[2024-01-24 11:43:25,078] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:25,081] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:25,082] [INFO] DQC Reference Directory: /var/lib/cwl/stgcafdbb22-7fd9-4d9b-8f07-bc8678bbc549/dqc_reference
[2024-01-24 11:43:30,056] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:30,057] [INFO] Task started: Prodigal
[2024-01-24 11:43:30,058] [INFO] Running command: gunzip -c /var/lib/cwl/stgaa94ccd1-3545-4b6c-a754-8da288e25cfc/GCF_002591895.1_ASM259189v1_genomic.fna.gz | prodigal -d GCF_002591895.1_ASM259189v1_genomic.fna/cds.fna -a GCF_002591895.1_ASM259189v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:41,295] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:41,295] [INFO] Task started: HMMsearch
[2024-01-24 11:43:41,295] [INFO] Running command: hmmsearch --tblout GCF_002591895.1_ASM259189v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcafdbb22-7fd9-4d9b-8f07-bc8678bbc549/dqc_reference/reference_markers.hmm GCF_002591895.1_ASM259189v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:41,605] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:41,607] [INFO] Found 6/6 markers.
[2024-01-24 11:43:41,644] [INFO] Query marker FASTA was written to GCF_002591895.1_ASM259189v1_genomic.fna/markers.fasta
[2024-01-24 11:43:41,645] [INFO] Task started: Blastn
[2024-01-24 11:43:41,645] [INFO] Running command: blastn -query GCF_002591895.1_ASM259189v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcafdbb22-7fd9-4d9b-8f07-bc8678bbc549/dqc_reference/reference_markers.fasta -out GCF_002591895.1_ASM259189v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:42,329] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:42,332] [INFO] Selected 21 target genomes.
[2024-01-24 11:43:42,333] [INFO] Target genome list was writen to GCF_002591895.1_ASM259189v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:42,361] [INFO] Task started: fastANI
[2024-01-24 11:43:42,361] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa94ccd1-3545-4b6c-a754-8da288e25cfc/GCF_002591895.1_ASM259189v1_genomic.fna.gz --refList GCF_002591895.1_ASM259189v1_genomic.fna/target_genomes.txt --output GCF_002591895.1_ASM259189v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:43:57,156] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:57,157] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcafdbb22-7fd9-4d9b-8f07-bc8678bbc549/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:43:57,157] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcafdbb22-7fd9-4d9b-8f07-bc8678bbc549/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:43:57,168] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:43:57,169] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:43:57,169] [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
Lacimicrobium alkaliphilum	strain=X13M-12	GCA_002591895.1	1526571	1526571	type	True	100.0	1409	1412	95	conclusive
Lacimicrobium alkaliphilum	strain=CGMCC 1.12923	GCA_014640135.1	1526571	1526571	type	True	99.9944	1406	1412	95	conclusive
Bowmanella dokdonensis	strain=JCM 30855	GCA_017254865.1	751969	751969	type	True	77.4167	260	1412	95	below_threshold
Bowmanella pacifica	strain=CGMCC 1.7086	GCA_014645355.1	502051	502051	type	True	77.371	203	1412	95	below_threshold
Saliniradius amylolyticus	strain=HMF8227	GCA_003143555.1	2183582	2183582	type	True	77.1216	138	1412	95	below_threshold
Salinimonas chungwhensis	strain=DSM 16280	GCA_000378185.1	265425	265425	type	True	77.1148	58	1412	95	below_threshold
Alteromonas aestuariivivens	strain=KCTC 52655	GCA_003367475.1	1938339	1938339	type	True	76.8922	84	1412	95	below_threshold
Alteromonas alba	strain=190	GCA_002993365.1	2079529	2079529	type	True	76.6018	79	1412	95	below_threshold
Salinimonas profundi	strain=HHU 13199	GCA_014750655.1	2729140	2729140	type	True	76.5632	67	1412	95	below_threshold
Neptunicella marina	strain=S27-2	GCA_014270035.1	2125989	2125989	type	True	76.435	85	1412	95	below_threshold
Oceanimonas smirnovii	strain=ATCC BAA-899	GCA_000381965.1	264574	264574	type	True	75.806	55	1412	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:43:57,170] [INFO] DFAST Taxonomy check result was written to GCF_002591895.1_ASM259189v1_genomic.fna/tc_result.tsv
[2024-01-24 11:43:57,171] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:43:57,171] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:43:57,171] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcafdbb22-7fd9-4d9b-8f07-bc8678bbc549/dqc_reference/checkm_data
[2024-01-24 11:43:57,172] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:43:57,212] [INFO] Task started: CheckM
[2024-01-24 11:43:57,213] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002591895.1_ASM259189v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002591895.1_ASM259189v1_genomic.fna/checkm_input GCF_002591895.1_ASM259189v1_genomic.fna/checkm_result
[2024-01-24 11:44:34,304] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:34,306] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:34,331] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:34,331] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:34,332] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002591895.1_ASM259189v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:34,332] [INFO] Task started: Blastn
[2024-01-24 11:44:34,332] [INFO] Running command: blastn -query GCF_002591895.1_ASM259189v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcafdbb22-7fd9-4d9b-8f07-bc8678bbc549/dqc_reference/reference_markers_gtdb.fasta -out GCF_002591895.1_ASM259189v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:35,491] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:35,496] [INFO] Selected 16 target genomes.
[2024-01-24 11:44:35,496] [INFO] Target genome list was writen to GCF_002591895.1_ASM259189v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:35,520] [INFO] Task started: fastANI
[2024-01-24 11:44:35,520] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa94ccd1-3545-4b6c-a754-8da288e25cfc/GCF_002591895.1_ASM259189v1_genomic.fna.gz --refList GCF_002591895.1_ASM259189v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002591895.1_ASM259189v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:48,063] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:48,076] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:48,076] [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_002591895.1	s__Lacimicrobium alkaliphilum	100.0	1409	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Lacimicrobium	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_001466725.1	s__Lacimicrobium alkaliphilum_B	84.0406	1041	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Lacimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002201535.1	s__Lacimicrobium sp002201535	79.7448	577	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Lacimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002887595.1	s__Bowmanella denitrificans	77.4787	253	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Bowmanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017254865.1	s__Bowmanella dokdonensis	77.4391	258	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Bowmanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018531185.1	s__Bowmanella sp018531185	77.3295	206	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Bowmanella	95.0	96.11	96.11	0.88	0.88	2	-
GCF_003143555.1	s__Saliniradius amylolyticus	77.1414	137	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Saliniradius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378185.1	s__Alteromonas chungwhensis	77.0703	59	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429145.1	s__Aestuariibacter salexigens	76.7634	80	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aestuariibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584565.2	s__Alteromonas sp002729795	76.7061	75	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.21	97.21	0.92	0.92	2	-
GCF_014750655.1	s__Alteromonas profundi_A	76.5315	68	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:48,078] [INFO] GTDB search result was written to GCF_002591895.1_ASM259189v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:48,078] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:48,081] [INFO] DFAST_QC result json was written to GCF_002591895.1_ASM259189v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:48,081] [INFO] DFAST_QC completed!
[2024-01-24 11:44:48,082] [INFO] Total running time: 0h1m23s