[2024-01-24 12:22:48,957] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:48,965] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:48,970] [INFO] DQC Reference Directory: /var/lib/cwl/stgede7d486-c44f-45fc-8a57-5e5a10a06c1a/dqc_reference
[2024-01-24 12:22:50,407] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:50,408] [INFO] Task started: Prodigal
[2024-01-24 12:22:50,409] [INFO] Running command: gunzip -c /var/lib/cwl/stg35c69a1c-4f31-44b8-a27a-a445c60c678b/GCF_017255015.1_ASM1725501v1_genomic.fna.gz | prodigal -d GCF_017255015.1_ASM1725501v1_genomic.fna/cds.fna -a GCF_017255015.1_ASM1725501v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:04,803] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:04,804] [INFO] Task started: HMMsearch
[2024-01-24 12:23:04,804] [INFO] Running command: hmmsearch --tblout GCF_017255015.1_ASM1725501v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgede7d486-c44f-45fc-8a57-5e5a10a06c1a/dqc_reference/reference_markers.hmm GCF_017255015.1_ASM1725501v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:05,110] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:05,111] [INFO] Found 6/6 markers.
[2024-01-24 12:23:05,156] [INFO] Query marker FASTA was written to GCF_017255015.1_ASM1725501v1_genomic.fna/markers.fasta
[2024-01-24 12:23:05,156] [INFO] Task started: Blastn
[2024-01-24 12:23:05,157] [INFO] Running command: blastn -query GCF_017255015.1_ASM1725501v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgede7d486-c44f-45fc-8a57-5e5a10a06c1a/dqc_reference/reference_markers.fasta -out GCF_017255015.1_ASM1725501v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:05,880] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:05,884] [INFO] Selected 23 target genomes.
[2024-01-24 12:23:05,884] [INFO] Target genome list was writen to GCF_017255015.1_ASM1725501v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:05,897] [INFO] Task started: fastANI
[2024-01-24 12:23:05,897] [INFO] Running command: fastANI --query /var/lib/cwl/stg35c69a1c-4f31-44b8-a27a-a445c60c678b/GCF_017255015.1_ASM1725501v1_genomic.fna.gz --refList GCF_017255015.1_ASM1725501v1_genomic.fna/target_genomes.txt --output GCF_017255015.1_ASM1725501v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:21,687] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:21,687] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgede7d486-c44f-45fc-8a57-5e5a10a06c1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:21,687] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgede7d486-c44f-45fc-8a57-5e5a10a06c1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:21,697] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:23:21,698] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:23:21,698] [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
Bowmanella pacifica	strain=CGMCC 1.7086	GCA_014645355.1	502051	502051	type	True	84.2105	1074	1543	95	below_threshold
Bowmanella dokdonensis	strain=JCM 30855	GCA_017254865.1	751969	751969	type	True	77.6762	303	1543	95	below_threshold
Lacimicrobium alkaliphilum	strain=X13M-12	GCA_002591895.1	1526571	1526571	type	True	77.2741	200	1543	95	below_threshold
Lacimicrobium alkaliphilum	strain=CGMCC 1.12923	GCA_014640135.1	1526571	1526571	type	True	77.2611	206	1543	95	below_threshold
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	77.2369	62	1543	95	below_threshold
Alteromonas antoniana	strain=MD_567	GCA_019249295.1	2803813	2803813	type	True	77.033	81	1543	95	below_threshold
Alteromonas portus	strain=HB161718	GCA_005117025.1	2565549	2565549	type	True	76.923	67	1543	95	below_threshold
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	76.8755	62	1543	95	below_threshold
Aestuariibacter halophilus	strain=JC2043	GCA_020687825.1	226011	226011	type	True	76.7851	109	1543	95	below_threshold
Photobacterium salinisoli	strain=LAM9072	GCA_003614885.1	1616783	1616783	type	True	76.2572	50	1543	95	below_threshold
Paraglaciecola hydrolytica	strain=S66	GCA_001565895.1	1799789	1799789	type	True	76.0841	73	1543	95	below_threshold
Arsukibacterium indicum	strain=SM2107	GCA_019100565.1	2848612	2848612	type	True	75.7613	60	1543	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:21,700] [INFO] DFAST Taxonomy check result was written to GCF_017255015.1_ASM1725501v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:21,700] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:21,700] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:21,700] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgede7d486-c44f-45fc-8a57-5e5a10a06c1a/dqc_reference/checkm_data
[2024-01-24 12:23:21,701] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:21,751] [INFO] Task started: CheckM
[2024-01-24 12:23:21,752] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017255015.1_ASM1725501v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017255015.1_ASM1725501v1_genomic.fna/checkm_input GCF_017255015.1_ASM1725501v1_genomic.fna/checkm_result
[2024-01-24 12:24:06,392] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:06,394] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:06,426] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:06,426] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:06,427] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017255015.1_ASM1725501v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:06,427] [INFO] Task started: Blastn
[2024-01-24 12:24:06,427] [INFO] Running command: blastn -query GCF_017255015.1_ASM1725501v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgede7d486-c44f-45fc-8a57-5e5a10a06c1a/dqc_reference/reference_markers_gtdb.fasta -out GCF_017255015.1_ASM1725501v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:07,483] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:07,487] [INFO] Selected 19 target genomes.
[2024-01-24 12:24:07,487] [INFO] Target genome list was writen to GCF_017255015.1_ASM1725501v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:07,500] [INFO] Task started: fastANI
[2024-01-24 12:24:07,500] [INFO] Running command: fastANI --query /var/lib/cwl/stg35c69a1c-4f31-44b8-a27a-a445c60c678b/GCF_017255015.1_ASM1725501v1_genomic.fna.gz --refList GCF_017255015.1_ASM1725501v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017255015.1_ASM1725501v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:21,415] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:21,430] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:21,430] [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_018531185.1	s__Bowmanella sp018531185	96.1079	1358	1543	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Bowmanella	95.0	96.11	96.11	0.88	0.88	2	conclusive
GCF_014645355.1	s__Bowmanella pacifica	84.2016	1075	1543	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Bowmanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002887595.1	s__Bowmanella denitrificans	80.9853	735	1543	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	77.6762	303	1543	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Bowmanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004329715.1	s__JS7-9 sp004329715	77.493	101	1543	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__JS7-9	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002201535.1	s__Lacimicrobium sp002201535	77.3459	188	1543	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Lacimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429145.1	s__Aestuariibacter salexigens	77.292	69	1543	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aestuariibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002591895.1	s__Lacimicrobium alkaliphilum	77.2741	200	1543	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Lacimicrobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001466725.1	s__Lacimicrobium alkaliphilum_B	77.1465	239	1543	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Lacimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019249295.1	s__Alteromonas antoniana	76.9711	83	1543	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014225.1	s__Paraglaciecola atlantica_A	76.7993	59	1543	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000314955.1	s__Paraglaciecola chathamensis	76.7629	50	1543	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	98.24	97.58	0.90	0.88	8	-
GCF_006494365.1	s__Alteromonas mangrovi	76.5205	96	1543	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 12:24:21,433] [INFO] GTDB search result was written to GCF_017255015.1_ASM1725501v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:21,434] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:21,439] [INFO] DFAST_QC result json was written to GCF_017255015.1_ASM1725501v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:21,439] [INFO] DFAST_QC completed!
[2024-01-24 12:24:21,439] [INFO] Total running time: 0h1m32s