[2024-01-24 11:12:39,652] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:39,654] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:39,654] [INFO] DQC Reference Directory: /var/lib/cwl/stgb176f07f-a92f-4fd7-802f-c9b211b87d51/dqc_reference
[2024-01-24 11:12:40,986] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:40,987] [INFO] Task started: Prodigal
[2024-01-24 11:12:40,988] [INFO] Running command: gunzip -c /var/lib/cwl/stgc31cfb89-ef01-485a-92b0-0c6e6d66b3c1/GCF_017571465.1_ASM1757146v1_genomic.fna.gz | prodigal -d GCF_017571465.1_ASM1757146v1_genomic.fna/cds.fna -a GCF_017571465.1_ASM1757146v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:47,603] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:47,604] [INFO] Task started: HMMsearch
[2024-01-24 11:12:47,604] [INFO] Running command: hmmsearch --tblout GCF_017571465.1_ASM1757146v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb176f07f-a92f-4fd7-802f-c9b211b87d51/dqc_reference/reference_markers.hmm GCF_017571465.1_ASM1757146v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:47,869] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:47,871] [INFO] Found 6/6 markers.
[2024-01-24 11:12:47,901] [INFO] Query marker FASTA was written to GCF_017571465.1_ASM1757146v1_genomic.fna/markers.fasta
[2024-01-24 11:12:47,901] [INFO] Task started: Blastn
[2024-01-24 11:12:47,902] [INFO] Running command: blastn -query GCF_017571465.1_ASM1757146v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb176f07f-a92f-4fd7-802f-c9b211b87d51/dqc_reference/reference_markers.fasta -out GCF_017571465.1_ASM1757146v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:48,588] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:48,628] [INFO] Selected 29 target genomes.
[2024-01-24 11:12:48,629] [INFO] Target genome list was writen to GCF_017571465.1_ASM1757146v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:48,744] [INFO] Task started: fastANI
[2024-01-24 11:12:48,744] [INFO] Running command: fastANI --query /var/lib/cwl/stgc31cfb89-ef01-485a-92b0-0c6e6d66b3c1/GCF_017571465.1_ASM1757146v1_genomic.fna.gz --refList GCF_017571465.1_ASM1757146v1_genomic.fna/target_genomes.txt --output GCF_017571465.1_ASM1757146v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:04,961] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:04,962] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb176f07f-a92f-4fd7-802f-c9b211b87d51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:04,962] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb176f07f-a92f-4fd7-802f-c9b211b87d51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:04,972] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:13:04,972] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:13:04,972] [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 indica	strain=13-15A	GCA_004293625.1	2267253	2267253	type	True	79.1766	159	911	95	below_threshold
Thiomicrorhabdus xiamenensis	strain=G2	GCA_013282625.1	2739063	2739063	type	True	79.1717	237	911	95	below_threshold
Thiosulfatimonas sediminis	strain=aks77	GCA_011398355.1	2675054	2675054	type	True	79.1376	364	911	95	below_threshold
Thiomicrorhabdus sediminis	strain=G1	GCA_005885815.1	2580412	2580412	type	True	78.6524	158	911	95	below_threshold
Thiomicrorhabdus immobilis	strain=Am19	GCA_021654855.1	2791037	2791037	type	True	78.5625	113	911	95	below_threshold
Thiomicrorhabdus heinhorstiae	strain=HH1	GCA_013391765.2	2748010	2748010	type	True	78.2898	168	911	95	below_threshold
Thiomicrorhabdus cannonii	strain=HH3	GCA_013391695.1	2748011	2748011	type	True	77.2638	104	911	95	below_threshold
Thiomicrorhabdus arctica	strain=DSM 13458	GCA_000381085.1	131540	131540	type	True	77.1102	82	911	95	below_threshold
Hydrogenovibrio marinus	strain=MH-110	GCA_013340845.1	28885	28885	type	True	77.0328	89	911	95	below_threshold
Hydrogenovibrio marinus	strain=DSM 11271	GCA_000711315.1	28885	28885	type	True	77.02	92	911	95	below_threshold
Hydrogenovibrio marinus	strain=MH-110	GCA_000696325.1	28885	28885	type	True	77.0059	88	911	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:04,975] [INFO] DFAST Taxonomy check result was written to GCF_017571465.1_ASM1757146v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:04,976] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:04,976] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:04,976] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb176f07f-a92f-4fd7-802f-c9b211b87d51/dqc_reference/checkm_data
[2024-01-24 11:13:04,978] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:05,009] [INFO] Task started: CheckM
[2024-01-24 11:13:05,010] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017571465.1_ASM1757146v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017571465.1_ASM1757146v1_genomic.fna/checkm_input GCF_017571465.1_ASM1757146v1_genomic.fna/checkm_result
[2024-01-24 11:13:31,244] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:31,245] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:31,269] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:31,269] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:31,270] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017571465.1_ASM1757146v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:31,270] [INFO] Task started: Blastn
[2024-01-24 11:13:31,270] [INFO] Running command: blastn -query GCF_017571465.1_ASM1757146v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb176f07f-a92f-4fd7-802f-c9b211b87d51/dqc_reference/reference_markers_gtdb.fasta -out GCF_017571465.1_ASM1757146v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:32,449] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:32,453] [INFO] Selected 16 target genomes.
[2024-01-24 11:13:32,453] [INFO] Target genome list was writen to GCF_017571465.1_ASM1757146v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:32,466] [INFO] Task started: fastANI
[2024-01-24 11:13:32,467] [INFO] Running command: fastANI --query /var/lib/cwl/stgc31cfb89-ef01-485a-92b0-0c6e6d66b3c1/GCF_017571465.1_ASM1757146v1_genomic.fna.gz --refList GCF_017571465.1_ASM1757146v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017571465.1_ASM1757146v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:39,998] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:40,009] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:40,009] [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_017571465.1	s__Thiomicrorhabdus sp017571465	100.0	909	911	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_017571475.1	s__Thiomicrorhabdus sp017571475	79.3384	230	911	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	79.1766	159	911	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013282625.1	s__Thiomicrorhabdus xiamenensis	79.1717	237	911	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011398355.1	s__Thiomicrorhabdus sp011398355	79.1247	365	911	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391765.2	s__Thiomicrorhabdus sp013391765	78.2898	168	911	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000478585.1	s__Thiomicrorhabdus sp000478585	78.207	116	911	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016936535.1	s__Thiomicrorhabdus sp016936535	77.9961	116	911	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	77.613	101	911	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	77.2369	105	911	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	77.084	79	911	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	99.61	99.61	0.87	0.87	2	-
GCA_006222135.1	s__Thiomicrorhabdus sp006222135	76.9375	73	911	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:40,011] [INFO] GTDB search result was written to GCF_017571465.1_ASM1757146v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:40,012] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:40,015] [INFO] DFAST_QC result json was written to GCF_017571465.1_ASM1757146v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:40,015] [INFO] DFAST_QC completed!
[2024-01-24 11:13:40,016] [INFO] Total running time: 0h1m0s