[2024-01-24 12:22:37,895] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:37,898] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:37,898] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f99e20b-9ff8-4ece-9afe-da49ac9b3a5f/dqc_reference
[2024-01-24 12:22:39,254] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:39,255] [INFO] Task started: Prodigal
[2024-01-24 12:22:39,255] [INFO] Running command: gunzip -c /var/lib/cwl/stgc590991a-b6e4-4c5e-bfa5-026d46a90bef/GCF_000696225.1_ASM69622v1_genomic.fna.gz | prodigal -d GCF_000696225.1_ASM69622v1_genomic.fna/cds.fna -a GCF_000696225.1_ASM69622v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:47,994] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:47,994] [INFO] Task started: HMMsearch
[2024-01-24 12:22:47,994] [INFO] Running command: hmmsearch --tblout GCF_000696225.1_ASM69622v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f99e20b-9ff8-4ece-9afe-da49ac9b3a5f/dqc_reference/reference_markers.hmm GCF_000696225.1_ASM69622v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:48,246] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:48,248] [INFO] Found 6/6 markers.
[2024-01-24 12:22:48,276] [INFO] Query marker FASTA was written to GCF_000696225.1_ASM69622v1_genomic.fna/markers.fasta
[2024-01-24 12:22:48,276] [INFO] Task started: Blastn
[2024-01-24 12:22:48,276] [INFO] Running command: blastn -query GCF_000696225.1_ASM69622v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f99e20b-9ff8-4ece-9afe-da49ac9b3a5f/dqc_reference/reference_markers.fasta -out GCF_000696225.1_ASM69622v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:49,159] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:49,164] [INFO] Selected 17 target genomes.
[2024-01-24 12:22:49,164] [INFO] Target genome list was writen to GCF_000696225.1_ASM69622v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:49,174] [INFO] Task started: fastANI
[2024-01-24 12:22:49,174] [INFO] Running command: fastANI --query /var/lib/cwl/stgc590991a-b6e4-4c5e-bfa5-026d46a90bef/GCF_000696225.1_ASM69622v1_genomic.fna.gz --refList GCF_000696225.1_ASM69622v1_genomic.fna/target_genomes.txt --output GCF_000696225.1_ASM69622v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:01,193] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:01,194] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f99e20b-9ff8-4ece-9afe-da49ac9b3a5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:01,194] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f99e20b-9ff8-4ece-9afe-da49ac9b3a5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:01,208] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:01,208] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:01,208] [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
Serpentinimonas barnesii	strain=H1	GCA_000696225.1	1458427	1458427	type	True	100.0	789	792	95	conclusive
Serpentinimonas raichei	strain=A1	GCA_000828895.1	1458425	1458425	type	True	93.3845	720	792	95	below_threshold
Serpentinimonas maccroryi	strain=B1	GCA_000828915.1	1458426	1458426	type	True	87.5511	668	792	95	below_threshold
Tepidicella baoligensis	strain=B18-50	GCA_013432195.1	2707016	2707016	type	True	79.7836	398	792	95	below_threshold
Tepidimonas thermarum	strain=AA-1	GCA_007556705.1	335431	335431	type	True	79.6949	407	792	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.5757	423	792	95	below_threshold
Tepidimonas fonticaldi	strain=AT-A2	GCA_007556755.1	1101373	1101373	type	True	79.5488	415	792	95	below_threshold
Malikia granosa	strain=P1	GCA_002980595.1	263067	263067	type	True	79.4486	374	792	95	below_threshold
Ottowia beijingensis	strain=GCS-AN-3	GCA_013423955.1	1207057	1207057	type	True	79.3292	377	792	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	79.3272	420	792	95	below_threshold
Hydrogenophaga intermedia	strain=DSM 5680	GCA_005938115.1	65786	65786	type	True	79.1309	391	792	95	below_threshold
Extensimonas perlucida	strain=HX2-24	GCA_007655255.1	2590786	2590786	type	True	78.8565	343	792	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	78.1013	303	792	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	78.0353	352	792	95	below_threshold
Simplicispira suum	strain=SC1-8	GCA_003008595.1	2109915	2109915	type	True	77.8336	295	792	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	77.8163	318	792	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	77.7076	327	792	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:01,210] [INFO] DFAST Taxonomy check result was written to GCF_000696225.1_ASM69622v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:01,211] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:01,211] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:01,211] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f99e20b-9ff8-4ece-9afe-da49ac9b3a5f/dqc_reference/checkm_data
[2024-01-24 12:23:01,212] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:01,240] [INFO] Task started: CheckM
[2024-01-24 12:23:01,241] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000696225.1_ASM69622v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000696225.1_ASM69622v1_genomic.fna/checkm_input GCF_000696225.1_ASM69622v1_genomic.fna/checkm_result
[2024-01-24 12:23:31,429] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:31,432] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:31,454] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:31,455] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:31,455] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000696225.1_ASM69622v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:31,456] [INFO] Task started: Blastn
[2024-01-24 12:23:31,456] [INFO] Running command: blastn -query GCF_000696225.1_ASM69622v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f99e20b-9ff8-4ece-9afe-da49ac9b3a5f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000696225.1_ASM69622v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:33,143] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:33,146] [INFO] Selected 15 target genomes.
[2024-01-24 12:23:33,146] [INFO] Target genome list was writen to GCF_000696225.1_ASM69622v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:33,156] [INFO] Task started: fastANI
[2024-01-24 12:23:33,157] [INFO] Running command: fastANI --query /var/lib/cwl/stgc590991a-b6e4-4c5e-bfa5-026d46a90bef/GCF_000696225.1_ASM69622v1_genomic.fna.gz --refList GCF_000696225.1_ASM69622v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000696225.1_ASM69622v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:42,357] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:42,374] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:42,375] [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_000696225.1	s__Serpentinomonas sp000696225	100.0	789	792	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Serpentinomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000828895.1	s__Serpentinomonas raichei	93.3845	720	792	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Serpentinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000828915.1	s__Serpentinomonas mccroryi	87.5708	667	792	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Serpentinomonas	95.0	98.21	97.99	0.96	0.95	3	-
GCF_002837145.1	s__BK-30 sp002837145	80.4464	450	792	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__BK-30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002291945.1	s__UBA997 sp002291945	79.9186	374	792	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA997	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013432195.1	s__Tepidicella baoligensis	79.7625	400	792	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363315.1	s__Tepidicella xavieri	79.7067	431	792	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007556705.1	s__Tepidimonas thermarum	79.6619	410	792	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002837135.1	s__Macromonas bipunctata	79.5895	358	792	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Macromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002980595.1	s__Malikia granosa	79.3965	378	792	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Malikia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002127215.1	s__Hydrogenophaga sp002127215	79.381	368	792	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007556675.1	s__Tepidimonas taiwanensis	79.1955	379	792	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	98.33	97.91	0.91	0.88	3	-
GCA_013693755.1	s__Tibeticola sp013693755	79.0527	370	792	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tibeticola	95.0	96.98	96.98	0.89	0.89	2	-
GCF_002245625.1	s__Acidovorax kalamii	78.0125	353	792	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016191995.1	s__Rubrivivax sp016191995	77.4141	291	792	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:42,378] [INFO] GTDB search result was written to GCF_000696225.1_ASM69622v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:42,378] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:42,382] [INFO] DFAST_QC result json was written to GCF_000696225.1_ASM69622v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:42,382] [INFO] DFAST_QC completed!
[2024-01-24 12:23:42,382] [INFO] Total running time: 0h1m4s