[2024-01-24 11:43:50,656] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:50,658] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:50,659] [INFO] DQC Reference Directory: /var/lib/cwl/stgde7ad826-398b-46d9-b62c-5fad64586ac3/dqc_reference
[2024-01-24 11:43:51,881] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:51,882] [INFO] Task started: Prodigal
[2024-01-24 11:43:51,882] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ac64ab1-0b8e-4a94-8483-22ac6b673a25/GCF_024623325.1_ASM2462332v1_genomic.fna.gz | prodigal -d GCF_024623325.1_ASM2462332v1_genomic.fna/cds.fna -a GCF_024623325.1_ASM2462332v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:07,085] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:07,085] [INFO] Task started: HMMsearch
[2024-01-24 11:44:07,085] [INFO] Running command: hmmsearch --tblout GCF_024623325.1_ASM2462332v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde7ad826-398b-46d9-b62c-5fad64586ac3/dqc_reference/reference_markers.hmm GCF_024623325.1_ASM2462332v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:07,360] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:07,361] [INFO] Found 6/6 markers.
[2024-01-24 11:44:07,408] [INFO] Query marker FASTA was written to GCF_024623325.1_ASM2462332v1_genomic.fna/markers.fasta
[2024-01-24 11:44:07,408] [INFO] Task started: Blastn
[2024-01-24 11:44:07,409] [INFO] Running command: blastn -query GCF_024623325.1_ASM2462332v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde7ad826-398b-46d9-b62c-5fad64586ac3/dqc_reference/reference_markers.fasta -out GCF_024623325.1_ASM2462332v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:08,048] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:08,052] [INFO] Selected 25 target genomes.
[2024-01-24 11:44:08,053] [INFO] Target genome list was writen to GCF_024623325.1_ASM2462332v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:08,064] [INFO] Task started: fastANI
[2024-01-24 11:44:08,065] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ac64ab1-0b8e-4a94-8483-22ac6b673a25/GCF_024623325.1_ASM2462332v1_genomic.fna.gz --refList GCF_024623325.1_ASM2462332v1_genomic.fna/target_genomes.txt --output GCF_024623325.1_ASM2462332v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:25,130] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:25,131] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde7ad826-398b-46d9-b62c-5fad64586ac3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:25,131] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde7ad826-398b-46d9-b62c-5fad64586ac3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:25,141] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:25,141] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:25,141] [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
Acetatifactor muris	strain=DSM 23669	GCA_024623325.1	879566	879566	type	True	100.0	1953	1955	95	conclusive
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	81.1205	76	1955	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	80.9256	77	1955	95	below_threshold
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	80.8858	129	1955	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	79.0479	152	1955	95	below_threshold
Clostridium porci	strain=WCA-389-WT-23D1	GCA_009696375.1	2605778	2605778	type	True	79.0029	69	1955	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	78.6083	132	1955	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	77.9195	137	1955	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	76.4883	58	1955	95	below_threshold
Murimonas intestini	strain=DSM 26524	GCA_024622195.1	1337051	1337051	type	True	76.3778	59	1955	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	76.3116	59	1955	95	below_threshold
Cuneatibacter caecimuris	strain=DSM 29486	GCA_004216775.1	1796618	1796618	type	True	76.1745	50	1955	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:25,143] [INFO] DFAST Taxonomy check result was written to GCF_024623325.1_ASM2462332v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:25,143] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:25,143] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:25,143] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde7ad826-398b-46d9-b62c-5fad64586ac3/dqc_reference/checkm_data
[2024-01-24 11:44:25,144] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:25,198] [INFO] Task started: CheckM
[2024-01-24 11:44:25,198] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024623325.1_ASM2462332v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024623325.1_ASM2462332v1_genomic.fna/checkm_input GCF_024623325.1_ASM2462332v1_genomic.fna/checkm_result
[2024-01-24 11:45:10,071] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:10,072] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:10,090] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:10,090] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:10,091] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024623325.1_ASM2462332v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:10,091] [INFO] Task started: Blastn
[2024-01-24 11:45:10,091] [INFO] Running command: blastn -query GCF_024623325.1_ASM2462332v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde7ad826-398b-46d9-b62c-5fad64586ac3/dqc_reference/reference_markers_gtdb.fasta -out GCF_024623325.1_ASM2462332v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:11,141] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:11,144] [INFO] Selected 16 target genomes.
[2024-01-24 11:45:11,144] [INFO] Target genome list was writen to GCF_024623325.1_ASM2462332v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:11,166] [INFO] Task started: fastANI
[2024-01-24 11:45:11,166] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ac64ab1-0b8e-4a94-8483-22ac6b673a25/GCF_024623325.1_ASM2462332v1_genomic.fna.gz --refList GCF_024623325.1_ASM2462332v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024623325.1_ASM2462332v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:24,506] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:24,519] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:24,520] [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_900248245.1	s__Acetatifactor muris	99.9877	1918	1955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910588225.1	s__Acetatifactor sp910588225	90.8148	1080	1955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910576125.1	s__Acetatifactor sp910576125	81.5019	532	1955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003612485.1	s__Acetatifactor sp003612485	81.2371	408	1955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	98.96	98.96	0.94	0.94	2	-
GCA_910580225.1	s__Acetatifactor sp910580225	79.477	440	1955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587555.1	s__Acetatifactor sp910587555	78.7518	415	1955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585805.1	s__Acetatifactor sp910585805	78.7433	405	1955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577185.1	s__Acetatifactor sp910577185	78.6189	442	1955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586515.1	s__Acetatifactor sp910586515	78.5116	394	1955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586775.1	s__Acetatifactor sp910586775	78.2845	397	1955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578995.1	s__Acetatifactor sp910578995	78.141	359	1955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002490995.1	s__Acetatifactor sp002490995	77.8557	378	1955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587755.1	s__Acetatifactor sp910587755	77.5676	230	1955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584435.1	s__Acetatifactor sp910584435	77.5396	270	1955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016303085.1	s__Acetatifactor sp016303085	76.586	131	1955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017478245.1	s__Acetatifactor sp017478245	76.0623	85	1955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:24,521] [INFO] GTDB search result was written to GCF_024623325.1_ASM2462332v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:24,522] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:24,525] [INFO] DFAST_QC result json was written to GCF_024623325.1_ASM2462332v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:24,525] [INFO] DFAST_QC completed!
[2024-01-24 11:45:24,525] [INFO] Total running time: 0h1m34s