[2024-01-24 12:05:59,065] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:05:59,071] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:05:59,071] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4a04953-5a0f-4d6b-b212-e42412b13d0a/dqc_reference
[2024-01-24 12:06:00,610] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:00,610] [INFO] Task started: Prodigal
[2024-01-24 12:06:00,611] [INFO] Running command: gunzip -c /var/lib/cwl/stg1e71848c-6029-46f7-9780-4c2caf6d31ea/GCF_001662875.1_ASM166287v1_genomic.fna.gz | prodigal -d GCF_001662875.1_ASM166287v1_genomic.fna/cds.fna -a GCF_001662875.1_ASM166287v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:14,902] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:14,902] [INFO] Task started: HMMsearch
[2024-01-24 12:06:14,903] [INFO] Running command: hmmsearch --tblout GCF_001662875.1_ASM166287v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4a04953-5a0f-4d6b-b212-e42412b13d0a/dqc_reference/reference_markers.hmm GCF_001662875.1_ASM166287v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:15,232] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:15,233] [INFO] Found 6/6 markers.
[2024-01-24 12:06:15,272] [INFO] Query marker FASTA was written to GCF_001662875.1_ASM166287v1_genomic.fna/markers.fasta
[2024-01-24 12:06:15,273] [INFO] Task started: Blastn
[2024-01-24 12:06:15,273] [INFO] Running command: blastn -query GCF_001662875.1_ASM166287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4a04953-5a0f-4d6b-b212-e42412b13d0a/dqc_reference/reference_markers.fasta -out GCF_001662875.1_ASM166287v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:16,104] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:16,107] [INFO] Selected 12 target genomes.
[2024-01-24 12:06:16,108] [INFO] Target genome list was writen to GCF_001662875.1_ASM166287v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:16,113] [INFO] Task started: fastANI
[2024-01-24 12:06:16,113] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e71848c-6029-46f7-9780-4c2caf6d31ea/GCF_001662875.1_ASM166287v1_genomic.fna.gz --refList GCF_001662875.1_ASM166287v1_genomic.fna/target_genomes.txt --output GCF_001662875.1_ASM166287v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:26,545] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:26,545] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4a04953-5a0f-4d6b-b212-e42412b13d0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:26,546] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4a04953-5a0f-4d6b-b212-e42412b13d0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:26,553] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:06:26,553] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:06:26,553] [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 tepidiphila	strain=MCCC 1A03514	GCA_001662875.1	393657	393657	type	True	100.0	1455	1457	95	inconclusive
Thalassospira tepidiphila	strain=DSM 18888	GCA_011927685.1	393657	393657	type	True	99.999	1455	1457	95	inconclusive
Thalassospira profundimaris	strain=WP0211	GCA_000300275.1	502049	502049	suspected-type	True	95.4912	1306	1457	95	inconclusive
Thalassospira indica	strain=PB8BT	GCA_003403095.1	1891279	1891279	type	True	94.6367	1323	1457	95	below_threshold
Thalassospira australica	strain=NP 3b2	GCA_000763295.1	1528106	1528106	type	True	84.743	1064	1457	95	below_threshold
Thalassospira povalilytica	strain=Zumi 95	GCA_002844235.1	732237	732237	type	True	83.9268	1109	1457	95	below_threshold
Thalassospira lohafexi	strain=139Z-12	GCA_002844275.1	744227	744227	type	True	82.072	1022	1457	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:26,555] [INFO] DFAST Taxonomy check result was written to GCF_001662875.1_ASM166287v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:26,555] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:26,555] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:26,556] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4a04953-5a0f-4d6b-b212-e42412b13d0a/dqc_reference/checkm_data
[2024-01-24 12:06:26,557] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:26,598] [INFO] Task started: CheckM
[2024-01-24 12:06:26,599] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001662875.1_ASM166287v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001662875.1_ASM166287v1_genomic.fna/checkm_input GCF_001662875.1_ASM166287v1_genomic.fna/checkm_result
[2024-01-24 12:07:12,156] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:12,157] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:12,177] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:12,177] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:12,178] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001662875.1_ASM166287v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:12,178] [INFO] Task started: Blastn
[2024-01-24 12:07:12,179] [INFO] Running command: blastn -query GCF_001662875.1_ASM166287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4a04953-5a0f-4d6b-b212-e42412b13d0a/dqc_reference/reference_markers_gtdb.fasta -out GCF_001662875.1_ASM166287v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:13,551] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:13,554] [INFO] Selected 8 target genomes.
[2024-01-24 12:07:13,554] [INFO] Target genome list was writen to GCF_001662875.1_ASM166287v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:13,560] [INFO] Task started: fastANI
[2024-01-24 12:07:13,560] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e71848c-6029-46f7-9780-4c2caf6d31ea/GCF_001662875.1_ASM166287v1_genomic.fna.gz --refList GCF_001662875.1_ASM166287v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001662875.1_ASM166287v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:22,387] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:22,396] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:22,396] [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_001662875.1	s__Thalassospira tepidiphila	100.0	1455	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.4963	96.58	95.57	0.94	0.88	15	conclusive
GCF_000300275.1	s__Thalassospira profundimaris	95.4912	1306	1457	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	95.2107	1343	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.2246	N/A	N/A	N/A	N/A	1	-
GCF_003403095.1	s__Thalassospira indica	94.6367	1323	1457	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	88.4344	1189	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	97.77	97.25	0.94	0.91	10	-
GCA_002709775.1	s__Thalassospira sp002709775	88.038	1102	1457	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	88.0072	1214	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011806525.1	s__Thalassospira sp011806525	87.6711	1214	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:22,398] [INFO] GTDB search result was written to GCF_001662875.1_ASM166287v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:22,398] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:22,401] [INFO] DFAST_QC result json was written to GCF_001662875.1_ASM166287v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:22,401] [INFO] DFAST_QC completed!
[2024-01-24 12:07:22,401] [INFO] Total running time: 0h1m23s