[2024-01-24 13:35:27,553] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:35:27,554] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:35:27,554] [INFO] DQC Reference Directory: /var/lib/cwl/stg01fc2fd6-8501-4557-9b89-1912d18823e3/dqc_reference
[2024-01-24 13:35:28,782] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:35:28,783] [INFO] Task started: Prodigal
[2024-01-24 13:35:28,783] [INFO] Running command: gunzip -c /var/lib/cwl/stgc7aa9f56-1c21-4ab9-bfea-07379777ed6a/GCF_030268065.1_ASM3026806v1_genomic.fna.gz | prodigal -d GCF_030268065.1_ASM3026806v1_genomic.fna/cds.fna -a GCF_030268065.1_ASM3026806v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:35:38,518] [INFO] Task succeeded: Prodigal
[2024-01-24 13:35:38,518] [INFO] Task started: HMMsearch
[2024-01-24 13:35:38,519] [INFO] Running command: hmmsearch --tblout GCF_030268065.1_ASM3026806v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01fc2fd6-8501-4557-9b89-1912d18823e3/dqc_reference/reference_markers.hmm GCF_030268065.1_ASM3026806v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:35:38,783] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:35:38,785] [INFO] Found 6/6 markers.
[2024-01-24 13:35:38,819] [INFO] Query marker FASTA was written to GCF_030268065.1_ASM3026806v1_genomic.fna/markers.fasta
[2024-01-24 13:35:38,820] [INFO] Task started: Blastn
[2024-01-24 13:35:38,820] [INFO] Running command: blastn -query GCF_030268065.1_ASM3026806v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01fc2fd6-8501-4557-9b89-1912d18823e3/dqc_reference/reference_markers.fasta -out GCF_030268065.1_ASM3026806v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:35:39,527] [INFO] Task succeeded: Blastn
[2024-01-24 13:35:39,531] [INFO] Selected 15 target genomes.
[2024-01-24 13:35:39,531] [INFO] Target genome list was writen to GCF_030268065.1_ASM3026806v1_genomic.fna/target_genomes.txt
[2024-01-24 13:35:39,576] [INFO] Task started: fastANI
[2024-01-24 13:35:39,576] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7aa9f56-1c21-4ab9-bfea-07379777ed6a/GCF_030268065.1_ASM3026806v1_genomic.fna.gz --refList GCF_030268065.1_ASM3026806v1_genomic.fna/target_genomes.txt --output GCF_030268065.1_ASM3026806v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:35:49,929] [INFO] Task succeeded: fastANI
[2024-01-24 13:35:49,930] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01fc2fd6-8501-4557-9b89-1912d18823e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:35:49,930] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01fc2fd6-8501-4557-9b89-1912d18823e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:35:49,940] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:35:49,940] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:35:49,941] [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
Geothrix fermentans	strain=DSM 14018	GCA_000428885.1	44676	44676	type	True	84.2597	785	1127	95	below_threshold
Holophaga foetida	strain=DSM 6591	GCA_000242615.3	35839	35839	type	True	78.3427	312	1127	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	75.8399	75	1127	95	below_threshold
Chromobacterium sphagni	strain=IIBBL 14B-1	GCA_001855555.1	1903179	1903179	type	True	75.4629	54	1127	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	75.3182	110	1127	95	below_threshold
Halorhodospira neutriphila	strain=DSM 15116	GCA_016584055.1	168379	168379	type	True	75.2353	68	1127	95	below_threshold
Dissulfurirhabdus thermomarina	strain=DSM 100025	GCA_010499435.1	1765737	1765737	type	True	75.1959	85	1127	95	below_threshold
Dissulfurirhabdus thermomarina	strain=SH388	GCA_012979235.1	1765737	1765737	type	True	75.1216	95	1127	95	below_threshold
Plesiocystis pacifica	strain=SIR-1	GCA_000170895.1	191768	191768	type	True	75.0645	170	1127	95	below_threshold
Chondromyces crocatus	strain=Cm c5	GCA_001189295.1	52	52	type	True	74.9185	91	1127	95	below_threshold
Deinococcus metalli	strain=DSM 27521	GCA_014201805.1	1141878	1141878	type	True	74.8791	79	1127	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:35:49,942] [INFO] DFAST Taxonomy check result was written to GCF_030268065.1_ASM3026806v1_genomic.fna/tc_result.tsv
[2024-01-24 13:35:49,943] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:35:49,943] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:35:49,943] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01fc2fd6-8501-4557-9b89-1912d18823e3/dqc_reference/checkm_data
[2024-01-24 13:35:49,944] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:35:49,985] [INFO] Task started: CheckM
[2024-01-24 13:35:49,985] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030268065.1_ASM3026806v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030268065.1_ASM3026806v1_genomic.fna/checkm_input GCF_030268065.1_ASM3026806v1_genomic.fna/checkm_result
[2024-01-24 13:36:26,441] [INFO] Task succeeded: CheckM
[2024-01-24 13:36:26,443] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:36:26,463] [INFO] ===== Completeness check finished =====
[2024-01-24 13:36:26,463] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:36:26,464] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030268065.1_ASM3026806v1_genomic.fna/markers.fasta)
[2024-01-24 13:36:26,464] [INFO] Task started: Blastn
[2024-01-24 13:36:26,464] [INFO] Running command: blastn -query GCF_030268065.1_ASM3026806v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01fc2fd6-8501-4557-9b89-1912d18823e3/dqc_reference/reference_markers_gtdb.fasta -out GCF_030268065.1_ASM3026806v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:27,538] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:27,543] [INFO] Selected 16 target genomes.
[2024-01-24 13:36:27,543] [INFO] Target genome list was writen to GCF_030268065.1_ASM3026806v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:36:27,660] [INFO] Task started: fastANI
[2024-01-24 13:36:27,660] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7aa9f56-1c21-4ab9-bfea-07379777ed6a/GCF_030268065.1_ASM3026806v1_genomic.fna.gz --refList GCF_030268065.1_ASM3026806v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030268065.1_ASM3026806v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:36:39,348] [INFO] Task succeeded: fastANI
[2024-01-24 13:36:39,361] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:36:39,361] [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_000428885.1	s__Geothrix fermentans	84.2791	783	1127	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003538615.1	s__Geothrix sp003538615	83.539	571	1127	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013390615.1	s__Geothrix sp013390615	83.1627	770	1127	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714685.1	s__Geothrix sp016714685	82.935	728	1127	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	98.39	97.91	0.89	0.88	4	-
GCA_903857495.1	s__Geothrix sp903857495	82.6966	699	1127	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.99	99.97	0.99	0.98	50	-
GCA_013334395.1	s__Geothrix sp013334395	82.6329	572	1127	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016721195.1	s__Geothrix sp016721195	82.6161	736	1127	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903863195.1	s__Geothrix sp903863195	82.5598	653	1127	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.63	99.47	0.91	0.90	5	-
GCA_903937385.1	s__Geothrix sp903937385	82.3176	669	1127	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.84	98.90	0.96	0.91	10	-
GCA_016195985.1	s__Geothrix sp016195985	81.9929	694	1127	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.98	99.98	0.99	0.99	2	-
GCA_903890595.1	s__Geothrix sp903890595	81.9774	475	1127	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.18	98.75	0.85	0.81	6	-
GCA_903840385.1	s__Geothrix sp903840385	81.8815	598	1127	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.80	99.80	0.94	0.94	2	-
GCA_903843705.1	s__Geothrix sp903843705	81.712	580	1127	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.09	98.86	0.88	0.85	6	-
GCA_903884655.1	s__Geothrix sp903884655	81.606	615	1127	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.96	99.93	0.97	0.97	3	-
GCA_903876615.1	s__Geothrix sp903876615	81.2464	381	1127	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903873655.1	s__Geothrix sp903873655	80.6219	536	1127	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.34	99.01	0.91	0.87	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:36:39,363] [INFO] GTDB search result was written to GCF_030268065.1_ASM3026806v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:36:39,364] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:36:39,367] [INFO] DFAST_QC result json was written to GCF_030268065.1_ASM3026806v1_genomic.fna/dqc_result.json
[2024-01-24 13:36:39,367] [INFO] DFAST_QC completed!
[2024-01-24 13:36:39,367] [INFO] Total running time: 0h1m12s