[2024-01-24 13:22:31,451] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:31,453] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:31,453] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1d83671-51bf-4263-8c84-a864f2fe599d/dqc_reference
[2024-01-24 13:22:32,850] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:32,851] [INFO] Task started: Prodigal
[2024-01-24 13:22:32,851] [INFO] Running command: gunzip -c /var/lib/cwl/stg3cb56e40-6d3f-4da5-b6b6-53b10db33393/GCF_025567445.1_ASM2556744v1_genomic.fna.gz | prodigal -d GCF_025567445.1_ASM2556744v1_genomic.fna/cds.fna -a GCF_025567445.1_ASM2556744v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:46,918] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:46,919] [INFO] Task started: HMMsearch
[2024-01-24 13:22:46,919] [INFO] Running command: hmmsearch --tblout GCF_025567445.1_ASM2556744v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1d83671-51bf-4263-8c84-a864f2fe599d/dqc_reference/reference_markers.hmm GCF_025567445.1_ASM2556744v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:47,257] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:47,259] [INFO] Found 6/6 markers.
[2024-01-24 13:22:47,308] [INFO] Query marker FASTA was written to GCF_025567445.1_ASM2556744v1_genomic.fna/markers.fasta
[2024-01-24 13:22:47,309] [INFO] Task started: Blastn
[2024-01-24 13:22:47,309] [INFO] Running command: blastn -query GCF_025567445.1_ASM2556744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1d83671-51bf-4263-8c84-a864f2fe599d/dqc_reference/reference_markers.fasta -out GCF_025567445.1_ASM2556744v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:47,987] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:47,991] [INFO] Selected 26 target genomes.
[2024-01-24 13:22:47,991] [INFO] Target genome list was writen to GCF_025567445.1_ASM2556744v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:49,426] [INFO] Task started: fastANI
[2024-01-24 13:22:49,426] [INFO] Running command: fastANI --query /var/lib/cwl/stg3cb56e40-6d3f-4da5-b6b6-53b10db33393/GCF_025567445.1_ASM2556744v1_genomic.fna.gz --refList GCF_025567445.1_ASM2556744v1_genomic.fna/target_genomes.txt --output GCF_025567445.1_ASM2556744v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:08,903] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:08,904] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1d83671-51bf-4263-8c84-a864f2fe599d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:08,905] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1d83671-51bf-4263-8c84-a864f2fe599d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:08,925] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:08,925] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:08,925] [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
Diplocloster agilis	strain=ASD5720	GCA_019042275.1	2850323	2850323	type	True	98.817	1634	1904	95	conclusive
Diplocloster modestus	strain=ASD4241	GCA_019042245.1	2850322	2850322	type	True	88.317	1315	1904	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	79.3434	64	1904	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	79.2634	117	1904	95	below_threshold
Qiania dongpingensis	strain=NSJ-38	GCA_014337195.1	2763669	2763669	type	True	79.0999	62	1904	95	below_threshold
Blautia producta	strain=ATCC 27340	GCA_000373885.1	33035	33035	suspected-type	True	78.9679	92	1904	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	77.7388	120	1904	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	77.33	60	1904	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_000173815.1	168384	168384	type	True	77.216	59	1904	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_002221555.2	1796616	1796616	type	True	77.1711	65	1904	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_001689125.2	1796616	1796616	type	True	77.0967	66	1904	95	below_threshold
Anaerobium acetethylicum	strain=GluBS11	GCA_900096945.1	1619234	1619234	type	True	77.0653	60	1904	95	below_threshold
Marvinbryantia formatexigens	strain=I-52	GCA_900102475.1	168384	168384	type	True	77.012	59	1904	95	below_threshold
Lacrimispora sphenoides	strain=NCTC507	GCA_900461315.1	29370	29370	type	True	76.9341	57	1904	95	below_threshold
Lacrimispora sphenoides	strain=ATCC 19403	GCA_900105615.1	29370	29370	type	True	76.7392	57	1904	95	below_threshold
Wansuia hejianensis	strain=NSJ-29	GCA_014337215.1	2763667	2763667	type	True	76.6756	82	1904	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	76.4257	90	1904	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	76.42	94	1904	95	below_threshold
Hungatella effluvii	strain=DSM 24995	GCA_003201875.1	1096246	1096246	type	True	76.4105	94	1904	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:08,927] [INFO] DFAST Taxonomy check result was written to GCF_025567445.1_ASM2556744v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:08,927] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:08,928] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:08,928] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1d83671-51bf-4263-8c84-a864f2fe599d/dqc_reference/checkm_data
[2024-01-24 13:23:08,929] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:08,984] [INFO] Task started: CheckM
[2024-01-24 13:23:08,984] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025567445.1_ASM2556744v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025567445.1_ASM2556744v1_genomic.fna/checkm_input GCF_025567445.1_ASM2556744v1_genomic.fna/checkm_result
[2024-01-24 13:23:52,997] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:52,998] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:53,023] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:53,023] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:53,023] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025567445.1_ASM2556744v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:53,024] [INFO] Task started: Blastn
[2024-01-24 13:23:53,024] [INFO] Running command: blastn -query GCF_025567445.1_ASM2556744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1d83671-51bf-4263-8c84-a864f2fe599d/dqc_reference/reference_markers_gtdb.fasta -out GCF_025567445.1_ASM2556744v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:54,093] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:54,098] [INFO] Selected 25 target genomes.
[2024-01-24 13:23:54,098] [INFO] Target genome list was writen to GCF_025567445.1_ASM2556744v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:54,137] [INFO] Task started: fastANI
[2024-01-24 13:23:54,138] [INFO] Running command: fastANI --query /var/lib/cwl/stg3cb56e40-6d3f-4da5-b6b6-53b10db33393/GCF_025567445.1_ASM2556744v1_genomic.fna.gz --refList GCF_025567445.1_ASM2556744v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025567445.1_ASM2556744v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:10,693] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:10,720] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:10,720] [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_902362855.1	s__GCA-900066755 sp900066755	100.0	1894	1904	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__GCA-900066755	95.0	99.21	98.73	0.90	0.82	4	conclusive
GCA_902363085.1	s__GCA-900066755 sp902363085	88.1959	1307	1904	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__GCA-900066755	95.0	99.73	99.73	0.92	0.92	2	-
GCF_000225345.1	s__Roseburia hominis	79.7115	76	1904	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.94	95.20	0.88	0.81	15	-
GCF_001881565.1	s__Eisenbergiella tayi	77.7456	121	1904	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	97.85	97.22	0.85	0.80	21	-
GCF_016901695.1	s__Lachnoclostridium_B massiliensis_A	77.218	61	1904	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002361955.1	s__CAG-56 sp002361955	77.2064	59	1904	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-56	95.0	99.90	99.85	0.92	0.90	5	-
GCA_019120315.1	s__Ruminococcus_G avistercoris	77.0907	66	1904	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_G	95.0	99.47	98.95	0.89	0.84	3	-
GCF_900096945.1	s__Anaerobium acetethylicum	77.0653	60	1904	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904379015.1	s__Paralachnospira caecorum	76.7779	57	1904	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Paralachnospira	95.0	99.98	99.98	0.92	0.92	2	-
GCA_900547735.1	s__Clostridium_Q sp900547735	76.6331	62	1904	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910575555.1	s__14-2 sp011960065	76.6183	82	1904	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	99.61	97.67	0.95	0.76	7	-
GCA_910583895.1	s__Choladocola sp910583895	76.486	54	1904	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018711275.1	s__Pullilachnospira intestinigallinarum	76.4382	76	1904	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pullilachnospira	95.0	99.92	99.92	0.90	0.90	2	-
GCA_009911175.1	s__Schaedlerella sp009911175	76.4154	88	1904	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	98.09	98.08	0.79	0.79	3	-
GCF_900626075.1	s__Clostridium_Q transplantifaecale	76.3555	70	1904	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019115665.1	s__Eisenbergiella pullistercoris	76.3318	76	1904	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900770325.1	s__Merdiplasma sp900770325	76.1895	55	1904	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdiplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018715565.1	s__Ventrimonas merdavium	76.1761	77	1904	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.46	99.46	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:10,721] [INFO] GTDB search result was written to GCF_025567445.1_ASM2556744v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:10,722] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:10,726] [INFO] DFAST_QC result json was written to GCF_025567445.1_ASM2556744v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:10,726] [INFO] DFAST_QC completed!
[2024-01-24 13:24:10,726] [INFO] Total running time: 0h1m39s