[2024-01-24 13:31:32,999] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:33,003] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:33,003] [INFO] DQC Reference Directory: /var/lib/cwl/stgacfe4e44-c6c9-47de-8004-5c95ea8a16bb/dqc_reference
[2024-01-24 13:31:34,449] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:34,450] [INFO] Task started: Prodigal
[2024-01-24 13:31:34,450] [INFO] Running command: gunzip -c /var/lib/cwl/stg2f82c643-0504-4e95-8e17-e12e4cbb9505/GCF_031451615.1_ASM3145161v1_genomic.fna.gz | prodigal -d GCF_031451615.1_ASM3145161v1_genomic.fna/cds.fna -a GCF_031451615.1_ASM3145161v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:46,212] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:46,212] [INFO] Task started: HMMsearch
[2024-01-24 13:31:46,212] [INFO] Running command: hmmsearch --tblout GCF_031451615.1_ASM3145161v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgacfe4e44-c6c9-47de-8004-5c95ea8a16bb/dqc_reference/reference_markers.hmm GCF_031451615.1_ASM3145161v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:46,514] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:46,515] [INFO] Found 6/6 markers.
[2024-01-24 13:31:46,567] [INFO] Query marker FASTA was written to GCF_031451615.1_ASM3145161v1_genomic.fna/markers.fasta
[2024-01-24 13:31:46,568] [INFO] Task started: Blastn
[2024-01-24 13:31:46,568] [INFO] Running command: blastn -query GCF_031451615.1_ASM3145161v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgacfe4e44-c6c9-47de-8004-5c95ea8a16bb/dqc_reference/reference_markers.fasta -out GCF_031451615.1_ASM3145161v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:47,407] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:47,411] [INFO] Selected 23 target genomes.
[2024-01-24 13:31:47,412] [INFO] Target genome list was writen to GCF_031451615.1_ASM3145161v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:47,420] [INFO] Task started: fastANI
[2024-01-24 13:31:47,420] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f82c643-0504-4e95-8e17-e12e4cbb9505/GCF_031451615.1_ASM3145161v1_genomic.fna.gz --refList GCF_031451615.1_ASM3145161v1_genomic.fna/target_genomes.txt --output GCF_031451615.1_ASM3145161v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:02,705] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:02,705] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgacfe4e44-c6c9-47de-8004-5c95ea8a16bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:02,706] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgacfe4e44-c6c9-47de-8004-5c95ea8a16bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:02,723] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:32:02,723] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:32:02,723] [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
Halomonas arcis	strain=CGMCC 1.6494	GCA_900103865.1	416873	416873	type	True	82.3112	853	1281	95	below_threshold
Halomonas meridiana	strain=ACAM 246	GCA_900129255.1	29570	29570	type	True	79.7927	459	1281	95	below_threshold
Halomonas meridiana	strain=NBRC 15608	GCA_006540125.1	29570	29570	type	True	79.7149	436	1281	95	below_threshold
Halomonas stevensii	strain=S18214	GCA_000275725.1	502821	502821	type	True	79.7017	509	1281	95	below_threshold
Halomonas hamiltonii	strain=KCTC 22154	GCA_014651775.1	502829	502829	type	True	79.6807	521	1281	95	below_threshold
Halomonas aquamarina	strain=558	GCA_900110265.1	77097	77097	type	True	79.5329	448	1281	95	below_threshold
Halomonas johnsoniae	strain=KCTC 22157	GCA_014651795.1	502832	502832	type	True	79.4955	522	1281	95	below_threshold
Halomonas songnenensis	strain=CGMCC 1.12152	GCA_003002925.1	1176243	1176243	type	True	79.3332	469	1281	95	below_threshold
Halomonas lionensis	strain=RHS90	GCA_002087295.1	1144478	1144478	type	True	79.2818	419	1281	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019722725.1	2852117	2852117	type	True	79.132	390	1281	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019504685.1	2852117	2852117	type	True	79.0965	398	1281	95	below_threshold
Halomonas lutescens	strain=CGMCC 1.15122	GCA_014640815.1	1602943	1602943	type	True	79.0463	469	1281	95	below_threshold
Halomonas populi	strain=MC	GCA_003989825.1	2498858	2498858	type	True	78.9851	423	1281	95	below_threshold
Halomonas nanhaiensis	strain=JCM 18142	GCA_003990185.1	1258546	1258546	type	True	78.9168	419	1281	95	below_threshold
Halomonas subglaciescola	strain=ACAM 12	GCA_900142895.1	29571	29571	type	True	78.4775	336	1281	95	below_threshold
Halomonas rituensis	strain=TQ8S	GCA_003336665.1	2282306	2282306	type	True	78.3901	343	1281	95	below_threshold
Halomonas jeotgali	strain=Hwa	GCA_000334215.1	553386	553386	type	True	78.1353	273	1281	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	78.1021	283	1281	95	below_threshold
Halomonas fontilapidosi	strain=CECT 7341	GCA_014192285.1	616675	616675	type	True	78.0275	303	1281	95	below_threshold
Halomonas taeanensis	strain=BH539	GCA_900100755.1	284577	284577	type	True	77.9449	282	1281	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	77.9136	285	1281	95	below_threshold
Halomonas montanilacus	strain=PYC7W	GCA_003336675.1	2282305	2282305	type	True	77.8861	304	1281	95	below_threshold
Halomonas halocynthiae	strain=DSM 14573	GCA_000425725.1	176290	176290	type	True	77.6106	113	1281	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:02,725] [INFO] DFAST Taxonomy check result was written to GCF_031451615.1_ASM3145161v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:02,726] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:02,726] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:02,726] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgacfe4e44-c6c9-47de-8004-5c95ea8a16bb/dqc_reference/checkm_data
[2024-01-24 13:32:02,727] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:02,770] [INFO] Task started: CheckM
[2024-01-24 13:32:02,770] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031451615.1_ASM3145161v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031451615.1_ASM3145161v1_genomic.fna/checkm_input GCF_031451615.1_ASM3145161v1_genomic.fna/checkm_result
[2024-01-24 13:32:40,801] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:40,802] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:40,819] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:40,819] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:40,820] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031451615.1_ASM3145161v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:40,820] [INFO] Task started: Blastn
[2024-01-24 13:32:40,820] [INFO] Running command: blastn -query GCF_031451615.1_ASM3145161v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgacfe4e44-c6c9-47de-8004-5c95ea8a16bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_031451615.1_ASM3145161v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:42,113] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:42,119] [INFO] Selected 7 target genomes.
[2024-01-24 13:32:42,119] [INFO] Target genome list was writen to GCF_031451615.1_ASM3145161v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:42,127] [INFO] Task started: fastANI
[2024-01-24 13:32:42,127] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f82c643-0504-4e95-8e17-e12e4cbb9505/GCF_031451615.1_ASM3145161v1_genomic.fna.gz --refList GCF_031451615.1_ASM3145161v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031451615.1_ASM3145161v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:49,304] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:49,311] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:49,312] [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_015767635.1	s__Halomonas sp002119345	98.2227	1123	1281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.32	98.32	0.86	0.86	2	conclusive
GCF_900111305.1	s__Halomonas subterranea	90.8742	1017	1281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.10	95.10	0.84	0.84	2	-
GCF_014263395.1	s__Halomonas sp014263395	90.0082	1018	1281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000686925.1	s__Halomonas sp000686925	83.4685	908	1281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900086985.1	s__Halomonas sp900086985	83.2849	930	1281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.32	98.66	0.96	0.94	3	-
GCF_900103865.1	s__Halomonas arcis	82.3112	853	1281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000275725.1	s__Halomonas stevensii	79.7223	507	1281	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.843	97.33	97.21	0.85	0.83	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:49,313] [INFO] GTDB search result was written to GCF_031451615.1_ASM3145161v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:49,314] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:49,317] [INFO] DFAST_QC result json was written to GCF_031451615.1_ASM3145161v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:49,317] [INFO] DFAST_QC completed!
[2024-01-24 13:32:49,317] [INFO] Total running time: 0h1m16s