[2024-01-25 18:09:35,385] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:09:35,388] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:09:35,388] [INFO] DQC Reference Directory: /var/lib/cwl/stg37e845d8-7f72-4062-8379-c443a461d6b3/dqc_reference
[2024-01-25 18:09:36,557] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:09:36,558] [INFO] Task started: Prodigal
[2024-01-25 18:09:36,558] [INFO] Running command: gunzip -c /var/lib/cwl/stgee8e5454-f55f-4880-8703-a0058c4fd616/GCF_025989185.1_ASM2598918v1_genomic.fna.gz | prodigal -d GCF_025989185.1_ASM2598918v1_genomic.fna/cds.fna -a GCF_025989185.1_ASM2598918v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:09:52,117] [INFO] Task succeeded: Prodigal
[2024-01-25 18:09:52,117] [INFO] Task started: HMMsearch
[2024-01-25 18:09:52,117] [INFO] Running command: hmmsearch --tblout GCF_025989185.1_ASM2598918v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37e845d8-7f72-4062-8379-c443a461d6b3/dqc_reference/reference_markers.hmm GCF_025989185.1_ASM2598918v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:09:52,399] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:09:52,400] [INFO] Found 6/6 markers.
[2024-01-25 18:09:52,443] [INFO] Query marker FASTA was written to GCF_025989185.1_ASM2598918v1_genomic.fna/markers.fasta
[2024-01-25 18:09:52,443] [INFO] Task started: Blastn
[2024-01-25 18:09:52,443] [INFO] Running command: blastn -query GCF_025989185.1_ASM2598918v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37e845d8-7f72-4062-8379-c443a461d6b3/dqc_reference/reference_markers.fasta -out GCF_025989185.1_ASM2598918v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:53,361] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:53,364] [INFO] Selected 22 target genomes.
[2024-01-25 18:09:53,364] [INFO] Target genome list was writen to GCF_025989185.1_ASM2598918v1_genomic.fna/target_genomes.txt
[2024-01-25 18:09:53,384] [INFO] Task started: fastANI
[2024-01-25 18:09:53,384] [INFO] Running command: fastANI --query /var/lib/cwl/stgee8e5454-f55f-4880-8703-a0058c4fd616/GCF_025989185.1_ASM2598918v1_genomic.fna.gz --refList GCF_025989185.1_ASM2598918v1_genomic.fna/target_genomes.txt --output GCF_025989185.1_ASM2598918v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:10:13,575] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:13,576] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37e845d8-7f72-4062-8379-c443a461d6b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:10:13,576] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37e845d8-7f72-4062-8379-c443a461d6b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:10:13,589] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:10:13,589] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:10:13,590] [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
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	79.7837	709	1750	95	below_threshold
Acidisphaera rubrifaciens	strain=HS-AP3	GCA_000964365.1	50715	50715	type	True	78.8171	329	1750	95	below_threshold
Rhodopila globiformis	strain=DSM 161	GCA_002937115.1	1071	1071	type	True	78.5551	600	1750	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	78.2966	545	1750	95	below_threshold
Roseomonas coralli	strain=M0104	GCA_009829925.1	2545983	2545983	type	True	78.1763	555	1750	95	below_threshold
Endobacter medicaginis	strain=LMG 26838	GCA_013376135.1	1181271	1181271	type	True	78.1417	225	1750	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	78.1153	563	1750	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	77.8908	536	1750	95	below_threshold
Endobacter medicaginis	strain=CECT 8088	GCA_014192375.1	1181271	1181271	type	True	77.8467	343	1750	95	below_threshold
Roseomonas wenyumeiae	strain=Z23	GCA_003696345.1	2478470	2478470	type	True	77.7007	524	1750	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	77.7003	594	1750	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	77.6778	531	1750	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	77.6648	463	1750	95	below_threshold
Siccirubricoccus deserti	strain=CGMCC 1.15936	GCA_014644195.1	2013562	2013562	type	True	77.6352	554	1750	95	below_threshold
Siccirubricoccus deserti	strain=SYSU D8009	GCA_014283215.1	2013562	2013562	type	True	77.6205	560	1750	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	77.5409	445	1750	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	77.5396	432	1750	95	below_threshold
Falsiroseomonas frigidaquae	strain=JCM 15073	GCA_012163145.1	487318	487318	type	True	77.4679	571	1750	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	77.373	311	1750	95	below_threshold
Roseomonas harenae	strain=CPCC 101081	GCA_009848505.1	2692566	2692566	type	True	77.1894	411	1750	95	below_threshold
Novacetimonas maltaceti	strain=LMG 1529	GCA_003206475.1	1203393	1203393	type	True	77.0971	192	1750	95	below_threshold
Novacetimonas maltaceti	strain=LMG 1529	GCA_002906255.1	1203393	1203393	type	True	77.0176	193	1750	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:10:13,591] [INFO] DFAST Taxonomy check result was written to GCF_025989185.1_ASM2598918v1_genomic.fna/tc_result.tsv
[2024-01-25 18:10:13,591] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:10:13,591] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:10:13,592] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37e845d8-7f72-4062-8379-c443a461d6b3/dqc_reference/checkm_data
[2024-01-25 18:10:13,592] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:10:13,641] [INFO] Task started: CheckM
[2024-01-25 18:10:13,641] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025989185.1_ASM2598918v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025989185.1_ASM2598918v1_genomic.fna/checkm_input GCF_025989185.1_ASM2598918v1_genomic.fna/checkm_result
[2024-01-25 18:11:13,667] [INFO] Task succeeded: CheckM
[2024-01-25 18:11:13,668] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:11:13,689] [INFO] ===== Completeness check finished =====
[2024-01-25 18:11:13,690] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:11:13,691] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025989185.1_ASM2598918v1_genomic.fna/markers.fasta)
[2024-01-25 18:11:13,691] [INFO] Task started: Blastn
[2024-01-25 18:11:13,691] [INFO] Running command: blastn -query GCF_025989185.1_ASM2598918v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37e845d8-7f72-4062-8379-c443a461d6b3/dqc_reference/reference_markers_gtdb.fasta -out GCF_025989185.1_ASM2598918v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:15,402] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:15,404] [INFO] Selected 19 target genomes.
[2024-01-25 18:11:15,405] [INFO] Target genome list was writen to GCF_025989185.1_ASM2598918v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:11:15,438] [INFO] Task started: fastANI
[2024-01-25 18:11:15,438] [INFO] Running command: fastANI --query /var/lib/cwl/stgee8e5454-f55f-4880-8703-a0058c4fd616/GCF_025989185.1_ASM2598918v1_genomic.fna.gz --refList GCF_025989185.1_ASM2598918v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025989185.1_ASM2598918v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:11:35,015] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:35,029] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:11:35,029] [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_001899585.1	s__70-18 sp001899585	81.6851	902	1750	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__70-18	95.0	99.94	99.94	0.98	0.98	2	-
GCA_018971455.1	s__REEB85 sp018971455	80.7786	422	1750	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__REEB85	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903907955.1	s__BOG-930 sp903907955	80.0164	590	1750	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930	95.0	99.93	99.75	0.97	0.94	12	-
GCA_003133265.1	s__PALSA-911 sp003133265	79.7416	495	1750	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__PALSA-911	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630155.1	s__Rhodovastum atsumiense	79.7295	705	1750	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodovastum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903918195.1	s__BOG-930 sp903918195	79.7022	614	1750	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930	95.0	99.84	99.84	0.94	0.94	2	-
GCA_903865895.1	s__CAIYPH01 sp903865895	79.3796	711	1750	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIYPH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240635.1	s__JAFEFJ01 sp018240635	79.0817	522	1750	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFEFJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304945.1	s__69-11 sp017304945	79.0367	644	1750	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__69-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903881515.1	s__CAIRTN01 sp903881515	79.0097	617	1750	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIRTN01	95.0	99.60	99.60	0.90	0.90	2	-
GCF_000964365.1	s__Acidisphaera rubrifaciens	78.8398	327	1750	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903928045.1	s__CAIYPH01 sp903928045	78.7636	509	1750	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIYPH01	95.0	98.55	98.55	0.76	0.76	2	-
GCA_903845065.1	s__CAIYPH01 sp903845065	78.7088	709	1750	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIYPH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307285.1	s__JAFKFI01 sp017307285	78.6698	549	1750	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFKFI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898425.1	s__69-11 sp001898425	78.5818	650	1750	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__69-11	95.0	99.84	99.84	0.96	0.96	2	-
GCF_002937115.1	s__Rhodopila globiformis	78.5564	600	1750	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004761865.1	s__Crenalkalicoccus roseus	78.1593	580	1750	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Crenalkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005844085.1	s__Lichenicoccus roseus	77.8989	413	1750	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Lichenicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464375.1	s__Roseomonas_B sp001464375	77.498	495	1750	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:11:35,031] [INFO] GTDB search result was written to GCF_025989185.1_ASM2598918v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:11:35,032] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:11:35,036] [INFO] DFAST_QC result json was written to GCF_025989185.1_ASM2598918v1_genomic.fna/dqc_result.json
[2024-01-25 18:11:35,036] [INFO] DFAST_QC completed!
[2024-01-25 18:11:35,036] [INFO] Total running time: 0h1m60s