[2024-01-24 11:35:10,896] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:10,898] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:10,899] [INFO] DQC Reference Directory: /var/lib/cwl/stgd168a65d-ed6f-46af-928e-200aed960e99/dqc_reference
[2024-01-24 11:35:12,253] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:12,254] [INFO] Task started: Prodigal
[2024-01-24 11:35:12,254] [INFO] Running command: gunzip -c /var/lib/cwl/stg78685872-22f2-49b4-98f4-883bb79cfefc/GCF_013391765.2_ASM1339176v2_genomic.fna.gz | prodigal -d GCF_013391765.2_ASM1339176v2_genomic.fna/cds.fna -a GCF_013391765.2_ASM1339176v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:18,913] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:18,914] [INFO] Task started: HMMsearch
[2024-01-24 11:35:18,914] [INFO] Running command: hmmsearch --tblout GCF_013391765.2_ASM1339176v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd168a65d-ed6f-46af-928e-200aed960e99/dqc_reference/reference_markers.hmm GCF_013391765.2_ASM1339176v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:19,152] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:19,153] [INFO] Found 6/6 markers.
[2024-01-24 11:35:19,179] [INFO] Query marker FASTA was written to GCF_013391765.2_ASM1339176v2_genomic.fna/markers.fasta
[2024-01-24 11:35:19,180] [INFO] Task started: Blastn
[2024-01-24 11:35:19,180] [INFO] Running command: blastn -query GCF_013391765.2_ASM1339176v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgd168a65d-ed6f-46af-928e-200aed960e99/dqc_reference/reference_markers.fasta -out GCF_013391765.2_ASM1339176v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:19,895] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:19,905] [INFO] Selected 23 target genomes.
[2024-01-24 11:35:19,906] [INFO] Target genome list was writen to GCF_013391765.2_ASM1339176v2_genomic.fna/target_genomes.txt
[2024-01-24 11:35:19,965] [INFO] Task started: fastANI
[2024-01-24 11:35:19,965] [INFO] Running command: fastANI --query /var/lib/cwl/stg78685872-22f2-49b4-98f4-883bb79cfefc/GCF_013391765.2_ASM1339176v2_genomic.fna.gz --refList GCF_013391765.2_ASM1339176v2_genomic.fna/target_genomes.txt --output GCF_013391765.2_ASM1339176v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:32,884] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:32,885] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd168a65d-ed6f-46af-928e-200aed960e99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:32,885] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd168a65d-ed6f-46af-928e-200aed960e99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:32,902] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:32,902] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:32,902] [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
Thiomicrorhabdus heinhorstiae	strain=HH1	GCA_013391765.2	2748010	2748010	type	True	100.0	832	836	95	conclusive
Thiomicrorhabdus xiamenensis	strain=G2	GCA_013282625.1	2739063	2739063	type	True	79.2314	229	836	95	below_threshold
Thiomicrorhabdus sediminis	strain=G1	GCA_005885815.1	2580412	2580412	type	True	78.4938	160	836	95	below_threshold
Thiomicrorhabdus indica	strain=13-15A	GCA_004293625.1	2267253	2267253	type	True	78.3626	104	836	95	below_threshold
Thiomicrorhabdus immobilis	strain=Am19	GCA_021654855.1	2791037	2791037	type	True	78.1715	116	836	95	below_threshold
Hydrogenovibrio kuenenii	strain=DSM 12350	GCA_000526715.1	63658	63658	type	True	77.8986	73	836	95	below_threshold
Thiomicrorhabdus cannonii	strain=HH3	GCA_013391695.1	2748011	2748011	type	True	77.7978	167	836	95	below_threshold
Thiomicrorhabdus aquaedulcis	strain=HaS4	GCA_004001325.1	2211106	2211106	type	True	77.5973	69	836	95	below_threshold
Thiomicrorhabdus chilensis	strain=DSM 12352	GCA_000483485.1	63656	63656	type	True	77.5561	147	836	95	below_threshold
Thiomicrorhabdus arctica	strain=DSM 13458	GCA_000381085.1	131540	131540	type	True	77.1154	73	836	95	below_threshold
Thiosulfativibrio zosterae	strain=AkT22	GCA_011398155.1	2675053	2675053	type	True	76.9222	69	836	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:32,904] [INFO] DFAST Taxonomy check result was written to GCF_013391765.2_ASM1339176v2_genomic.fna/tc_result.tsv
[2024-01-24 11:35:32,905] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:32,905] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:32,906] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd168a65d-ed6f-46af-928e-200aed960e99/dqc_reference/checkm_data
[2024-01-24 11:35:32,907] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:32,934] [INFO] Task started: CheckM
[2024-01-24 11:35:32,935] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013391765.2_ASM1339176v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013391765.2_ASM1339176v2_genomic.fna/checkm_input GCF_013391765.2_ASM1339176v2_genomic.fna/checkm_result
[2024-01-24 11:35:58,809] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:58,810] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:58,830] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:58,830] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:58,830] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013391765.2_ASM1339176v2_genomic.fna/markers.fasta)
[2024-01-24 11:35:58,831] [INFO] Task started: Blastn
[2024-01-24 11:35:58,831] [INFO] Running command: blastn -query GCF_013391765.2_ASM1339176v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgd168a65d-ed6f-46af-928e-200aed960e99/dqc_reference/reference_markers_gtdb.fasta -out GCF_013391765.2_ASM1339176v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:59,984] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:59,988] [INFO] Selected 22 target genomes.
[2024-01-24 11:35:59,989] [INFO] Target genome list was writen to GCF_013391765.2_ASM1339176v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:00,010] [INFO] Task started: fastANI
[2024-01-24 11:36:00,011] [INFO] Running command: fastANI --query /var/lib/cwl/stg78685872-22f2-49b4-98f4-883bb79cfefc/GCF_013391765.2_ASM1339176v2_genomic.fna.gz --refList GCF_013391765.2_ASM1339176v2_genomic.fna/target_genomes_gtdb.txt --output GCF_013391765.2_ASM1339176v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:11,192] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:11,207] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:11,207] [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_013391765.2	s__Thiomicrorhabdus sp013391765	100.0	832	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013282625.1	s__Thiomicrorhabdus xiamenensis	79.2314	229	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017571475.1	s__Thiomicrorhabdus sp017571475	79.0833	238	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005885815.1	s__Thiomicrorhabdus sediminis	78.4696	161	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000702325.1	s__Thiomicrorhabdus sp000702325	78.4522	80	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017571465.1	s__Thiomicrorhabdus sp017571465	78.4389	160	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004293625.1	s__Thiomicrorhabdus indica	78.3626	104	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391695.1	s__Thiomicrorhabdus sp013391695	77.817	166	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763835.1	s__Thiomicrorhabdus sp014763835	77.7365	109	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	99.61	99.61	0.87	0.87	2	-
GCF_004001325.1	s__Thiomicrorhabdus aquaedulcis	77.5973	69	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000483485.1	s__Thiomicrorhabdus chilensis	77.556	147	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004028275.1	s__Hydrogenovibrio thermophilus	77.1795	122	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Hydrogenovibrio	95.0	96.88	96.83	0.89	0.89	3	-
GCA_016938655.1	s__Thiomicrorhabdus sp016938655	77.1554	78	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381085.1	s__Thiomicrorhabdus arctica	77.1485	72	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002299245.1	s__Thiomicrorhabdus sp002299245	77.1376	62	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	99.68	99.68	0.83	0.83	2	-
GCF_001507555.1	s__Hydrogenovibrio sp001507555	77.0381	127	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Hydrogenovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744875.1	s__Hydrogenovibrio sp000744875	76.9724	79	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Hydrogenovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011398155.1	s__Thiosulfativibrio zosterae	76.9222	69	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiosulfativibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:11,210] [INFO] GTDB search result was written to GCF_013391765.2_ASM1339176v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:11,211] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:11,215] [INFO] DFAST_QC result json was written to GCF_013391765.2_ASM1339176v2_genomic.fna/dqc_result.json
[2024-01-24 11:36:11,215] [INFO] DFAST_QC completed!
[2024-01-24 11:36:11,216] [INFO] Total running time: 0h1m0s