[2024-01-25 18:41:05,640] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:41:05,641] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:41:05,642] [INFO] DQC Reference Directory: /var/lib/cwl/stga283d3d3-5a65-47a0-beb5-3f62bb1bb96d/dqc_reference
[2024-01-25 18:41:06,767] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:41:06,768] [INFO] Task started: Prodigal
[2024-01-25 18:41:06,768] [INFO] Running command: gunzip -c /var/lib/cwl/stg1cfe97e7-7ee8-4eb0-b729-b6134ed30cd4/GCF_030409305.1_ASM3040930v1_genomic.fna.gz | prodigal -d GCF_030409305.1_ASM3040930v1_genomic.fna/cds.fna -a GCF_030409305.1_ASM3040930v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:41:18,088] [INFO] Task succeeded: Prodigal
[2024-01-25 18:41:18,088] [INFO] Task started: HMMsearch
[2024-01-25 18:41:18,088] [INFO] Running command: hmmsearch --tblout GCF_030409305.1_ASM3040930v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga283d3d3-5a65-47a0-beb5-3f62bb1bb96d/dqc_reference/reference_markers.hmm GCF_030409305.1_ASM3040930v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:41:18,336] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:41:18,337] [INFO] Found 6/6 markers.
[2024-01-25 18:41:18,384] [INFO] Query marker FASTA was written to GCF_030409305.1_ASM3040930v1_genomic.fna/markers.fasta
[2024-01-25 18:41:18,384] [INFO] Task started: Blastn
[2024-01-25 18:41:18,384] [INFO] Running command: blastn -query GCF_030409305.1_ASM3040930v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga283d3d3-5a65-47a0-beb5-3f62bb1bb96d/dqc_reference/reference_markers.fasta -out GCF_030409305.1_ASM3040930v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:19,407] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:19,411] [INFO] Selected 15 target genomes.
[2024-01-25 18:41:19,411] [INFO] Target genome list was writen to GCF_030409305.1_ASM3040930v1_genomic.fna/target_genomes.txt
[2024-01-25 18:41:19,416] [INFO] Task started: fastANI
[2024-01-25 18:41:19,416] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cfe97e7-7ee8-4eb0-b729-b6134ed30cd4/GCF_030409305.1_ASM3040930v1_genomic.fna.gz --refList GCF_030409305.1_ASM3040930v1_genomic.fna/target_genomes.txt --output GCF_030409305.1_ASM3040930v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:41:34,427] [INFO] Task succeeded: fastANI
[2024-01-25 18:41:34,427] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga283d3d3-5a65-47a0-beb5-3f62bb1bb96d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:41:34,428] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga283d3d3-5a65-47a0-beb5-3f62bb1bb96d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:41:34,437] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:41:34,437] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:41:34,437] [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 stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	93.6555	1166	1442	95	below_threshold
Halomonas nitroreducens	strain=11S	GCA_003966155.1	447425	447425	type	True	91.5013	1109	1442	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	86.504	844	1442	95	below_threshold
Halomonas halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	86.4679	885	1442	95	below_threshold
Halomonas organivorans	strain=CECT 5995	GCA_014192055.1	257772	257772	type	True	86.0293	1013	1442	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	85.9057	907	1442	95	below_threshold
Halomonas borealis	strain=ATF 5.2	GCA_004798905.1	2508710	2508710	type	True	85.0762	788	1442	95	below_threshold
Halomonas aestuarii	strain=Hb3	GCA_001886615.1	1897729	1897729	type	True	85.0356	849	1442	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	84.4031	967	1442	95	below_threshold
Halomonas heilongjiangensis	strain=DSM 26881	GCA_002879645.1	1387883	1387883	type	True	84.2717	953	1442	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	83.48	815	1442	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	83.0806	802	1442	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	82.9459	830	1442	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	82.2385	769	1442	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	81.9899	769	1442	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:41:34,439] [INFO] DFAST Taxonomy check result was written to GCF_030409305.1_ASM3040930v1_genomic.fna/tc_result.tsv
[2024-01-25 18:41:34,439] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:41:34,439] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:41:34,440] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga283d3d3-5a65-47a0-beb5-3f62bb1bb96d/dqc_reference/checkm_data
[2024-01-25 18:41:34,440] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:41:34,492] [INFO] Task started: CheckM
[2024-01-25 18:41:34,492] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030409305.1_ASM3040930v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030409305.1_ASM3040930v1_genomic.fna/checkm_input GCF_030409305.1_ASM3040930v1_genomic.fna/checkm_result
[2024-01-25 18:42:12,409] [INFO] Task succeeded: CheckM
[2024-01-25 18:42:12,410] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:42:12,427] [INFO] ===== Completeness check finished =====
[2024-01-25 18:42:12,428] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:42:12,428] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030409305.1_ASM3040930v1_genomic.fna/markers.fasta)
[2024-01-25 18:42:12,429] [INFO] Task started: Blastn
[2024-01-25 18:42:12,429] [INFO] Running command: blastn -query GCF_030409305.1_ASM3040930v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga283d3d3-5a65-47a0-beb5-3f62bb1bb96d/dqc_reference/reference_markers_gtdb.fasta -out GCF_030409305.1_ASM3040930v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:14,361] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:14,365] [INFO] Selected 9 target genomes.
[2024-01-25 18:42:14,365] [INFO] Target genome list was writen to GCF_030409305.1_ASM3040930v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:42:14,369] [INFO] Task started: fastANI
[2024-01-25 18:42:14,370] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cfe97e7-7ee8-4eb0-b729-b6134ed30cd4/GCF_030409305.1_ASM3040930v1_genomic.fna.gz --refList GCF_030409305.1_ASM3040930v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030409305.1_ASM3040930v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:42:24,003] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:24,010] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:42:24,010] [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_014192275.1	s__Halomonas stenophila	93.6555	1166	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966155.1	s__Halomonas nitroreducens	91.5361	1106	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002549795.1	s__Halomonas beimenensis	87.1409	988	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265245.1	s__Halomonas smyrnensis	86.504	844	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.45	98.45	0.89	0.89	2	-
GCF_007989465.1	s__Halomonas halophila	86.4903	883	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.43	97.59	0.92	0.89	4	-
GCF_014192055.1	s__Halomonas organivorans	86.0755	1009	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056305.1	s__Halomonas denitrificans	85.933	905	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363755.1	s__Halomonas sp009363755	85.7281	846	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002879645.1	s__Halomonas heilongjiangensis	84.2591	955	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:42:24,011] [INFO] GTDB search result was written to GCF_030409305.1_ASM3040930v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:42:24,012] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:42:24,015] [INFO] DFAST_QC result json was written to GCF_030409305.1_ASM3040930v1_genomic.fna/dqc_result.json
[2024-01-25 18:42:24,015] [INFO] DFAST_QC completed!
[2024-01-25 18:42:24,015] [INFO] Total running time: 0h1m18s