[2024-01-25 19:38:05,867] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:38:05,868] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:38:05,869] [INFO] DQC Reference Directory: /var/lib/cwl/stgd89a6ae6-7b1e-442b-ad30-4b50f3e47b5b/dqc_reference
[2024-01-25 19:38:07,065] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:38:07,066] [INFO] Task started: Prodigal
[2024-01-25 19:38:07,066] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d23f535-4a9d-45ca-94b5-2127ab2db6e2/GCF_001403635.1_Clostridium_massilioamazoniensis_genomic.fna.gz | prodigal -d GCF_001403635.1_Clostridium_massilioamazoniensis_genomic.fna/cds.fna -a GCF_001403635.1_Clostridium_massilioamazoniensis_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:38:11,915] [INFO] Task succeeded: Prodigal
[2024-01-25 19:38:11,916] [INFO] Task started: HMMsearch
[2024-01-25 19:38:11,916] [INFO] Running command: hmmsearch --tblout GCF_001403635.1_Clostridium_massilioamazoniensis_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd89a6ae6-7b1e-442b-ad30-4b50f3e47b5b/dqc_reference/reference_markers.hmm GCF_001403635.1_Clostridium_massilioamazoniensis_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:38:12,165] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:38:12,166] [INFO] Found 6/6 markers.
[2024-01-25 19:38:12,193] [INFO] Query marker FASTA was written to GCF_001403635.1_Clostridium_massilioamazoniensis_genomic.fna/markers.fasta
[2024-01-25 19:38:12,193] [INFO] Task started: Blastn
[2024-01-25 19:38:12,193] [INFO] Running command: blastn -query GCF_001403635.1_Clostridium_massilioamazoniensis_genomic.fna/markers.fasta -db /var/lib/cwl/stgd89a6ae6-7b1e-442b-ad30-4b50f3e47b5b/dqc_reference/reference_markers.fasta -out GCF_001403635.1_Clostridium_massilioamazoniensis_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:38:12,754] [INFO] Task succeeded: Blastn
[2024-01-25 19:38:12,757] [INFO] Selected 19 target genomes.
[2024-01-25 19:38:12,757] [INFO] Target genome list was writen to GCF_001403635.1_Clostridium_massilioamazoniensis_genomic.fna/target_genomes.txt
[2024-01-25 19:38:12,774] [INFO] Task started: fastANI
[2024-01-25 19:38:12,774] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d23f535-4a9d-45ca-94b5-2127ab2db6e2/GCF_001403635.1_Clostridium_massilioamazoniensis_genomic.fna.gz --refList GCF_001403635.1_Clostridium_massilioamazoniensis_genomic.fna/target_genomes.txt --output GCF_001403635.1_Clostridium_massilioamazoniensis_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:38:28,746] [INFO] Task succeeded: fastANI
[2024-01-25 19:38:28,747] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd89a6ae6-7b1e-442b-ad30-4b50f3e47b5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:38:28,747] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd89a6ae6-7b1e-442b-ad30-4b50f3e47b5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:38:28,758] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:38:28,759] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:38:28,759] [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 massiliamazoniense	strain=ND2	GCA_001403635.1	1347366	1347366	type	True	100.0	1238	1239	95	conclusive
Clostridium mediterraneense	strain=Marseille-P2434	GCA_900091705.1	1805472	1805472	type	True	79.2784	397	1239	95	below_threshold
Clostridium perfringens	strain=ATCC 13124	GCA_000013285.1	1502	1502	type	True	78.7712	300	1239	95	below_threshold
Clostridium perfringens	strain=FDAARGOS_903	GCA_016027375.1	1502	1502	type	True	78.6637	305	1239	95	below_threshold
Sarcina ventriculi	strain=NCTC12966	GCA_900456775.1	1267	1267	type	True	77.7734	266	1239	95	below_threshold
Clostridium tarantellae	strain=DSM 3997	GCA_009295725.1	39493	39493	type	True	77.6448	273	1239	95	below_threshold
Clostridium manihotivorum	strain=CT4	GCA_004015185.1	2320868	2320868	type	True	77.4661	168	1239	95	below_threshold
Clostridium swellfunianum	strain=CICC 10730	GCA_023656515.1	1367462	1367462	type	True	77.2383	104	1239	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_018223745.1	1520	1520	suspected-type	True	77.2006	222	1239	95	below_threshold
Clostridium moniliforme	strain=DSM 3984	GCA_017873235.1	39489	39489	type	True	77.1626	235	1239	95	below_threshold
Clostridium sardiniense	strain=DSM 2632	GCA_016907995.1	29369	29369	type	True	76.9386	254	1239	95	below_threshold
Clostridium cagae	strain=Marseille-P4344	GCA_900290265.1	2080751	2080751	type	True	76.7732	235	1239	95	below_threshold
Clostridium felsineum	strain=DSM 793	GCA_002006235.2	36839	36839	type	True	76.7536	141	1239	95	below_threshold
Clostridium intestinale	strain=DSM 6191	GCA_900130055.1	36845	36845	type	True	76.74	196	1239	95	below_threshold
Clostridium celatum	strain=DSM 1785	GCA_000320405.1	36834	36834	type	True	76.693	221	1239	95	below_threshold
Clostridium cibarium	strain=Sa3CVN1	GCA_014836335.1	2762247	2762247	type	True	76.5919	182	1239	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	76.5883	247	1239	95	below_threshold
Clostridium felsineum	strain=DSM 7320	GCA_002006215.2	36839	36839	type	True	76.5397	147	1239	95	below_threshold
Clostridium simiarum	strain=MSJ-4	GCA_018919175.1	2841506	2841506	type	True	75.9287	149	1239	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:38:28,761] [INFO] DFAST Taxonomy check result was written to GCF_001403635.1_Clostridium_massilioamazoniensis_genomic.fna/tc_result.tsv
[2024-01-25 19:38:28,761] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:38:28,761] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:38:28,761] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd89a6ae6-7b1e-442b-ad30-4b50f3e47b5b/dqc_reference/checkm_data
[2024-01-25 19:38:28,762] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:38:28,801] [INFO] Task started: CheckM
[2024-01-25 19:38:28,801] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001403635.1_Clostridium_massilioamazoniensis_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001403635.1_Clostridium_massilioamazoniensis_genomic.fna/checkm_input GCF_001403635.1_Clostridium_massilioamazoniensis_genomic.fna/checkm_result
[2024-01-25 19:38:48,182] [INFO] Task succeeded: CheckM
[2024-01-25 19:38:48,186] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:38:48,237] [INFO] ===== Completeness check finished =====
[2024-01-25 19:38:48,237] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:38:48,238] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001403635.1_Clostridium_massilioamazoniensis_genomic.fna/markers.fasta)
[2024-01-25 19:38:48,238] [INFO] Task started: Blastn
[2024-01-25 19:38:48,238] [INFO] Running command: blastn -query GCF_001403635.1_Clostridium_massilioamazoniensis_genomic.fna/markers.fasta -db /var/lib/cwl/stgd89a6ae6-7b1e-442b-ad30-4b50f3e47b5b/dqc_reference/reference_markers_gtdb.fasta -out GCF_001403635.1_Clostridium_massilioamazoniensis_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:38:49,012] [INFO] Task succeeded: Blastn
[2024-01-25 19:38:49,014] [INFO] Selected 19 target genomes.
[2024-01-25 19:38:49,014] [INFO] Target genome list was writen to GCF_001403635.1_Clostridium_massilioamazoniensis_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:38:49,040] [INFO] Task started: fastANI
[2024-01-25 19:38:49,040] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d23f535-4a9d-45ca-94b5-2127ab2db6e2/GCF_001403635.1_Clostridium_massilioamazoniensis_genomic.fna.gz --refList GCF_001403635.1_Clostridium_massilioamazoniensis_genomic.fna/target_genomes_gtdb.txt --output GCF_001403635.1_Clostridium_massilioamazoniensis_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:39:02,117] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:02,128] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:39:02,128] [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_001403635.1	s__Clostridium_P massiliamazoniense	100.0	1238	1239	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900091705.1	s__Clostridium_P mediterraneense	79.2886	398	1239	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000013285.1	s__Clostridium_P perfringens	78.7061	300	1239	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	98.05	95.74	0.91	0.81	315	-
GCF_900456775.1	s__Clostridium_P ventriculi	77.8801	268	1239	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	98.93	98.34	0.95	0.94	8	-
GCF_009295725.1	s__Clostridium_P tarantellae	77.6545	272	1239	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002050515.1	s__Clostridium thermobutyricum	77.3899	291	1239	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.10	97.10	0.91	0.89	3	-
GCF_001405015.1	s__Clostridium disporicum	77.1135	200	1239	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.24	98.87	0.93	0.88	4	-
GCF_000498355.1	s__Clostridium sp000498355	77.106	254	1239	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004353185.1	s__Clostridium cuniculi	77.0916	257	1239	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.75	97.60	0.86	0.82	5	-
GCF_018918325.1	s__Clostridium sp018918325	77.0164	152	1239	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907995.1	s__Clostridium sardiniense	76.9485	253	1239	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900130055.1	s__Clostridium_T intestinale	76.7285	194	1239	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_T	95.0	95.87	95.52	0.87	0.83	4	-
GCA_900543325.1	s__Clostridium sp900543325	76.5911	213	1239	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900539375.1	s__Clostridium sp900539375	76.5814	226	1239	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.09	99.02	0.89	0.86	4	-
GCA_902785295.1	s__Clostridium sp902785295	76.552	185	1239	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007115085.1	s__Clostridium sp007115085	76.5492	183	1239	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.42	99.42	0.90	0.90	2	-
GCA_017383505.1	s__Clostridium sp017383505	76.4931	118	1239	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015058405.1	s__Clostridium sp015058405	76.4505	185	1239	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000633595.2	s__Clostridium_AM drakei	75.848	147	1239	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	96.092	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:39:02,129] [INFO] GTDB search result was written to GCF_001403635.1_Clostridium_massilioamazoniensis_genomic.fna/result_gtdb.tsv
[2024-01-25 19:39:02,130] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:39:02,133] [INFO] DFAST_QC result json was written to GCF_001403635.1_Clostridium_massilioamazoniensis_genomic.fna/dqc_result.json
[2024-01-25 19:39:02,133] [INFO] DFAST_QC completed!
[2024-01-25 19:39:02,133] [INFO] Total running time: 0h0m56s