[2024-01-24 15:02:33,569] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:33,572] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:33,572] [INFO] DQC Reference Directory: /var/lib/cwl/stg260ba8d4-0564-4988-b619-bbcc72e223ea/dqc_reference
[2024-01-24 15:02:34,826] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:34,827] [INFO] Task started: Prodigal
[2024-01-24 15:02:34,828] [INFO] Running command: gunzip -c /var/lib/cwl/stgeef1d8d6-5a2e-47be-892a-e1cb05503e25/GCF_000987775.1_ASM98777v1_genomic.fna.gz | prodigal -d GCF_000987775.1_ASM98777v1_genomic.fna/cds.fna -a GCF_000987775.1_ASM98777v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:45,034] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:45,034] [INFO] Task started: HMMsearch
[2024-01-24 15:02:45,034] [INFO] Running command: hmmsearch --tblout GCF_000987775.1_ASM98777v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg260ba8d4-0564-4988-b619-bbcc72e223ea/dqc_reference/reference_markers.hmm GCF_000987775.1_ASM98777v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:45,355] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:45,357] [INFO] Found 6/6 markers.
[2024-01-24 15:02:45,396] [INFO] Query marker FASTA was written to GCF_000987775.1_ASM98777v1_genomic.fna/markers.fasta
[2024-01-24 15:02:45,397] [INFO] Task started: Blastn
[2024-01-24 15:02:45,397] [INFO] Running command: blastn -query GCF_000987775.1_ASM98777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg260ba8d4-0564-4988-b619-bbcc72e223ea/dqc_reference/reference_markers.fasta -out GCF_000987775.1_ASM98777v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:46,187] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:46,190] [INFO] Selected 16 target genomes.
[2024-01-24 15:02:46,190] [INFO] Target genome list was writen to GCF_000987775.1_ASM98777v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:46,196] [INFO] Task started: fastANI
[2024-01-24 15:02:46,197] [INFO] Running command: fastANI --query /var/lib/cwl/stgeef1d8d6-5a2e-47be-892a-e1cb05503e25/GCF_000987775.1_ASM98777v1_genomic.fna.gz --refList GCF_000987775.1_ASM98777v1_genomic.fna/target_genomes.txt --output GCF_000987775.1_ASM98777v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:58,583] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:58,583] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg260ba8d4-0564-4988-b619-bbcc72e223ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:58,584] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg260ba8d4-0564-4988-b619-bbcc72e223ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:58,597] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:02:58,597] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:02:58,598] [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
Arsukibacterium perlucidum	strain=DSM 18276	GCA_000382165.1	368811	368811	type	True	82.0816	855	1356	95	below_threshold
Arsukibacterium tuosuense	strain=CGMCC 1.12461	GCA_900215315.1	1323745	1323745	type	True	81.7224	854	1356	95	below_threshold
Arsukibacterium indicum	strain=SM2107	GCA_019100565.1	2848612	2848612	type	True	81.0571	812	1356	95	below_threshold
Rheinheimera pacifica	strain=DSM 17616	GCA_900108485.1	173990	173990	type	True	79.4113	506	1356	95	below_threshold
Rheinheimera pleomorphica	strain=PKS7	GCA_011634895.1	2703963	2703963	type	True	79.0624	479	1356	95	below_threshold
Rheinheimera lutimaris	strain=YQF-2	GCA_013283795.1	2740584	2740584	type	True	79.0259	498	1356	95	below_threshold
Rheinheimera nanhaiensis	strain=E407-8	GCA_000296695.1	1163621	1163621	type	True	78.9737	458	1356	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_016918075.2	2793282	2793282	type	True	78.9205	406	1356	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_017824735.1	2793282	2793282	type	True	78.8988	408	1356	95	below_threshold
Rheinheimera hassiensis	strain=LMG 27268	GCA_022436675.1	1193627	1193627	type	True	78.8971	461	1356	95	below_threshold
Alishewanella agri	strain=BL06	GCA_000272005.1	553384	553384	type	True	78.7713	367	1356	95	below_threshold
Alishewanella longhuensis	strain=CGMCC 1.7003	GCA_014653435.1	1091037	1091037	type	True	78.5792	341	1356	95	below_threshold
Rheinheimera baltica	strain=DSM 14885	GCA_000425345.1	67576	67576	type	True	78.4806	320	1356	95	below_threshold
Rheinheimera tangshanensis	strain=JA3-B52	GCA_008017875.1	400153	400153	type	True	77.6191	184	1356	95	below_threshold
Rheinheimera tangshanensis	strain=CGMCC 1.6362	GCA_014645135.1	400153	400153	type	True	77.5342	182	1356	95	below_threshold
Pararheinheimera texasensis	strain=DSM 17496	GCA_000711985.1	306205	306205	type	True	77.3619	186	1356	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:58,599] [INFO] DFAST Taxonomy check result was written to GCF_000987775.1_ASM98777v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:58,600] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:58,600] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:58,600] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg260ba8d4-0564-4988-b619-bbcc72e223ea/dqc_reference/checkm_data
[2024-01-24 15:02:58,601] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:58,643] [INFO] Task started: CheckM
[2024-01-24 15:02:58,643] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000987775.1_ASM98777v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000987775.1_ASM98777v1_genomic.fna/checkm_input GCF_000987775.1_ASM98777v1_genomic.fna/checkm_result
[2024-01-24 15:03:34,649] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:34,651] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:34,669] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:34,670] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:34,670] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000987775.1_ASM98777v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:34,670] [INFO] Task started: Blastn
[2024-01-24 15:03:34,671] [INFO] Running command: blastn -query GCF_000987775.1_ASM98777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg260ba8d4-0564-4988-b619-bbcc72e223ea/dqc_reference/reference_markers_gtdb.fasta -out GCF_000987775.1_ASM98777v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:35,895] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:35,899] [INFO] Selected 9 target genomes.
[2024-01-24 15:03:35,899] [INFO] Target genome list was writen to GCF_000987775.1_ASM98777v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:35,905] [INFO] Task started: fastANI
[2024-01-24 15:03:35,905] [INFO] Running command: fastANI --query /var/lib/cwl/stgeef1d8d6-5a2e-47be-892a-e1cb05503e25/GCF_000987775.1_ASM98777v1_genomic.fna.gz --refList GCF_000987775.1_ASM98777v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000987775.1_ASM98777v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:44,560] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:44,570] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:44,570] [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_000987775.1	s__Arsukibacterium ikkense	100.0	1356	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000382165.1	s__Arsukibacterium perlucidum	82.0622	857	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402695.1	s__Arsukibacterium sp018402695	81.7376	875	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215315.1	s__Arsukibacterium tuosuense	81.731	853	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019100565.1	s__Arsukibacterium sp019100565	81.0493	813	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364615.1	s__Arsukibacterium sp002364615	80.8383	750	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	99.93	99.93	0.99	0.99	2	-
GCA_002415085.1	s__Arsukibacterium sp002415085	80.6986	767	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	99.96	99.86	0.96	0.90	7	-
GCF_000987765.1	s__Arsukibacterium sp000987765	80.1255	679	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108485.1	s__Rheinheimera pacifica	79.4061	506	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:44,572] [INFO] GTDB search result was written to GCF_000987775.1_ASM98777v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:44,572] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:44,576] [INFO] DFAST_QC result json was written to GCF_000987775.1_ASM98777v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:44,576] [INFO] DFAST_QC completed!
[2024-01-24 15:03:44,576] [INFO] Total running time: 0h1m11s