[2024-01-24 12:37:09,330] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:09,333] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:09,333] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2d3d30e-a072-48b9-91ef-a09960dcb395/dqc_reference
[2024-01-24 12:37:10,760] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:10,761] [INFO] Task started: Prodigal
[2024-01-24 12:37:10,762] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e80df42-436d-4a1c-869b-638d703b804f/GCF_019431045.1_ASM1943104v1_genomic.fna.gz | prodigal -d GCF_019431045.1_ASM1943104v1_genomic.fna/cds.fna -a GCF_019431045.1_ASM1943104v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:16,366] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:16,367] [INFO] Task started: HMMsearch
[2024-01-24 12:37:16,367] [INFO] Running command: hmmsearch --tblout GCF_019431045.1_ASM1943104v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2d3d30e-a072-48b9-91ef-a09960dcb395/dqc_reference/reference_markers.hmm GCF_019431045.1_ASM1943104v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:16,669] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:16,671] [INFO] Found 6/6 markers.
[2024-01-24 12:37:16,708] [INFO] Query marker FASTA was written to GCF_019431045.1_ASM1943104v1_genomic.fna/markers.fasta
[2024-01-24 12:37:16,709] [INFO] Task started: Blastn
[2024-01-24 12:37:16,709] [INFO] Running command: blastn -query GCF_019431045.1_ASM1943104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2d3d30e-a072-48b9-91ef-a09960dcb395/dqc_reference/reference_markers.fasta -out GCF_019431045.1_ASM1943104v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:17,314] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:17,318] [INFO] Selected 18 target genomes.
[2024-01-24 12:37:17,319] [INFO] Target genome list was writen to GCF_019431045.1_ASM1943104v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:17,384] [INFO] Task started: fastANI
[2024-01-24 12:37:17,385] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e80df42-436d-4a1c-869b-638d703b804f/GCF_019431045.1_ASM1943104v1_genomic.fna.gz --refList GCF_019431045.1_ASM1943104v1_genomic.fna/target_genomes.txt --output GCF_019431045.1_ASM1943104v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:32,222] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:32,223] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2d3d30e-a072-48b9-91ef-a09960dcb395/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:32,224] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2d3d30e-a072-48b9-91ef-a09960dcb395/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:32,243] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:32,244] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:32,244] [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 weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	100.0	1296	1299	95	conclusive
Clostridium uliginosum	strain=DSM 12992	GCA_900112485.1	119641	119641	type	True	82.5895	750	1299	95	below_threshold
Clostridium cagae	strain=Marseille-P4344	GCA_900290265.1	2080751	2080751	type	True	82.0824	752	1299	95	below_threshold
Clostridium saccharobutylicum	strain=DSM 13864	GCA_000473995.1	169679	169679	type	True	79.1175	523	1299	95	below_threshold
Clostridium saccharobutylicum	strain=DSM 13864	GCA_001657435.1	169679	169679	type	True	79.0845	488	1299	95	below_threshold
Clostridium gelidum	strain=C5S11	GCA_019977655.1	704125	704125	type	True	78.8546	528	1299	95	below_threshold
Clostridium saccharoperbutylacetonicum	strain=ATCC 27021	GCA_000334435.1	36745	36745	type	True	78.5592	504	1299	95	below_threshold
Clostridium saccharoperbutylacetonicum	strain=N1-4(HMT)	GCA_000340885.1	36745	36745	type	True	78.5397	520	1299	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_018223745.1	1520	1520	suspected-type	True	78.4424	461	1299	95	below_threshold
Clostridium neonatale	strain=LCDC 99A005	GCA_002553615.1	137838	137838	type	True	78.1657	440	1299	95	below_threshold
Clostridium neonatale	strain=LCDC no.99-A-005	GCA_001458595.1	137838	137838	type	True	78.162	440	1299	95	below_threshold
Clostridium cibarium	strain=Sa3CVN1	GCA_014836335.1	2762247	2762247	type	True	77.6323	279	1299	95	below_threshold
Clostridium moniliforme	strain=DSM 3984	GCA_017873235.1	39489	39489	type	True	77.6042	302	1299	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	77.274	293	1299	95	below_threshold
Clostridium celatum	strain=DSM 1785	GCA_000320405.1	36834	36834	type	True	77.1049	277	1299	95	below_threshold
Clostridium chrysemydis	strain=PT	GCA_015234215.1	2665504	2665504	type	True	76.9138	248	1299	95	below_threshold
Clostridium simiarum	strain=MSJ-4	GCA_018919175.1	2841506	2841506	type	True	76.573	151	1299	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:32,247] [INFO] DFAST Taxonomy check result was written to GCF_019431045.1_ASM1943104v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:32,247] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:32,247] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:32,248] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2d3d30e-a072-48b9-91ef-a09960dcb395/dqc_reference/checkm_data
[2024-01-24 12:37:32,249] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:32,289] [INFO] Task started: CheckM
[2024-01-24 12:37:32,289] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019431045.1_ASM1943104v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019431045.1_ASM1943104v1_genomic.fna/checkm_input GCF_019431045.1_ASM1943104v1_genomic.fna/checkm_result
[2024-01-24 12:37:55,783] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:55,785] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:55,809] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:55,809] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:55,810] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019431045.1_ASM1943104v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:55,810] [INFO] Task started: Blastn
[2024-01-24 12:37:55,810] [INFO] Running command: blastn -query GCF_019431045.1_ASM1943104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2d3d30e-a072-48b9-91ef-a09960dcb395/dqc_reference/reference_markers_gtdb.fasta -out GCF_019431045.1_ASM1943104v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:56,609] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:56,614] [INFO] Selected 17 target genomes.
[2024-01-24 12:37:56,614] [INFO] Target genome list was writen to GCF_019431045.1_ASM1943104v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:56,631] [INFO] Task started: fastANI
[2024-01-24 12:37:56,631] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e80df42-436d-4a1c-869b-638d703b804f/GCF_019431045.1_ASM1943104v1_genomic.fna.gz --refList GCF_019431045.1_ASM1943104v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019431045.1_ASM1943104v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:10,910] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:10,932] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:38:10,932] [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_900112485.1	s__Clostridium uliginosum	82.5321	755	1299	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_001735765.2	s__Clostridium taeniosporum	82.272	791	1299	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_900290265.1	s__Clostridium cagae	82.0699	753	1299	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.09	97.56	0.90	0.85	15	-
GCF_000827935.1	s__Clostridium botulinum_A	81.5526	737	1299	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.05	97.92	0.91	0.85	31	-
GCF_000473995.1	s__Clostridium saccharobutylicum	79.0991	525	1299	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.89	95.82	0.99	0.83	65	-
GCA_003129525.1	s__Clostridium beijerinckii_D	78.8922	500	1299	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_015058475.1	s__Clostridium butyricum_B	78.8377	346	1299	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_015058525.1	s__Clostridium butyricum_A	78.6226	281	1299	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_009928485.1	s__Clostridium sp009928485	78.595	468	1299	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_000340885.1	s__Clostridium saccharoperbutylacetonicum	78.5458	518	1299	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.35	98.00	0.96	0.89	7	-
GCF_018223745.1	s__Clostridium beijerinckii	78.4601	460	1299	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.01	95.18	0.85	0.79	244	-
GCF_000230835.1	s__Clostridium sp000230835	78.429	462	1299	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	96.12	96.12	0.82	0.82	2	-
GCF_001458595.1	s__Clostridium neonatale	78.1553	440	1299	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.07	98.42	0.91	0.80	11	-
GCF_007115085.1	s__Clostridium sp007115085	77.5884	286	1299	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_900547475.1	s__Clostridium sp900547475	77.3624	285	1299	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	96.47	95.30	0.88	0.84	3	-
GCF_000401215.1	s__Clostridium sartagoforme_A	77.1062	311	1299	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.25	98.25	0.85	0.85	2	-
GCF_001405015.1	s__Clostridium disporicum	77.0868	258	1299	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.24	98.87	0.93	0.88	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:10,934] [INFO] GTDB search result was written to GCF_019431045.1_ASM1943104v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:10,934] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:10,938] [INFO] DFAST_QC result json was written to GCF_019431045.1_ASM1943104v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:10,939] [INFO] DFAST_QC completed!
[2024-01-24 12:38:10,939] [INFO] Total running time: 0h1m2s