[2024-01-24 13:31:26,247] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:26,249] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:26,249] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a4d962b-e44f-4925-bd1d-5c439d9f77cd/dqc_reference
[2024-01-24 13:31:27,449] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:27,450] [INFO] Task started: Prodigal
[2024-01-24 13:31:27,450] [INFO] Running command: gunzip -c /var/lib/cwl/stg5782fda3-3457-4108-a507-a4c2dc4f735a/GCF_004959935.1_ASM495993v1_genomic.fna.gz | prodigal -d GCF_004959935.1_ASM495993v1_genomic.fna/cds.fna -a GCF_004959935.1_ASM495993v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:39,376] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:39,377] [INFO] Task started: HMMsearch
[2024-01-24 13:31:39,377] [INFO] Running command: hmmsearch --tblout GCF_004959935.1_ASM495993v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a4d962b-e44f-4925-bd1d-5c439d9f77cd/dqc_reference/reference_markers.hmm GCF_004959935.1_ASM495993v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:39,666] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:39,668] [INFO] Found 6/6 markers.
[2024-01-24 13:31:39,713] [INFO] Query marker FASTA was written to GCF_004959935.1_ASM495993v1_genomic.fna/markers.fasta
[2024-01-24 13:31:39,714] [INFO] Task started: Blastn
[2024-01-24 13:31:39,714] [INFO] Running command: blastn -query GCF_004959935.1_ASM495993v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a4d962b-e44f-4925-bd1d-5c439d9f77cd/dqc_reference/reference_markers.fasta -out GCF_004959935.1_ASM495993v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:40,726] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:40,730] [INFO] Selected 23 target genomes.
[2024-01-24 13:31:40,730] [INFO] Target genome list was writen to GCF_004959935.1_ASM495993v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:40,849] [INFO] Task started: fastANI
[2024-01-24 13:31:40,850] [INFO] Running command: fastANI --query /var/lib/cwl/stg5782fda3-3457-4108-a507-a4c2dc4f735a/GCF_004959935.1_ASM495993v1_genomic.fna.gz --refList GCF_004959935.1_ASM495993v1_genomic.fna/target_genomes.txt --output GCF_004959935.1_ASM495993v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:58,850] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:58,851] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a4d962b-e44f-4925-bd1d-5c439d9f77cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:58,851] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a4d962b-e44f-4925-bd1d-5c439d9f77cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:58,870] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:31:58,870] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:31:58,870] [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 changlensis	strain=JA139	GCA_003034985.1	402884	402884	type	True	79.769	531	1292	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	79.7268	477	1292	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	79.7028	565	1292	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	79.3016	459	1292	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	79.2774	471	1292	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	79.2677	472	1292	95	below_threshold
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	79.2154	495	1292	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009908165.1	1465486	1465486	type	True	79.1829	489	1292	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009881095.1	1465486	1465486	type	True	79.1559	492	1292	95	below_threshold
Frigidibacter albus	strain=CGMCC 1.13995	GCA_014640395.1	1465486	1465486	type	True	79.118	501	1292	95	below_threshold
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	79.0478	458	1292	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	78.9243	478	1292	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	78.8256	460	1292	95	below_threshold
Gemmobacter serpentinus	strain=HB-1	GCA_008973825.1	2652247	2652247	type	True	78.745	444	1292	95	below_threshold
Gemmobacter lanyuensis	strain=KCTC 23714	GCA_014652355.1	1054497	1054497	type	True	78.6527	443	1292	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	78.562	415	1292	95	below_threshold
Gemmobacter aquarius	strain=HYN0069	GCA_003060865.1	2169400	2169400	type	True	78.5332	401	1292	95	below_threshold
Paracoccus gahaiensis	strain=KCTC 42687	GCA_005048225.1	1706839	1706839	type	True	78.5082	429	1292	95	below_threshold
Gemmobacter aquaticus	strain=CGMCC 1.7029	GCA_014645295.1	490185	490185	type	True	78.4174	400	1292	95	below_threshold
Gemmobacter aquaticus	strain=A1-9	GCA_007859075.1	490185	490185	type	True	78.3965	403	1292	95	below_threshold
Allgaiera indica	strain=CGMCC 1.10859	GCA_014653075.1	765699	765699	type	True	78.2191	388	1292	95	below_threshold
Allgaiera indica	strain=DSM 24802	GCA_900106675.1	765699	765699	type	True	78.1958	380	1292	95	below_threshold
Roseicitreum antarcticum	strain=ZS2-28	GCA_014681765.1	564137	564137	type	True	77.4509	285	1292	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:58,872] [INFO] DFAST Taxonomy check result was written to GCF_004959935.1_ASM495993v1_genomic.fna/tc_result.tsv
[2024-01-24 13:31:58,873] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:58,873] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:58,873] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a4d962b-e44f-4925-bd1d-5c439d9f77cd/dqc_reference/checkm_data
[2024-01-24 13:31:58,874] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:58,918] [INFO] Task started: CheckM
[2024-01-24 13:31:58,918] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004959935.1_ASM495993v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004959935.1_ASM495993v1_genomic.fna/checkm_input GCF_004959935.1_ASM495993v1_genomic.fna/checkm_result
[2024-01-24 13:32:43,111] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:43,113] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:43,138] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:43,138] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:43,139] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004959935.1_ASM495993v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:43,140] [INFO] Task started: Blastn
[2024-01-24 13:32:43,140] [INFO] Running command: blastn -query GCF_004959935.1_ASM495993v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a4d962b-e44f-4925-bd1d-5c439d9f77cd/dqc_reference/reference_markers_gtdb.fasta -out GCF_004959935.1_ASM495993v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:45,055] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:45,058] [INFO] Selected 16 target genomes.
[2024-01-24 13:32:45,059] [INFO] Target genome list was writen to GCF_004959935.1_ASM495993v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:45,112] [INFO] Task started: fastANI
[2024-01-24 13:32:45,112] [INFO] Running command: fastANI --query /var/lib/cwl/stg5782fda3-3457-4108-a507-a4c2dc4f735a/GCF_004959935.1_ASM495993v1_genomic.fna.gz --refList GCF_004959935.1_ASM495993v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004959935.1_ASM495993v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:57,016] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:57,036] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:57,037] [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_004959935.1	s__Falsirhodobacter xinxiangensis	100.0	1284	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Falsirhodobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004015795.1	s__Falsirhodobacter deserti	81.1824	530	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Falsirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018279165.1	s__Falsirhodobacter sp018279165	81.0615	536	1292	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	79.7496	533	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter	95.0	98.07	96.18	0.89	0.78	3	-
GCF_900207575.1	s__Cereibacter_A ovatus	79.7272	477	1292	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_009908265.2	s__Gemmobacter_B sp009908265	79.2775	471	1292	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_003993775.1	s__Frigidibacter sp003993775	79.2434	517	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110025.1	s__Gemmobacter aquatilis	79.2345	493	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001620265.1	s__Frigidibacter mobilis	78.9231	478	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054195.1	s__Gemmobacter caeni	78.8589	470	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	98.77	98.23	0.88	0.79	5	-
GCF_000739715.2	s__Falsirhodobacter sp000739715	78.8467	341	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Falsirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018798885.1	s__Gemmobacter sp018798885	78.8355	459	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014652355.1	s__Gemmobacter lanyuensis	78.6297	446	1292	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	78.6053	376	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869875.1	s__Paracoccus sp016869875	77.8413	274	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314715.1	s__Pararhodobacter sp001314715	77.3868	295	1292	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:57,039] [INFO] GTDB search result was written to GCF_004959935.1_ASM495993v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:57,040] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:57,047] [INFO] DFAST_QC result json was written to GCF_004959935.1_ASM495993v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:57,047] [INFO] DFAST_QC completed!
[2024-01-24 13:32:57,047] [INFO] Total running time: 0h1m31s