[2024-01-24 12:31:58,508] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:58,513] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:58,513] [INFO] DQC Reference Directory: /var/lib/cwl/stge397370a-03a8-4f43-aa84-c5024a1aeda4/dqc_reference
[2024-01-24 12:31:59,937] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:59,938] [INFO] Task started: Prodigal
[2024-01-24 12:31:59,938] [INFO] Running command: gunzip -c /var/lib/cwl/stgf7760aef-bb48-442f-ba9a-49923116ece9/GCF_000577335.1_JCD_genomic.fna.gz | prodigal -d GCF_000577335.1_JCD_genomic.fna/cds.fna -a GCF_000577335.1_JCD_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:09,405] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:09,405] [INFO] Task started: HMMsearch
[2024-01-24 12:32:09,405] [INFO] Running command: hmmsearch --tblout GCF_000577335.1_JCD_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge397370a-03a8-4f43-aa84-c5024a1aeda4/dqc_reference/reference_markers.hmm GCF_000577335.1_JCD_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:09,670] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:09,671] [INFO] Found 6/6 markers.
[2024-01-24 12:32:09,705] [INFO] Query marker FASTA was written to GCF_000577335.1_JCD_genomic.fna/markers.fasta
[2024-01-24 12:32:09,705] [INFO] Task started: Blastn
[2024-01-24 12:32:09,705] [INFO] Running command: blastn -query GCF_000577335.1_JCD_genomic.fna/markers.fasta -db /var/lib/cwl/stge397370a-03a8-4f43-aa84-c5024a1aeda4/dqc_reference/reference_markers.fasta -out GCF_000577335.1_JCD_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:10,424] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:10,429] [INFO] Selected 16 target genomes.
[2024-01-24 12:32:10,430] [INFO] Target genome list was writen to GCF_000577335.1_JCD_genomic.fna/target_genomes.txt
[2024-01-24 12:32:10,436] [INFO] Task started: fastANI
[2024-01-24 12:32:10,436] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7760aef-bb48-442f-ba9a-49923116ece9/GCF_000577335.1_JCD_genomic.fna.gz --refList GCF_000577335.1_JCD_genomic.fna/target_genomes.txt --output GCF_000577335.1_JCD_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:18,602] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:18,602] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge397370a-03a8-4f43-aa84-c5024a1aeda4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:18,603] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge397370a-03a8-4f43-aa84-c5024a1aeda4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:18,608] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:18,609] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:18,609] [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
Clostridium jeddahense	strain=JCD	GCA_000577335.1	1414721	1414721	type	True	100.0	1141	1151	95	conclusive
Clostridium merdae	strain=Marseille-P2953	GCA_900176635.1	1958780	1958780	type	True	80.4481	487	1151	95	below_threshold
Clostridium minihomine	strain=Marseille-P4642	GCA_900240385.1	2045012	2045012	type	True	78.8138	298	1151	95	below_threshold
Caproicibacter fermentans	strain=EA1	GCA_009746625.1	2576756	2576756	type	True	77.3583	97	1151	95	below_threshold
Anaeromassilibacillus senegalensis	strain=mt9	GCA_001261775.1	1673717	1673717	type	True	77.2521	101	1151	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:18,611] [INFO] DFAST Taxonomy check result was written to GCF_000577335.1_JCD_genomic.fna/tc_result.tsv
[2024-01-24 12:32:18,612] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:18,612] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:18,613] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge397370a-03a8-4f43-aa84-c5024a1aeda4/dqc_reference/checkm_data
[2024-01-24 12:32:18,614] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:18,660] [INFO] Task started: CheckM
[2024-01-24 12:32:18,660] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000577335.1_JCD_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000577335.1_JCD_genomic.fna/checkm_input GCF_000577335.1_JCD_genomic.fna/checkm_result
[2024-01-24 12:32:52,415] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:52,417] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:52,436] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:52,437] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:52,437] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000577335.1_JCD_genomic.fna/markers.fasta)
[2024-01-24 12:32:52,438] [INFO] Task started: Blastn
[2024-01-24 12:32:52,438] [INFO] Running command: blastn -query GCF_000577335.1_JCD_genomic.fna/markers.fasta -db /var/lib/cwl/stge397370a-03a8-4f43-aa84-c5024a1aeda4/dqc_reference/reference_markers_gtdb.fasta -out GCF_000577335.1_JCD_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:53,687] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:53,691] [INFO] Selected 10 target genomes.
[2024-01-24 12:32:53,691] [INFO] Target genome list was writen to GCF_000577335.1_JCD_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:53,739] [INFO] Task started: fastANI
[2024-01-24 12:32:53,740] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7760aef-bb48-442f-ba9a-49923116ece9/GCF_000577335.1_JCD_genomic.fna.gz --refList GCF_000577335.1_JCD_genomic.fna/target_genomes_gtdb.txt --output GCF_000577335.1_JCD_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:59,164] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:59,172] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:59,172] [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_000577335.1	s__Clostridium_E jeddahense	100.0	1141	1151	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Clostridium_E	95.0	97.87	96.05	0.91	0.86	8	conclusive
GCA_000383295.1	s__Clostridium_E sporosphaeroides	90.6514	843	1151	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Clostridium_E	95.0	99.23	99.22	0.94	0.93	3	-
GCF_900176635.1	s__Clostridium_E merdae	80.4602	485	1151	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Clostridium_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900240385.1	s__Clostridium_E minihomine	78.8138	298	1151	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Clostridium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902810075.1	s__Clostridium_E sp002397665	77.7483	262	1151	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Clostridium_E	95.0	97.21	97.21	0.87	0.87	2	-
GCF_015667585.1	s__Anaeromassilibacillus sp015667585	77.3163	108	1151	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Anaeromassilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018712265.1	s__Gallacutalibacter pullicola	77.1065	87	1151	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Gallacutalibacter	95.0	98.09	98.02	0.89	0.86	4	-
GCA_012517675.1	s__Caproiciproducens sp012517675	76.8841	103	1151	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproiciproducens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:59,174] [INFO] GTDB search result was written to GCF_000577335.1_JCD_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:59,175] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:59,177] [INFO] DFAST_QC result json was written to GCF_000577335.1_JCD_genomic.fna/dqc_result.json
[2024-01-24 12:32:59,177] [INFO] DFAST_QC completed!
[2024-01-24 12:32:59,177] [INFO] Total running time: 0h1m1s