247	type	True	78.3838	330	1023	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	78.3833	399	1023	95	below_threshold
Paracoccus fontiphilus	strain=MVW-1	GCA_017356265.1	1815556	1815556	type	True	78.3548	339	1023	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	78.2581	324	1023	95	below_threshold
Gemmobacter nectariphilus	strain=DSM 15620	GCA_000429765.1	220343	220343	type	True	78.2221	348	1023	95	below_threshold
Allgaiera indica	strain=CGMCC 1.10859	GCA_014653075.1	765699	765699	type	True	78.2029	321	1023	95	below_threshold
Allgaiera indica	strain=DSM 24802	GCA_900106675.1	765699	765699	type	True	78.1982	318	1023	95	below_threshold
Gemmobacter aquaticus	strain=CGMCC 1.7029	GCA_014645295.1	490185	490185	type	True	78.1939	313	1023	95	below_threshold
Gemmobacter aquaticus	strain=A1-9	GCA_007859075.1	490185	490185	type	True	78.1704	311	1023	95	below_threshold
Thioclava marina	strain=11.10-0-13	GCA_002020135.1	1915077	1915077	type	True	77.916	267	1023	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	77.8791	309	1023	95	below_threshold
Thioclava pacifica	strain=DSM 10166	GCA_000714535.1	285109	285109	type	True	77.825	259	1023	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:48:34,743] [INFO] DFAST Taxonomy check result was written to GCF_022899245.1_ASM2289924v1_genomic.fna/tc_result.tsv
[2024-01-25 17:48:34,743] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:48:34,743] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:48:34,744] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg765c51f7-a659-4b85-aa55-a14e6d95deb8/dqc_reference/checkm_data
[2024-01-25 17:48:34,744] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:48:34,782] [INFO] Task started: CheckM
[2024-01-25 17:48:34,782] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022899245.1_ASM2289924v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022899245.1_ASM2289924v1_genomic.fna/checkm_input GCF_022899245.1_ASM2289924v1_genomic.fna/checkm_result
[2024-01-25 17:49:25,861] [INFO] Task succeeded: CheckM
[2024-01-25 17:49:25,862] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:49:25,874] [INFO] ===== Completeness check finished =====
[2024-01-25 17:49:25,874] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:49:25,874] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022899245.1_ASM2289924v1_genomic.fna/markers.fasta)
[2024-01-25 17:49:25,875] [INFO] Task started: Blastn
[2024-01-25 17:49:25,875] [INFO] Running command: blastn -query GCF_022899245.1_ASM2289924v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg765c51f7-a659-4b85-aa55-a14e6d95deb8/dqc_reference/reference_markers_gtdb.fasta -out GCF_022899245.1_ASM2289924v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:27,665] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:27,667] [INFO] Selected 16 target genomes.
[2024-01-25 17:49:27,668] [INFO] Target genome list was writen to GCF_022899245.1_ASM2289924v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:49:27,692] [INFO] Task started: fastANI
[2024-01-25 17:49:27,692] [INFO] Running command: fastANI --query /var/lib/cwl/stg1179872e-8d6b-4b23-b1dd-3e7e2ca93dbf/GCF_022899245.1_ASM2289924v1_genomic.fna.gz --refList GCF_022899245.1_ASM2289924v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022899245.1_ASM2289924v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:49:39,086] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:39,096] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:49:39,096] [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_018279165.1	s__Falsirhodobacter sp018279165	81.887	541	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Falsirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004015795.1	s__Falsirhodobacter deserti	81.6876	529	1023	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	81.2537	583	1023	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	79.5223	427	1023	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	79.1641	438	1023	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	78.9851	359	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002407205.1	s__Cereibacter_A sp002407205	78.9253	392	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003993775.1	s__Frigidibacter sp003993775	78.9069	429	1023	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	78.5724	352	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017356265.1	s__Paracoccus fontiphilus	78.4141	334	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011008935.1	s__KMS-5 sp011008935	78.3389	355	1023	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_900106675.1	s__Acidimangrovimonas indica	78.1866	319	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Acidimangrovimonas	95.0	99.99	99.99	1.00	0.99	3	-
GCF_018860625.1	s__Paracoccus sp018860625	78.1432	331	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649175.1	s__Rhodovulum strictum	77.8679	310	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314715.1	s__Pararhodobacter sp001314715	77.5049	249	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000220565.1	s__Pseudooceanicola sp000220565	77.2962	283	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:49:39,097] [INFO] GTDB search result was written to GCF_022899245.1_ASM2289924v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:49:39,098] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:49:39,101] [INFO] DFAST_QC result json was written to GCF_022899245.1_ASM2289924v1_genomic.fna/dqc_result.json
[2024-01-25 17:49:39,101] [INFO] DFAST_QC completed!
[2024-01-25 17:49:39,101] [INFO] Total running time: 0h1m33s