[2024-01-24 13:57:56,501] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:56,503] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:56,503] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ac8e325-9313-4bbe-b6b8-7dfadfd62ae3/dqc_reference
[2024-01-24 13:57:57,894] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:57,895] [INFO] Task started: Prodigal
[2024-01-24 13:57:57,895] [INFO] Running command: gunzip -c /var/lib/cwl/stg91b2b3a5-7450-470c-9c55-2db80c64513b/GCF_002844235.1_ASM284423v1_genomic.fna.gz | prodigal -d GCF_002844235.1_ASM284423v1_genomic.fna/cds.fna -a GCF_002844235.1_ASM284423v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:12,743] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:12,743] [INFO] Task started: HMMsearch
[2024-01-24 13:58:12,743] [INFO] Running command: hmmsearch --tblout GCF_002844235.1_ASM284423v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ac8e325-9313-4bbe-b6b8-7dfadfd62ae3/dqc_reference/reference_markers.hmm GCF_002844235.1_ASM284423v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:13,020] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:13,022] [INFO] Found 6/6 markers.
[2024-01-24 13:58:13,062] [INFO] Query marker FASTA was written to GCF_002844235.1_ASM284423v1_genomic.fna/markers.fasta
[2024-01-24 13:58:13,062] [INFO] Task started: Blastn
[2024-01-24 13:58:13,062] [INFO] Running command: blastn -query GCF_002844235.1_ASM284423v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ac8e325-9313-4bbe-b6b8-7dfadfd62ae3/dqc_reference/reference_markers.fasta -out GCF_002844235.1_ASM284423v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:13,847] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:13,861] [INFO] Selected 16 target genomes.
[2024-01-24 13:58:13,862] [INFO] Target genome list was writen to GCF_002844235.1_ASM284423v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:13,869] [INFO] Task started: fastANI
[2024-01-24 13:58:13,869] [INFO] Running command: fastANI --query /var/lib/cwl/stg91b2b3a5-7450-470c-9c55-2db80c64513b/GCF_002844235.1_ASM284423v1_genomic.fna.gz --refList GCF_002844235.1_ASM284423v1_genomic.fna/target_genomes.txt --output GCF_002844235.1_ASM284423v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:27,163] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:27,163] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ac8e325-9313-4bbe-b6b8-7dfadfd62ae3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:27,164] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ac8e325-9313-4bbe-b6b8-7dfadfd62ae3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:27,174] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:27,174] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:27,175] [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
Thalassospira povalilytica	strain=Zumi 95	GCA_002844235.1	732237	732237	type	True	100.0	1471	1471	95	conclusive
Thalassospira tepidiphila	strain=DSM 18888	GCA_011927685.1	393657	393657	type	True	84.0301	1089	1471	95	below_threshold
Thalassospira profundimaris	strain=WP0211	GCA_000300275.1	502049	502049	suspected-type	True	83.9745	1067	1471	95	below_threshold
Thalassospira tepidiphila	strain=MCCC 1A03514	GCA_001662875.1	393657	393657	type	True	83.9485	1100	1471	95	below_threshold
Thalassospira indica	strain=PB8BT	GCA_003403095.1	1891279	1891279	type	True	83.8526	1090	1471	95	below_threshold
Thalassospira australica	strain=NP 3b2	GCA_000763295.1	1528106	1528106	type	True	83.2093	1017	1471	95	below_threshold
Thalassospira lucentensis	strain=MCCC 1A00383	GCA_003326595.1	168935	168935	type	True	82.3033	1002	1471	95	below_threshold
Thalassospira lucentensis	strain=DSM 14000	GCA_000421265.1	168935	168935	type	True	82.2464	1021	1471	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:27,176] [INFO] DFAST Taxonomy check result was written to GCF_002844235.1_ASM284423v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:27,177] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:27,177] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:27,177] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ac8e325-9313-4bbe-b6b8-7dfadfd62ae3/dqc_reference/checkm_data
[2024-01-24 13:58:27,179] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:27,219] [INFO] Task started: CheckM
[2024-01-24 13:58:27,219] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002844235.1_ASM284423v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002844235.1_ASM284423v1_genomic.fna/checkm_input GCF_002844235.1_ASM284423v1_genomic.fna/checkm_result
[2024-01-24 13:59:13,377] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:13,379] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:13,399] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:13,399] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:13,400] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002844235.1_ASM284423v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:13,400] [INFO] Task started: Blastn
[2024-01-24 13:59:13,400] [INFO] Running command: blastn -query GCF_002844235.1_ASM284423v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ac8e325-9313-4bbe-b6b8-7dfadfd62ae3/dqc_reference/reference_markers_gtdb.fasta -out GCF_002844235.1_ASM284423v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:14,783] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:14,791] [INFO] Selected 10 target genomes.
[2024-01-24 13:59:14,791] [INFO] Target genome list was writen to GCF_002844235.1_ASM284423v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:14,809] [INFO] Task started: fastANI
[2024-01-24 13:59:14,809] [INFO] Running command: fastANI --query /var/lib/cwl/stg91b2b3a5-7450-470c-9c55-2db80c64513b/GCF_002844235.1_ASM284423v1_genomic.fna.gz --refList GCF_002844235.1_ASM284423v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002844235.1_ASM284423v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:26,446] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:26,463] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:26,463] [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_002844235.1	s__Thalassospira povalilytica	100.0	1471	1471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	97.81	97.62	0.94	0.91	8	conclusive
GCF_003326675.1	s__Thalassospira profundimaris_D	87.3357	1226	1471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003326795.1	s__Thalassospira profundimaris_C	86.4574	1181	1471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000948415.1	s__Thalassospira sp000948415	84.1407	1080	1471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001662875.1	s__Thalassospira tepidiphila	83.9571	1099	1471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.4963	96.58	95.57	0.94	0.88	15	-
GCF_000300275.1	s__Thalassospira profundimaris	83.9569	1069	1471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.4963	N/A	N/A	N/A	N/A	1	-
GCF_017922435.1	s__Thalassospira sp017922435	83.9102	1103	1471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.2246	N/A	N/A	N/A	N/A	1	-
GCA_002709775.1	s__Thalassospira sp002709775	83.8738	994	1471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003403095.1	s__Thalassospira indica	83.8491	1090	1471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001613795.1	s__Thalassospira sp001613795	83.6323	1009	1471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	97.77	97.25	0.94	0.91	10	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:26,465] [INFO] GTDB search result was written to GCF_002844235.1_ASM284423v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:26,465] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:26,469] [INFO] DFAST_QC result json was written to GCF_002844235.1_ASM284423v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:26,470] [INFO] DFAST_QC completed!
[2024-01-24 13:59:26,470] [INFO] Total running time: 0h1m30s