[2024-01-24 14:06:07,196] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:07,198] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:07,199] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c10ef4c-cdc6-420f-a3b6-dfe095178702/dqc_reference
[2024-01-24 14:06:08,517] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:08,518] [INFO] Task started: Prodigal
[2024-01-24 14:06:08,518] [INFO] Running command: gunzip -c /var/lib/cwl/stgb3dbb15c-95f7-434f-8bf5-642955aa6cd1/GCF_000175215.2_ASM17521v2_genomic.fna.gz | prodigal -d GCF_000175215.2_ASM17521v2_genomic.fna/cds.fna -a GCF_000175215.2_ASM17521v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:21,442] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:21,442] [INFO] Task started: HMMsearch
[2024-01-24 14:06:21,442] [INFO] Running command: hmmsearch --tblout GCF_000175215.2_ASM17521v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c10ef4c-cdc6-420f-a3b6-dfe095178702/dqc_reference/reference_markers.hmm GCF_000175215.2_ASM17521v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:21,810] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:21,811] [INFO] Found 6/6 markers.
[2024-01-24 14:06:21,851] [INFO] Query marker FASTA was written to GCF_000175215.2_ASM17521v2_genomic.fna/markers.fasta
[2024-01-24 14:06:21,852] [INFO] Task started: Blastn
[2024-01-24 14:06:21,852] [INFO] Running command: blastn -query GCF_000175215.2_ASM17521v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c10ef4c-cdc6-420f-a3b6-dfe095178702/dqc_reference/reference_markers.fasta -out GCF_000175215.2_ASM17521v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:22,749] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:22,753] [INFO] Selected 16 target genomes.
[2024-01-24 14:06:22,754] [INFO] Target genome list was writen to GCF_000175215.2_ASM17521v2_genomic.fna/target_genomes.txt
[2024-01-24 14:06:22,759] [INFO] Task started: fastANI
[2024-01-24 14:06:22,759] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3dbb15c-95f7-434f-8bf5-642955aa6cd1/GCF_000175215.2_ASM17521v2_genomic.fna.gz --refList GCF_000175215.2_ASM17521v2_genomic.fna/target_genomes.txt --output GCF_000175215.2_ASM17521v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:36,122] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:36,122] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c10ef4c-cdc6-420f-a3b6-dfe095178702/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:36,123] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c10ef4c-cdc6-420f-a3b6-dfe095178702/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:36,142] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:36,142] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:36,143] [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
Asticcacaulis excentricus	strain=CB 48	GCA_000175215.2	78587	78587	type	True	100.0	1434	1434	95	conclusive
Asticcacaulis tiandongensis	strain=3.1105	GCA_006475605.1	2565365	2565365	type	True	78.3821	340	1434	95	below_threshold
Asticcacaulis taihuensis	strain=CGMCC 1.3431	GCA_900100255.1	260084	260084	type	True	78.295	351	1434	95	below_threshold
Asticcacaulis benevestitus	strain=DSM 16100	GCA_000376105.1	347481	347481	type	True	78.0733	387	1434	95	below_threshold
Asticcacaulis endophyticus	strain=KCTC 32296	GCA_014652575.1	1395890	1395890	type	True	77.8052	396	1434	95	below_threshold
Asticcacaulis biprosthecium	strain=C19	GCA_000204015.1	76891	76891	type	True	77.6106	356	1434	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	77.3614	184	1434	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	77.1758	124	1434	95	below_threshold
Caulobacter soli	strain=Ji-3-8	GCA_011045195.1	2708539	2708539	type	True	77.1562	171	1434	95	below_threshold
Caulobacter flavus	strain=RHGG3	GCA_003722335.1	1679497	1679497	type	True	77.1201	205	1434	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	77.0981	162	1434	95	below_threshold
Caulobacter zeae	strain=410	GCA_002858925.1	2055137	2055137	type	True	76.9958	191	1434	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	76.9595	185	1434	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	76.4816	81	1434	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	75.886	72	1434	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	75.6848	69	1434	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:36,144] [INFO] DFAST Taxonomy check result was written to GCF_000175215.2_ASM17521v2_genomic.fna/tc_result.tsv
[2024-01-24 14:06:36,145] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:36,145] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:36,145] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c10ef4c-cdc6-420f-a3b6-dfe095178702/dqc_reference/checkm_data
[2024-01-24 14:06:36,146] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:36,190] [INFO] Task started: CheckM
[2024-01-24 14:06:36,190] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000175215.2_ASM17521v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000175215.2_ASM17521v2_genomic.fna/checkm_input GCF_000175215.2_ASM17521v2_genomic.fna/checkm_result
[2024-01-24 14:07:16,108] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:16,109] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:16,130] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:16,130] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:16,131] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000175215.2_ASM17521v2_genomic.fna/markers.fasta)
[2024-01-24 14:07:16,131] [INFO] Task started: Blastn
[2024-01-24 14:07:16,131] [INFO] Running command: blastn -query GCF_000175215.2_ASM17521v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c10ef4c-cdc6-420f-a3b6-dfe095178702/dqc_reference/reference_markers_gtdb.fasta -out GCF_000175215.2_ASM17521v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:17,703] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:17,706] [INFO] Selected 11 target genomes.
[2024-01-24 14:07:17,706] [INFO] Target genome list was writen to GCF_000175215.2_ASM17521v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:17,714] [INFO] Task started: fastANI
[2024-01-24 14:07:17,714] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3dbb15c-95f7-434f-8bf5-642955aa6cd1/GCF_000175215.2_ASM17521v2_genomic.fna.gz --refList GCF_000175215.2_ASM17521v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000175215.2_ASM17521v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:26,942] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:26,955] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:26,955] [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_000175215.2	s__Asticcacaulis excentricus	100.0	1434	1434	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003966695.1	s__Asticcacaulis excentricus_A	90.5462	1060	1434	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053985.1	s__Asticcacaulis sp003053985	83.899	943	1434	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000495855.1	s__Asticcacaulis sp000495855	80.4687	731	1434	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006475605.1	s__Asticcacaulis tiandongensis	78.3821	340	1434	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017875235.1	s__Asticcacaulis solisilvae	78.1043	431	1434	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873225.1	s__Asticcacaulis sp014873225	78.0499	394	1434	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002342035.1	s__Asticcacaulis sp002342035	77.9805	371	1434	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652575.1	s__Asticcacaulis endophyticus	77.7884	398	1434	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000204015.1	s__Asticcacaulis biprosthecium	77.6286	354	1434	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011064825.1	s__Brevundimonas mediterranea_A	77.4287	154	1434	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0657	98.11	97.23	0.89	0.83	17	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:26,957] [INFO] GTDB search result was written to GCF_000175215.2_ASM17521v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:26,958] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:26,962] [INFO] DFAST_QC result json was written to GCF_000175215.2_ASM17521v2_genomic.fna/dqc_result.json
[2024-01-24 14:07:26,962] [INFO] DFAST_QC completed!
[2024-01-24 14:07:26,962] [INFO] Total running time: 0h1m20s