[2023-06-27 10:19:49,605] [INFO] DFAST_QC pipeline started.
[2023-06-27 10:19:49,618] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 10:19:49,619] [INFO] DQC Reference Directory: /var/lib/cwl/stgcbfa48b4-9bdc-44ac-846d-399432fc7b15/dqc_reference
[2023-06-27 10:19:51,265] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 10:19:51,267] [INFO] Task started: Prodigal
[2023-06-27 10:19:51,267] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d61f80a-5748-4aff-9b91-f206f10f16e6/GCA_026400105.1_ASM2640010v1_genomic.fna.gz | prodigal -d GCA_026400105.1_ASM2640010v1_genomic.fna/cds.fna -a GCA_026400105.1_ASM2640010v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 10:19:59,843] [INFO] Task succeeded: Prodigal
[2023-06-27 10:19:59,843] [INFO] Task started: HMMsearch
[2023-06-27 10:19:59,843] [INFO] Running command: hmmsearch --tblout GCA_026400105.1_ASM2640010v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcbfa48b4-9bdc-44ac-846d-399432fc7b15/dqc_reference/reference_markers.hmm GCA_026400105.1_ASM2640010v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 10:20:00,106] [INFO] Task succeeded: HMMsearch
[2023-06-27 10:20:00,108] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2d61f80a-5748-4aff-9b91-f206f10f16e6/GCA_026400105.1_ASM2640010v1_genomic.fna.gz]
[2023-06-27 10:20:00,151] [INFO] Query marker FASTA was written to GCA_026400105.1_ASM2640010v1_genomic.fna/markers.fasta
[2023-06-27 10:20:00,151] [INFO] Task started: Blastn
[2023-06-27 10:20:00,151] [INFO] Running command: blastn -query GCA_026400105.1_ASM2640010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcbfa48b4-9bdc-44ac-846d-399432fc7b15/dqc_reference/reference_markers.fasta -out GCA_026400105.1_ASM2640010v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 10:20:01,205] [INFO] Task succeeded: Blastn
[2023-06-27 10:20:01,221] [INFO] Selected 19 target genomes.
[2023-06-27 10:20:01,221] [INFO] Target genome list was writen to GCA_026400105.1_ASM2640010v1_genomic.fna/target_genomes.txt
[2023-06-27 10:20:01,226] [INFO] Task started: fastANI
[2023-06-27 10:20:01,226] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d61f80a-5748-4aff-9b91-f206f10f16e6/GCA_026400105.1_ASM2640010v1_genomic.fna.gz --refList GCA_026400105.1_ASM2640010v1_genomic.fna/target_genomes.txt --output GCA_026400105.1_ASM2640010v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 10:20:19,871] [INFO] Task succeeded: fastANI
[2023-06-27 10:20:19,872] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcbfa48b4-9bdc-44ac-846d-399432fc7b15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 10:20:19,872] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcbfa48b4-9bdc-44ac-846d-399432fc7b15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 10:20:19,899] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 10:20:19,900] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 10:20:19,900] [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
Malikia spinosa	strain=83	GCA_002980625.1	86180	86180	type	True	94.8525	841	972	95	below_threshold
Malikia granosa	strain=P1	GCA_002980595.1	263067	263067	type	True	91.6492	823	972	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.9743	491	972	95	below_threshold
Hydrogenophaga pseudoflava	strain=NBRC 102511	GCA_001592285.1	47421	47421	type	True	80.7667	501	972	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	80.5431	470	972	95	below_threshold
Tepidimonas sediminis	strain=YIM 72259	GCA_007556605.1	2588941	2588941	type	True	80.1453	437	972	95	below_threshold
Tepidicella baoligensis	strain=B18-50	GCA_013432195.1	2707016	2707016	type	True	80.0106	373	972	95	below_threshold
Hydrogenophaga intermedia	strain=DSM 5680	GCA_005938115.1	65786	65786	type	True	79.9411	468	972	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	79.8661	523	972	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.7964	462	972	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	79.7911	506	972	95	below_threshold
Variovorax guangxiensis	strain=DSM 27352	GCA_003952165.1	1775474	1775474	type	True	79.6815	490	972	95	below_threshold
Tepidimonas taiwanensis	strain=LMG 22826	GCA_020162115.1	307486	307486	type	True	79.5194	386	972	95	below_threshold
Ramlibacter henchirensis	strain=DSM 14656	GCA_004682015.1	204072	204072	type	True	79.4807	396	972	95	below_threshold
Serpentinimonas maccroryi	strain=B1	GCA_000828915.1	1458426	1458426	type	True	79.344	355	972	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	79.2375	488	972	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	79.1678	498	972	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	78.9226	398	972	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	78.8673	377	972	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 10:20:19,905] [INFO] DFAST Taxonomy check result was written to GCA_026400105.1_ASM2640010v1_genomic.fna/tc_result.tsv
[2023-06-27 10:20:19,905] [INFO] ===== Taxonomy check completed =====
[2023-06-27 10:20:19,906] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 10:20:19,906] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcbfa48b4-9bdc-44ac-846d-399432fc7b15/dqc_reference/checkm_data
[2023-06-27 10:20:19,907] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 10:20:19,947] [INFO] Task started: CheckM
[2023-06-27 10:20:19,947] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026400105.1_ASM2640010v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026400105.1_ASM2640010v1_genomic.fna/checkm_input GCA_026400105.1_ASM2640010v1_genomic.fna/checkm_result
[2023-06-27 10:20:52,298] [INFO] Task succeeded: CheckM
[2023-06-27 10:20:52,299] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-27 10:20:52,323] [INFO] ===== Completeness check finished =====
[2023-06-27 10:20:52,323] [INFO] ===== Start GTDB Search =====
[2023-06-27 10:20:52,324] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026400105.1_ASM2640010v1_genomic.fna/markers.fasta)
[2023-06-27 10:20:52,324] [INFO] Task started: Blastn
[2023-06-27 10:20:52,324] [INFO] Running command: blastn -query GCA_026400105.1_ASM2640010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcbfa48b4-9bdc-44ac-846d-399432fc7b15/dqc_reference/reference_markers_gtdb.fasta -out GCA_026400105.1_ASM2640010v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 10:20:54,166] [INFO] Task succeeded: Blastn
[2023-06-27 10:20:54,173] [INFO] Selected 17 target genomes.
[2023-06-27 10:20:54,173] [INFO] Target genome list was writen to GCA_026400105.1_ASM2640010v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 10:20:54,185] [INFO] Task started: fastANI
[2023-06-27 10:20:54,186] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d61f80a-5748-4aff-9b91-f206f10f16e6/GCA_026400105.1_ASM2640010v1_genomic.fna.gz --refList GCA_026400105.1_ASM2640010v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026400105.1_ASM2640010v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 10:21:08,436] [INFO] Task succeeded: fastANI
[2023-06-27 10:21:08,454] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 10:21:08,455] [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_002980625.1	s__Malikia spinosa	94.8525	841	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Malikia	95.0	97.79	97.60	0.88	0.88	3	-
GCF_002980595.1	s__Malikia granosa	91.6492	823	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Malikia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002837145.1	s__BK-30 sp002837145	81.792	492	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__BK-30	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011388215.1	s__Hydrogenophaga sp011388215	80.9798	490	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	99.06	99.06	0.95	0.95	2	-
GCF_002837135.1	s__Macromonas bipunctata	80.51	408	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Macromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016741995.1	s__Hydrogenophaga sp016741995	80.2058	414	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013432195.1	s__Tepidicella baoligensis	80.0552	370	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003569765.1	s__Aquabacterium_B tepidiphilum	79.9559	486	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016702555.1	s__Ottowia sp016702555	79.7876	428	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	99.62	99.62	0.96	0.96	2	-
GCA_019233055.1	s__Curvibacter sp019233055	79.7875	426	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Curvibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013693755.1	s__Tibeticola sp013693755	79.7319	415	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tibeticola	95.0	96.98	96.98	0.89	0.89	2	-
GCF_000382045.1	s__Variovorax paradoxus_A	79.6919	495	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	98.57	98.47	0.92	0.91	6	-
GCF_001424545.1	s__Ramlibacter sp001424545	79.6484	441	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000834655.1	s__Variovorax paradoxus_F	79.4802	451	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000828915.1	s__Serpentinomonas mccroryi	79.2843	360	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Serpentinomonas	95.0	98.21	97.99	0.96	0.95	3	-
GCF_003574675.1	s__Calidifontimicrobium sediminis	79.1346	421	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Calidifontimicrobium	95.0	96.54	96.54	0.86	0.86	2	-
GCA_019232985.1	s__JAFAMW01 sp019232985	79.0004	304	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAFAMW01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 10:21:08,457] [INFO] GTDB search result was written to GCA_026400105.1_ASM2640010v1_genomic.fna/result_gtdb.tsv
[2023-06-27 10:21:08,458] [INFO] ===== GTDB Search completed =====
[2023-06-27 10:21:08,462] [INFO] DFAST_QC result json was written to GCA_026400105.1_ASM2640010v1_genomic.fna/dqc_result.json
[2023-06-27 10:21:08,462] [INFO] DFAST_QC completed!
[2023-06-27 10:21:08,462] [INFO] Total running time: 0h1m19s