[2023-06-30 04:20:55,971] [INFO] DFAST_QC pipeline started.
[2023-06-30 04:20:55,973] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 04:20:55,973] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e18b863-d4c8-4f5b-a34f-fb0bae6b5944/dqc_reference
[2023-06-30 04:20:57,342] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 04:20:57,344] [INFO] Task started: Prodigal
[2023-06-30 04:20:57,345] [INFO] Running command: gunzip -c /var/lib/cwl/stg1975f129-92a3-4c0a-80fa-b407a044b3f6/GCA_019746735.1_ASM1974673v1_genomic.fna.gz | prodigal -d GCA_019746735.1_ASM1974673v1_genomic.fna/cds.fna -a GCA_019746735.1_ASM1974673v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 04:21:04,839] [INFO] Task succeeded: Prodigal
[2023-06-30 04:21:04,840] [INFO] Task started: HMMsearch
[2023-06-30 04:21:04,840] [INFO] Running command: hmmsearch --tblout GCA_019746735.1_ASM1974673v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e18b863-d4c8-4f5b-a34f-fb0bae6b5944/dqc_reference/reference_markers.hmm GCA_019746735.1_ASM1974673v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 04:21:05,024] [INFO] Task succeeded: HMMsearch
[2023-06-30 04:21:05,025] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1975f129-92a3-4c0a-80fa-b407a044b3f6/GCA_019746735.1_ASM1974673v1_genomic.fna.gz]
[2023-06-30 04:21:05,052] [INFO] Query marker FASTA was written to GCA_019746735.1_ASM1974673v1_genomic.fna/markers.fasta
[2023-06-30 04:21:05,052] [INFO] Task started: Blastn
[2023-06-30 04:21:05,052] [INFO] Running command: blastn -query GCA_019746735.1_ASM1974673v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e18b863-d4c8-4f5b-a34f-fb0bae6b5944/dqc_reference/reference_markers.fasta -out GCA_019746735.1_ASM1974673v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:21:05,844] [INFO] Task succeeded: Blastn
[2023-06-30 04:21:05,848] [INFO] Selected 21 target genomes.
[2023-06-30 04:21:05,848] [INFO] Target genome list was writen to GCA_019746735.1_ASM1974673v1_genomic.fna/target_genomes.txt
[2023-06-30 04:21:05,849] [INFO] Task started: fastANI
[2023-06-30 04:21:05,849] [INFO] Running command: fastANI --query /var/lib/cwl/stg1975f129-92a3-4c0a-80fa-b407a044b3f6/GCA_019746735.1_ASM1974673v1_genomic.fna.gz --refList GCA_019746735.1_ASM1974673v1_genomic.fna/target_genomes.txt --output GCA_019746735.1_ASM1974673v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 04:21:23,206] [INFO] Task succeeded: fastANI
[2023-06-30 04:21:23,206] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e18b863-d4c8-4f5b-a34f-fb0bae6b5944/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 04:21:23,207] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e18b863-d4c8-4f5b-a34f-fb0bae6b5944/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 04:21:23,222] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 04:21:23,223] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 04:21:23,223] [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
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	80.5727	388	706	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.453	394	706	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	80.2523	389	706	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	80.1457	402	706	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	80.096	359	706	95	below_threshold
Pseudorhodoferax soli	strain=DSM 21634	GCA_003337555.1	545864	545864	type	True	79.9107	395	706	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.8109	379	706	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	79.7183	346	706	95	below_threshold
Ramlibacter henchirensis	strain=DSM 14656	GCA_004682015.1	204072	204072	type	True	79.6059	332	706	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	79.5787	375	706	95	below_threshold
Xylophilus rhododendri	strain=KACC 21265	GCA_009906855.1	2697032	2697032	type	True	79.5621	341	706	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	79.5462	380	706	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	79.4448	367	706	95	below_threshold
Tepidicella baoligensis	strain=B18-50	GCA_013432195.1	2707016	2707016	type	True	79.391	252	706	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	79.2225	281	706	95	below_threshold
Xylophilus ampelinus	strain=CECT 7646	GCA_003217575.1	54067	54067	type	True	79.2052	280	706	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	79.0628	301	706	95	below_threshold
Acidovorax konjaci	strain=DSM 7481	GCA_900112675.1	32040	32040	type	True	78.9955	315	706	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	78.9894	303	706	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	78.9508	243	706	95	below_threshold
Brachymonas denitrificans	strain=DSM 15123	GCA_900110225.1	28220	28220	type	True	78.8328	221	706	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 04:21:23,225] [INFO] DFAST Taxonomy check result was written to GCA_019746735.1_ASM1974673v1_genomic.fna/tc_result.tsv
[2023-06-30 04:21:23,225] [INFO] ===== Taxonomy check completed =====
[2023-06-30 04:21:23,226] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 04:21:23,226] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e18b863-d4c8-4f5b-a34f-fb0bae6b5944/dqc_reference/checkm_data
[2023-06-30 04:21:23,227] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 04:21:23,255] [INFO] Task started: CheckM
[2023-06-30 04:21:23,255] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019746735.1_ASM1974673v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019746735.1_ASM1974673v1_genomic.fna/checkm_input GCA_019746735.1_ASM1974673v1_genomic.fna/checkm_result
[2023-06-30 04:21:51,002] [INFO] Task succeeded: CheckM
[2023-06-30 04:21:51,003] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 04:21:51,019] [INFO] ===== Completeness check finished =====
[2023-06-30 04:21:51,019] [INFO] ===== Start GTDB Search =====
[2023-06-30 04:21:51,019] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019746735.1_ASM1974673v1_genomic.fna/markers.fasta)
[2023-06-30 04:21:51,019] [INFO] Task started: Blastn
[2023-06-30 04:21:51,019] [INFO] Running command: blastn -query GCA_019746735.1_ASM1974673v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e18b863-d4c8-4f5b-a34f-fb0bae6b5944/dqc_reference/reference_markers_gtdb.fasta -out GCA_019746735.1_ASM1974673v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:21:52,512] [INFO] Task succeeded: Blastn
[2023-06-30 04:21:52,516] [INFO] Selected 12 target genomes.
[2023-06-30 04:21:52,516] [INFO] Target genome list was writen to GCA_019746735.1_ASM1974673v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 04:21:52,519] [INFO] Task started: fastANI
[2023-06-30 04:21:52,519] [INFO] Running command: fastANI --query /var/lib/cwl/stg1975f129-92a3-4c0a-80fa-b407a044b3f6/GCA_019746735.1_ASM1974673v1_genomic.fna.gz --refList GCA_019746735.1_ASM1974673v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019746735.1_ASM1974673v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 04:22:00,512] [INFO] Task succeeded: fastANI
[2023-06-30 04:22:00,522] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 04:22:00,522] [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
GCA_003500955.1	s__Hylemonella sp003500955	89.4576	529	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013334205.1	s__Hylemonella sp013334205	85.4078	557	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001432305.1	s__Hylemonella sp001432305	84.7461	545	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185015.1	s__Hylemonella sp016185015	84.7151	544	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001797315.1	s__Hylemonella sp001797315	82.0971	442	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	99.98	99.98	0.98	0.98	2	-
GCA_005503335.1	s__SCMQ01 sp005503335	81.3756	400	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCMQ01	95.0	99.99	99.99	1.00	1.00	3	-
GCF_000215705.1	s__Ramlibacter tataouinensis	80.5414	390	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002127215.1	s__Hydrogenophaga sp002127215	80.1762	363	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003013695.1	s__Pulveribacter suum	79.5647	331	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pulveribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016721925.1	s__JAABQG01 sp016721925	79.299	308	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAABQG01	95.0	98.62	98.32	0.93	0.90	9	-
GCF_900112675.1	s__Acidovorax_A konjaci	79.0324	313	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110225.1	s__Brachymonas denitrificans	78.8328	221	706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Brachymonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 04:22:00,524] [INFO] GTDB search result was written to GCA_019746735.1_ASM1974673v1_genomic.fna/result_gtdb.tsv
[2023-06-30 04:22:00,525] [INFO] ===== GTDB Search completed =====
[2023-06-30 04:22:00,528] [INFO] DFAST_QC result json was written to GCA_019746735.1_ASM1974673v1_genomic.fna/dqc_result.json
[2023-06-30 04:22:00,528] [INFO] DFAST_QC completed!
[2023-06-30 04:22:00,529] [INFO] Total running time: 0h1m5s