[2024-01-25 20:07:50,567] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:07:50,569] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:07:50,569] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a4151ab-53a0-46a1-acde-e71820af6ac2/dqc_reference
[2024-01-25 20:07:51,667] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:07:51,668] [INFO] Task started: Prodigal
[2024-01-25 20:07:51,668] [INFO] Running command: gunzip -c /var/lib/cwl/stg210a2e97-4221-4510-bde0-3ed5127a8f41/GCF_900182845.1_IMG-taxon_2706794916_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900182845.1_IMG-taxon_2706794916_annotated_assembly_genomic.fna/cds.fna -a GCF_900182845.1_IMG-taxon_2706794916_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:08:01,310] [INFO] Task succeeded: Prodigal
[2024-01-25 20:08:01,310] [INFO] Task started: HMMsearch
[2024-01-25 20:08:01,310] [INFO] Running command: hmmsearch --tblout GCF_900182845.1_IMG-taxon_2706794916_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a4151ab-53a0-46a1-acde-e71820af6ac2/dqc_reference/reference_markers.hmm GCF_900182845.1_IMG-taxon_2706794916_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:08:01,527] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:08:01,528] [INFO] Found 6/6 markers.
[2024-01-25 20:08:01,554] [INFO] Query marker FASTA was written to GCF_900182845.1_IMG-taxon_2706794916_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 20:08:01,555] [INFO] Task started: Blastn
[2024-01-25 20:08:01,555] [INFO] Running command: blastn -query GCF_900182845.1_IMG-taxon_2706794916_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a4151ab-53a0-46a1-acde-e71820af6ac2/dqc_reference/reference_markers.fasta -out GCF_900182845.1_IMG-taxon_2706794916_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:08:02,084] [INFO] Task succeeded: Blastn
[2024-01-25 20:08:02,087] [INFO] Selected 11 target genomes.
[2024-01-25 20:08:02,087] [INFO] Target genome list was writen to GCF_900182845.1_IMG-taxon_2706794916_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 20:08:02,110] [INFO] Task started: fastANI
[2024-01-25 20:08:02,110] [INFO] Running command: fastANI --query /var/lib/cwl/stg210a2e97-4221-4510-bde0-3ed5127a8f41/GCF_900182845.1_IMG-taxon_2706794916_annotated_assembly_genomic.fna.gz --refList GCF_900182845.1_IMG-taxon_2706794916_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900182845.1_IMG-taxon_2706794916_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:08:08,641] [INFO] Task succeeded: fastANI
[2024-01-25 20:08:08,641] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a4151ab-53a0-46a1-acde-e71820af6ac2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:08:08,642] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a4151ab-53a0-46a1-acde-e71820af6ac2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:08:08,646] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:08:08,646] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:08:08,646] [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
Sphaerochaeta associata	strain=GLS2T	GCA_022869165.1	1129264	1129264	type	True	99.9995	1151	1164	95	conclusive
Sphaerochaeta globosa	strain=Buddy	GCA_000190435.1	1131703	1131703	type	True	82.1945	721	1164	95	below_threshold
Sphaerochaeta pleomorpha	strain=Grapes	GCA_000236685.1	1131707	1131707	type	True	79.5593	128	1164	95	below_threshold
Sphaerochaeta halotolerans	strain=4-11	GCA_003429665.1	2293840	2293840	type	True	78.0684	218	1164	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:08:08,648] [INFO] DFAST Taxonomy check result was written to GCF_900182845.1_IMG-taxon_2706794916_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 20:08:08,648] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:08:08,648] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:08:08,648] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a4151ab-53a0-46a1-acde-e71820af6ac2/dqc_reference/checkm_data
[2024-01-25 20:08:08,649] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:08:08,684] [INFO] Task started: CheckM
[2024-01-25 20:08:08,684] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900182845.1_IMG-taxon_2706794916_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900182845.1_IMG-taxon_2706794916_annotated_assembly_genomic.fna/checkm_input GCF_900182845.1_IMG-taxon_2706794916_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 20:08:40,009] [INFO] Task succeeded: CheckM
[2024-01-25 20:08:40,010] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:08:40,026] [INFO] ===== Completeness check finished =====
[2024-01-25 20:08:40,026] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:08:40,027] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900182845.1_IMG-taxon_2706794916_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 20:08:40,027] [INFO] Task started: Blastn
[2024-01-25 20:08:40,027] [INFO] Running command: blastn -query GCF_900182845.1_IMG-taxon_2706794916_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a4151ab-53a0-46a1-acde-e71820af6ac2/dqc_reference/reference_markers_gtdb.fasta -out GCF_900182845.1_IMG-taxon_2706794916_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:08:40,788] [INFO] Task succeeded: Blastn
[2024-01-25 20:08:40,791] [INFO] Selected 13 target genomes.
[2024-01-25 20:08:40,791] [INFO] Target genome list was writen to GCF_900182845.1_IMG-taxon_2706794916_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:08:40,807] [INFO] Task started: fastANI
[2024-01-25 20:08:40,807] [INFO] Running command: fastANI --query /var/lib/cwl/stg210a2e97-4221-4510-bde0-3ed5127a8f41/GCF_900182845.1_IMG-taxon_2706794916_annotated_assembly_genomic.fna.gz --refList GCF_900182845.1_IMG-taxon_2706794916_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900182845.1_IMG-taxon_2706794916_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:08:48,351] [INFO] Task succeeded: fastANI
[2024-01-25 20:08:48,359] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:08:48,359] [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
GCA_012511235.1	s__Sphaerochaeta sp012511235	98.3539	533	1164	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	98.08	98.08	0.92	0.92	2	conclusive
GCA_012514185.1	s__Sphaerochaeta sp012514185	84.7131	607	1164	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002432715.1	s__Sphaerochaeta sp002432715	84.2107	746	1164	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	98.32	97.53	0.87	0.80	11	-
GCF_000190435.1	s__Sphaerochaeta globosa	82.2053	720	1164	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012519125.1	s__Sphaerochaeta sp012519125	79.4859	259	1164	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001603115.1	s__Sphaerochaeta sp001603115	79.4275	324	1164	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009930195.1	s__Sphaerochaeta sp009930195	79.4041	313	1164	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	99.24	99.24	0.76	0.76	2	-
GCF_016406725.1	s__Sphaerochaeta sp016406725	78.3516	224	1164	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003429665.1	s__Sphaerochaeta halotolerans	78.0684	218	1164	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	98.82	98.46	0.91	0.89	4	-
GCA_003247345.1	s__Sphaerochaeta sp003247345	77.8995	132	1164	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018399495.1	s__Sphaerochaeta sp018399495	77.6774	186	1164	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016342655.1	s__Sphaerochaeta sp016342655	77.3348	142	1164	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__Sphaerochaeta	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:08:48,361] [INFO] GTDB search result was written to GCF_900182845.1_IMG-taxon_2706794916_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 20:08:48,361] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:08:48,363] [INFO] DFAST_QC result json was written to GCF_900182845.1_IMG-taxon_2706794916_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 20:08:48,364] [INFO] DFAST_QC completed!
[2024-01-25 20:08:48,364] [INFO] Total running time: 0h0m58s