[2024-01-24 15:02:18,698] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:18,702] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:18,702] [INFO] DQC Reference Directory: /var/lib/cwl/stg163a4877-2df7-4b05-b8d8-b468d8fd85cb/dqc_reference
[2024-01-24 15:02:20,836] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:20,836] [INFO] Task started: Prodigal
[2024-01-24 15:02:20,837] [INFO] Running command: gunzip -c /var/lib/cwl/stge6da58bf-a50e-4189-bbbf-f25c0ba62332/GCF_005885815.1_ASM588581v1_genomic.fna.gz | prodigal -d GCF_005885815.1_ASM588581v1_genomic.fna/cds.fna -a GCF_005885815.1_ASM588581v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:27,600] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:27,600] [INFO] Task started: HMMsearch
[2024-01-24 15:02:27,600] [INFO] Running command: hmmsearch --tblout GCF_005885815.1_ASM588581v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg163a4877-2df7-4b05-b8d8-b468d8fd85cb/dqc_reference/reference_markers.hmm GCF_005885815.1_ASM588581v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:27,863] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:27,865] [INFO] Found 6/6 markers.
[2024-01-24 15:02:27,896] [INFO] Query marker FASTA was written to GCF_005885815.1_ASM588581v1_genomic.fna/markers.fasta
[2024-01-24 15:02:27,897] [INFO] Task started: Blastn
[2024-01-24 15:02:27,897] [INFO] Running command: blastn -query GCF_005885815.1_ASM588581v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg163a4877-2df7-4b05-b8d8-b468d8fd85cb/dqc_reference/reference_markers.fasta -out GCF_005885815.1_ASM588581v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:28,640] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:28,644] [INFO] Selected 22 target genomes.
[2024-01-24 15:02:28,644] [INFO] Target genome list was writen to GCF_005885815.1_ASM588581v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:28,738] [INFO] Task started: fastANI
[2024-01-24 15:02:28,739] [INFO] Running command: fastANI --query /var/lib/cwl/stge6da58bf-a50e-4189-bbbf-f25c0ba62332/GCF_005885815.1_ASM588581v1_genomic.fna.gz --refList GCF_005885815.1_ASM588581v1_genomic.fna/target_genomes.txt --output GCF_005885815.1_ASM588581v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:41,943] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:41,944] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg163a4877-2df7-4b05-b8d8-b468d8fd85cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:41,944] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg163a4877-2df7-4b05-b8d8-b468d8fd85cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:41,951] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:02:41,952] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:41,952] [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 sediminis	strain=G1	GCA_005885815.1	2580412	2580412	type	True	100.0	791	791	95	conclusive
Thiomicrorhabdus immobilis	strain=Am19	GCA_021654855.1	2791037	2791037	type	True	78.7206	200	791	95	below_threshold
Thiomicrorhabdus chilensis	strain=DSM 12352	GCA_000483485.1	63656	63656	type	True	78.6795	123	791	95	below_threshold
Thiomicrorhabdus xiamenensis	strain=G2	GCA_013282625.1	2739063	2739063	type	True	78.6689	157	791	95	below_threshold
Thiomicrorhabdus heinhorstiae	strain=HH1	GCA_013391765.2	2748010	2748010	type	True	78.6014	157	791	95	below_threshold
Thiomicrorhabdus indica	strain=13-15A	GCA_004293625.1	2267253	2267253	type	True	78.5974	121	791	95	below_threshold
Thiomicrorhabdus cannonii	strain=HH3	GCA_013391695.1	2748011	2748011	type	True	77.9251	132	791	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:41,954] [INFO] DFAST Taxonomy check result was written to GCF_005885815.1_ASM588581v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:41,954] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:41,954] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:41,954] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg163a4877-2df7-4b05-b8d8-b468d8fd85cb/dqc_reference/checkm_data
[2024-01-24 15:02:41,956] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:41,987] [INFO] Task started: CheckM
[2024-01-24 15:02:41,987] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005885815.1_ASM588581v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005885815.1_ASM588581v1_genomic.fna/checkm_input GCF_005885815.1_ASM588581v1_genomic.fna/checkm_result
[2024-01-24 15:03:08,562] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:08,564] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:08,587] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:08,587] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:08,588] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005885815.1_ASM588581v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:08,588] [INFO] Task started: Blastn
[2024-01-24 15:03:08,588] [INFO] Running command: blastn -query GCF_005885815.1_ASM588581v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg163a4877-2df7-4b05-b8d8-b468d8fd85cb/dqc_reference/reference_markers_gtdb.fasta -out GCF_005885815.1_ASM588581v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:09,692] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:09,695] [INFO] Selected 21 target genomes.
[2024-01-24 15:03:09,695] [INFO] Target genome list was writen to GCF_005885815.1_ASM588581v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:09,714] [INFO] Task started: fastANI
[2024-01-24 15:03:09,714] [INFO] Running command: fastANI --query /var/lib/cwl/stge6da58bf-a50e-4189-bbbf-f25c0ba62332/GCF_005885815.1_ASM588581v1_genomic.fna.gz --refList GCF_005885815.1_ASM588581v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005885815.1_ASM588581v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:21,596] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:21,617] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:21,617] [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_005885815.1	s__Thiomicrorhabdus sediminis	100.0	790	791	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_000702325.1	s__Thiomicrorhabdus sp000702325	78.8392	132	791	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	78.8159	166	791	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	78.7155	158	791	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	78.6113	123	791	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	78.6014	157	791	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	78.4464	156	791	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	77.9251	132	791	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507555.1	s__Hydrogenovibrio sp001507555	77.7934	94	791	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Hydrogenovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004786015.1	s__Hydrogenovibrio crunogenus_B	77.6508	83	791	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Hydrogenovibrio	95.0	96.95	96.95	0.90	0.90	2	-
GCA_006222135.1	s__Thiomicrorhabdus sp006222135	77.5269	93	791	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	77.5248	109	791	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Hydrogenovibrio	95.0	96.88	96.83	0.89	0.89	3	-
GCA_014763835.1	s__Thiomicrorhabdus sp014763835	77.4883	87	791	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	99.61	99.61	0.87	0.87	2	-
GCA_002299245.1	s__Thiomicrorhabdus sp002299245	77.3287	85	791	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	99.68	99.68	0.83	0.83	2	-
GCA_014859555.1	s__Thiomicrospira sp014859555	76.6015	58	791	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrospira	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:21,619] [INFO] GTDB search result was written to GCF_005885815.1_ASM588581v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:21,619] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:21,622] [INFO] DFAST_QC result json was written to GCF_005885815.1_ASM588581v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:21,623] [INFO] DFAST_QC completed!
[2024-01-24 15:03:21,623] [INFO] Total running time: 0h1m3s