[2024-01-25 20:18:50,645] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:18:50,646] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:18:50,646] [INFO] DQC Reference Directory: /var/lib/cwl/stg269f1001-8c7b-4b92-a8ef-5494b5cdb633/dqc_reference
[2024-01-25 20:18:51,775] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:18:51,775] [INFO] Task started: Prodigal
[2024-01-25 20:18:51,776] [INFO] Running command: gunzip -c /var/lib/cwl/stg7a329feb-9d42-4092-80b3-0cf3f9135356/GCF_001261775.1_Anaeromassilibacillus_senegalense_genomic.fna.gz | prodigal -d GCF_001261775.1_Anaeromassilibacillus_senegalense_genomic.fna/cds.fna -a GCF_001261775.1_Anaeromassilibacillus_senegalense_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:19:00,888] [INFO] Task succeeded: Prodigal
[2024-01-25 20:19:00,889] [INFO] Task started: HMMsearch
[2024-01-25 20:19:00,889] [INFO] Running command: hmmsearch --tblout GCF_001261775.1_Anaeromassilibacillus_senegalense_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg269f1001-8c7b-4b92-a8ef-5494b5cdb633/dqc_reference/reference_markers.hmm GCF_001261775.1_Anaeromassilibacillus_senegalense_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:19:01,124] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:19:01,126] [INFO] Found 6/6 markers.
[2024-01-25 20:19:01,154] [INFO] Query marker FASTA was written to GCF_001261775.1_Anaeromassilibacillus_senegalense_genomic.fna/markers.fasta
[2024-01-25 20:19:01,155] [INFO] Task started: Blastn
[2024-01-25 20:19:01,155] [INFO] Running command: blastn -query GCF_001261775.1_Anaeromassilibacillus_senegalense_genomic.fna/markers.fasta -db /var/lib/cwl/stg269f1001-8c7b-4b92-a8ef-5494b5cdb633/dqc_reference/reference_markers.fasta -out GCF_001261775.1_Anaeromassilibacillus_senegalense_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:01,746] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:01,749] [INFO] Selected 23 target genomes.
[2024-01-25 20:19:01,749] [INFO] Target genome list was writen to GCF_001261775.1_Anaeromassilibacillus_senegalense_genomic.fna/target_genomes.txt
[2024-01-25 20:19:01,771] [INFO] Task started: fastANI
[2024-01-25 20:19:01,771] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a329feb-9d42-4092-80b3-0cf3f9135356/GCF_001261775.1_Anaeromassilibacillus_senegalense_genomic.fna.gz --refList GCF_001261775.1_Anaeromassilibacillus_senegalense_genomic.fna/target_genomes.txt --output GCF_001261775.1_Anaeromassilibacillus_senegalense_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:19:15,204] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:15,204] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg269f1001-8c7b-4b92-a8ef-5494b5cdb633/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:19:15,204] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg269f1001-8c7b-4b92-a8ef-5494b5cdb633/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:19:15,210] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:19:15,211] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:19:15,211] [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
Anaeromassilibacillus senegalensis	strain=mt9	GCA_001261775.1	1673717	1673717	type	True	100.0	1165	1166	95	conclusive
Caproicibacter fermentans	strain=EA1	GCA_009746625.1	2576756	2576756	type	True	77.505	97	1166	95	below_threshold
Clostridium jeddahense	strain=JCD	GCA_000577335.1	1414721	1414721	type	True	77.3219	99	1166	95	below_threshold
Anaerotruncus massiliensis	strain=AT3	GCA_900199635.1	1673720	1673720	type	True	77.2682	60	1166	95	below_threshold
Hydrogeniiclostridium mannosilyticum	strain=ASD2818	GCA_003268275.1	2764322	2764322	type	True	77.2486	89	1166	95	below_threshold
Caproiciproducens galactitolivorans	strain=BS-1	GCA_004768785.1	642589	642589	type	True	77.2169	99	1166	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:19:15,213] [INFO] DFAST Taxonomy check result was written to GCF_001261775.1_Anaeromassilibacillus_senegalense_genomic.fna/tc_result.tsv
[2024-01-25 20:19:15,213] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:19:15,213] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:19:15,213] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg269f1001-8c7b-4b92-a8ef-5494b5cdb633/dqc_reference/checkm_data
[2024-01-25 20:19:15,214] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:19:15,262] [INFO] Task started: CheckM
[2024-01-25 20:19:15,262] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001261775.1_Anaeromassilibacillus_senegalense_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001261775.1_Anaeromassilibacillus_senegalense_genomic.fna/checkm_input GCF_001261775.1_Anaeromassilibacillus_senegalense_genomic.fna/checkm_result
[2024-01-25 20:19:45,906] [INFO] Task succeeded: CheckM
[2024-01-25 20:19:45,907] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:19:45,924] [INFO] ===== Completeness check finished =====
[2024-01-25 20:19:45,924] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:19:45,925] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001261775.1_Anaeromassilibacillus_senegalense_genomic.fna/markers.fasta)
[2024-01-25 20:19:45,925] [INFO] Task started: Blastn
[2024-01-25 20:19:45,925] [INFO] Running command: blastn -query GCF_001261775.1_Anaeromassilibacillus_senegalense_genomic.fna/markers.fasta -db /var/lib/cwl/stg269f1001-8c7b-4b92-a8ef-5494b5cdb633/dqc_reference/reference_markers_gtdb.fasta -out GCF_001261775.1_Anaeromassilibacillus_senegalense_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:46,826] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:46,829] [INFO] Selected 15 target genomes.
[2024-01-25 20:19:46,829] [INFO] Target genome list was writen to GCF_001261775.1_Anaeromassilibacillus_senegalense_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:19:46,851] [INFO] Task started: fastANI
[2024-01-25 20:19:46,851] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a329feb-9d42-4092-80b3-0cf3f9135356/GCF_001261775.1_Anaeromassilibacillus_senegalense_genomic.fna.gz --refList GCF_001261775.1_Anaeromassilibacillus_senegalense_genomic.fna/target_genomes_gtdb.txt --output GCF_001261775.1_Anaeromassilibacillus_senegalense_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:19:55,528] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:55,538] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:19:55,539] [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_001261775.1	s__Anaeromassilibacillus senegalensis	100.0	1165	1166	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Anaeromassilibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015667585.1	s__Anaeromassilibacillus sp015667585	90.2865	922	1166	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Anaeromassilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159845.1	s__Anaeromassilibacillus stercoravium	79.1038	340	1166	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Anaeromassilibacillus	95.0	98.79	98.27	0.94	0.87	13	-
GCA_001305115.1	s__Anaeromassilibacillus sp001305115	78.249	216	1166	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Anaeromassilibacillus	95.0	99.50	98.92	0.91	0.81	5	-
GCA_018712435.1	s__Caccousia avicola	77.7318	118	1166	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caccousia	95.0	98.29	98.29	0.88	0.88	2	-
GCA_902810075.1	s__Clostridium_E sp002397665	77.5414	106	1166	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	-
GCA_000752215.1	s__Caproiciproducens sp000752215	77.4916	155	1166	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproiciproducens	95.0	98.70	97.09	0.94	0.88	5	-
GCA_012517675.1	s__Caproiciproducens sp012517675	77.4666	134	1166	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproiciproducens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012516295.1	s__Caproiciproducens sp012516295	77.462	72	1166	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproiciproducens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000577335.1	s__Clostridium_E jeddahense	77.3489	98	1166	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	-
GCA_018712265.1	s__Gallacutalibacter pullicola	77.3314	104	1166	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_000383295.1	s__Clostridium_E sporosphaeroides	77.2961	106	1166	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	-
GCA_012839345.1	s__Caproiciproducens sp012839345	77.0453	91	1166	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproiciproducens	95.0	99.55	99.55	0.92	0.92	2	-
GCA_900546895.1	s__Caproiciproducens sp900546895	76.7743	123	1166	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproiciproducens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904377855.1	s__Avimonas merdigallinarum	76.5644	62	1166	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Avimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:19:55,542] [INFO] GTDB search result was written to GCF_001261775.1_Anaeromassilibacillus_senegalense_genomic.fna/result_gtdb.tsv
[2024-01-25 20:19:55,542] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:19:55,548] [INFO] DFAST_QC result json was written to GCF_001261775.1_Anaeromassilibacillus_senegalense_genomic.fna/dqc_result.json
[2024-01-25 20:19:55,548] [INFO] DFAST_QC completed!
[2024-01-25 20:19:55,548] [INFO] Total running time: 0h1m5s