[2024-01-24 13:21:46,161] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:46,162] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:46,163] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a14a086-05de-4981-bb2a-392cf02982b7/dqc_reference
[2024-01-24 13:21:47,526] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:47,527] [INFO] Task started: Prodigal
[2024-01-24 13:21:47,527] [INFO] Running command: gunzip -c /var/lib/cwl/stg8e8b3b84-4844-4a78-9060-364b7ec0b705/GCF_003096335.1_ASM309633v1_genomic.fna.gz | prodigal -d GCF_003096335.1_ASM309633v1_genomic.fna/cds.fna -a GCF_003096335.1_ASM309633v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:21:57,664] [INFO] Task succeeded: Prodigal
[2024-01-24 13:21:57,664] [INFO] Task started: HMMsearch
[2024-01-24 13:21:57,664] [INFO] Running command: hmmsearch --tblout GCF_003096335.1_ASM309633v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a14a086-05de-4981-bb2a-392cf02982b7/dqc_reference/reference_markers.hmm GCF_003096335.1_ASM309633v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:21:57,966] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:21:57,967] [INFO] Found 6/6 markers.
[2024-01-24 13:21:57,996] [INFO] Query marker FASTA was written to GCF_003096335.1_ASM309633v1_genomic.fna/markers.fasta
[2024-01-24 13:21:57,997] [INFO] Task started: Blastn
[2024-01-24 13:21:57,997] [INFO] Running command: blastn -query GCF_003096335.1_ASM309633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a14a086-05de-4981-bb2a-392cf02982b7/dqc_reference/reference_markers.fasta -out GCF_003096335.1_ASM309633v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:58,602] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:58,605] [INFO] Selected 11 target genomes.
[2024-01-24 13:21:58,605] [INFO] Target genome list was writen to GCF_003096335.1_ASM309633v1_genomic.fna/target_genomes.txt
[2024-01-24 13:21:58,617] [INFO] Task started: fastANI
[2024-01-24 13:21:58,617] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e8b3b84-4844-4a78-9060-364b7ec0b705/GCF_003096335.1_ASM309633v1_genomic.fna.gz --refList GCF_003096335.1_ASM309633v1_genomic.fna/target_genomes.txt --output GCF_003096335.1_ASM309633v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:06,040] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:06,041] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a14a086-05de-4981-bb2a-392cf02982b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:06,041] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a14a086-05de-4981-bb2a-392cf02982b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:06,050] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:22:06,050] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:06,050] [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
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	100.0	1048	1050	95	conclusive
Intestinimonas butyriciproducens	strain=SRB-521-5-I	GCA_004154955.1	1297617	1297617	type	True	99.996	1043	1050	95	conclusive
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	99.9913	1024	1050	95	conclusive
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	80.6659	148	1050	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	79.2035	345	1050	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	79.165	364	1050	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	79.1207	268	1050	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	78.2687	219	1050	95	below_threshold
Bittarella massiliensis	strain=GD6	GCA_001486165.1	1720313	1720313	type	True	76.8567	83	1050	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:06,052] [INFO] DFAST Taxonomy check result was written to GCF_003096335.1_ASM309633v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:06,052] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:06,052] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:06,053] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a14a086-05de-4981-bb2a-392cf02982b7/dqc_reference/checkm_data
[2024-01-24 13:22:06,054] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:06,085] [INFO] Task started: CheckM
[2024-01-24 13:22:06,085] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003096335.1_ASM309633v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003096335.1_ASM309633v1_genomic.fna/checkm_input GCF_003096335.1_ASM309633v1_genomic.fna/checkm_result
[2024-01-24 13:22:39,188] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:39,190] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:39,214] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:39,214] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:39,215] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003096335.1_ASM309633v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:39,216] [INFO] Task started: Blastn
[2024-01-24 13:22:39,216] [INFO] Running command: blastn -query GCF_003096335.1_ASM309633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a14a086-05de-4981-bb2a-392cf02982b7/dqc_reference/reference_markers_gtdb.fasta -out GCF_003096335.1_ASM309633v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:40,262] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:40,266] [INFO] Selected 16 target genomes.
[2024-01-24 13:22:40,266] [INFO] Target genome list was writen to GCF_003096335.1_ASM309633v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:40,287] [INFO] Task started: fastANI
[2024-01-24 13:22:40,288] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e8b3b84-4844-4a78-9060-364b7ec0b705/GCF_003096335.1_ASM309633v1_genomic.fna.gz --refList GCF_003096335.1_ASM309633v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003096335.1_ASM309633v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:49,264] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:49,290] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:49,290] [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_004154955.1	s__Intestinimonas butyriciproducens	99.996	1043	1050	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	98.73	98.09	0.87	0.79	17	conclusive
GCF_900626145.1	s__Intestinimonas timonensis	81.8896	481	1050	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001244995.1	s__Intestinimonas massiliensis	80.8067	439	1050	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	99.15	98.60	0.93	0.82	6	-
GCA_019117605.1	s__Intestinimonas stercoravium	80.4752	375	1050	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	98.97	98.96	0.85	0.84	3	-
GCA_900540545.1	s__Intestinimonas sp900540545	80.3682	414	1050	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119795.1	s__Intestinimonas pullistercoris	80.3205	339	1050	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	99.29	99.15	0.85	0.82	4	-
GCF_014287895.1	s__NSJ-51 sp900549795	80.2001	325	1050	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__NSJ-51	95.0	99.27	99.06	0.90	0.89	3	-
GCF_017811815.1	s__Flavonifractor sp017811815	79.9028	312	1050	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019115785.1	s__Intestinimonas merdavium	79.7212	371	1050	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	98.39	98.39	0.88	0.88	2	-
GCF_900199495.1	s__An92 sp900199495	79.3617	273	1050	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	98.28	97.84	0.85	0.79	7	-
GCA_019119165.1	s__Flavonifractor intestinigallinarum	78.9032	261	1050	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	98.85	97.85	0.90	0.88	3	-
GCA_018374635.1	s__An92 sp018374635	78.8607	266	1050	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549405.1	s__Lawsonibacter sp900549405	78.4837	169	1050	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	97.96	97.96	0.89	0.89	2	-
GCA_910579155.1	s__Enterenecus sp910579155	77.7352	186	1050	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900756495.1	s__HGM12998 sp900756495	77.7294	167	1050	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__HGM12998	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017416685.1	s__Lawsonibacter sp017416685	77.1157	124	1050	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:22:49,292] [INFO] GTDB search result was written to GCF_003096335.1_ASM309633v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:49,293] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:49,297] [INFO] DFAST_QC result json was written to GCF_003096335.1_ASM309633v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:49,297] [INFO] DFAST_QC completed!
[2024-01-24 13:22:49,297] [INFO] Total running time: 0h1m3s