[2024-01-25 20:22:05,872] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:22:05,879] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:22:05,879] [INFO] DQC Reference Directory: /var/lib/cwl/stgd316482f-a196-4066-8873-45fc4b2bdaed/dqc_reference
[2024-01-25 20:22:07,100] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:22:07,101] [INFO] Task started: Prodigal
[2024-01-25 20:22:07,101] [INFO] Running command: gunzip -c /var/lib/cwl/stg766422dd-e1aa-4462-b29d-80a997ced492/GCF_021432385.1_ASM2143238v1_genomic.fna.gz | prodigal -d GCF_021432385.1_ASM2143238v1_genomic.fna/cds.fna -a GCF_021432385.1_ASM2143238v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:22:15,430] [INFO] Task succeeded: Prodigal
[2024-01-25 20:22:15,430] [INFO] Task started: HMMsearch
[2024-01-25 20:22:15,430] [INFO] Running command: hmmsearch --tblout GCF_021432385.1_ASM2143238v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd316482f-a196-4066-8873-45fc4b2bdaed/dqc_reference/reference_markers.hmm GCF_021432385.1_ASM2143238v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:22:15,724] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:22:15,725] [INFO] Found 6/6 markers.
[2024-01-25 20:22:15,768] [INFO] Query marker FASTA was written to GCF_021432385.1_ASM2143238v1_genomic.fna/markers.fasta
[2024-01-25 20:22:15,768] [INFO] Task started: Blastn
[2024-01-25 20:22:15,768] [INFO] Running command: blastn -query GCF_021432385.1_ASM2143238v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd316482f-a196-4066-8873-45fc4b2bdaed/dqc_reference/reference_markers.fasta -out GCF_021432385.1_ASM2143238v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:16,319] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:16,322] [INFO] Selected 15 target genomes.
[2024-01-25 20:22:16,322] [INFO] Target genome list was writen to GCF_021432385.1_ASM2143238v1_genomic.fna/target_genomes.txt
[2024-01-25 20:22:16,327] [INFO] Task started: fastANI
[2024-01-25 20:22:16,327] [INFO] Running command: fastANI --query /var/lib/cwl/stg766422dd-e1aa-4462-b29d-80a997ced492/GCF_021432385.1_ASM2143238v1_genomic.fna.gz --refList GCF_021432385.1_ASM2143238v1_genomic.fna/target_genomes.txt --output GCF_021432385.1_ASM2143238v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:22:37,371] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:37,371] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd316482f-a196-4066-8873-45fc4b2bdaed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:22:37,372] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd316482f-a196-4066-8873-45fc4b2bdaed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:22:37,380] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:22:37,380] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:22:37,381] [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 hydrogenum	strain=CUEA01	GCA_021432385.1	2855764	2855764	type	True	100.0	1830	1832	95	conclusive
Clostridium felsineum	strain=DSM 7320	GCA_002006215.2	36839	36839	type	True	78.3188	393	1832	95	below_threshold
Clostridium acetobutylicum	strain=ATCC 824	GCA_000008765.1	1488	1488	type	True	78.2696	308	1832	95	below_threshold
Clostridium felsineum	strain=DSM 793	GCA_002006235.2	36839	36839	type	True	78.1997	396	1832	95	below_threshold
Clostridium felsineum	strain=DSM 794	GCA_002006355.2	36839	36839	type	True	78.0611	375	1832	95	below_threshold
Clostridium pasteurianum	strain=DSM 525	GCA_000807255.1	1501	1501	type	True	77.2549	212	1832	95	below_threshold
Clostridium arbusti	strain=SL206	GCA_000246895.2	1137848	1137848	type	True	76.6044	202	1832	95	below_threshold
Clostridium prolinivorans	strain=PYR-10	GCA_004011155.1	2769420	2769420	type	True	76.0087	176	1832	95	below_threshold
Clostridium cavendishii	strain=DSM 21758	GCA_900141845.1	349931	349931	type	True	75.9952	203	1832	95	below_threshold
Clostridium tetanomorphum	strain=DSM 4474	GCA_017873215.1	1553	1553	type	True	75.9452	186	1832	95	below_threshold
Clostridium tertium	strain=DSM 2485	GCA_017873245.1	1559	1559	type	True	75.8057	151	1832	95	below_threshold
Clostridium chrysemydis	strain=PT	GCA_015234215.1	2665504	2665504	type	True	75.7921	123	1832	95	below_threshold
Clostridium collagenovorans	strain=DSM 3089	GCA_900130005.1	29357	29357	type	True	75.7744	110	1832	95	below_threshold
Clostridium faecium	strain=N37	GCA_014836835.1	2762223	2762223	type	True	75.7397	152	1832	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:22:37,382] [INFO] DFAST Taxonomy check result was written to GCF_021432385.1_ASM2143238v1_genomic.fna/tc_result.tsv
[2024-01-25 20:22:37,383] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:22:37,383] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:22:37,383] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd316482f-a196-4066-8873-45fc4b2bdaed/dqc_reference/checkm_data
[2024-01-25 20:22:37,384] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:22:37,435] [INFO] Task started: CheckM
[2024-01-25 20:22:37,436] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021432385.1_ASM2143238v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021432385.1_ASM2143238v1_genomic.fna/checkm_input GCF_021432385.1_ASM2143238v1_genomic.fna/checkm_result
[2024-01-25 20:23:06,275] [INFO] Task succeeded: CheckM
[2024-01-25 20:23:06,275] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:23:06,301] [INFO] ===== Completeness check finished =====
[2024-01-25 20:23:06,301] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:23:06,302] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021432385.1_ASM2143238v1_genomic.fna/markers.fasta)
[2024-01-25 20:23:06,302] [INFO] Task started: Blastn
[2024-01-25 20:23:06,302] [INFO] Running command: blastn -query GCF_021432385.1_ASM2143238v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd316482f-a196-4066-8873-45fc4b2bdaed/dqc_reference/reference_markers_gtdb.fasta -out GCF_021432385.1_ASM2143238v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:07,118] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:07,120] [INFO] Selected 27 target genomes.
[2024-01-25 20:23:07,121] [INFO] Target genome list was writen to GCF_021432385.1_ASM2143238v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:23:07,142] [INFO] Task started: fastANI
[2024-01-25 20:23:07,142] [INFO] Running command: fastANI --query /var/lib/cwl/stg766422dd-e1aa-4462-b29d-80a997ced492/GCF_021432385.1_ASM2143238v1_genomic.fna.gz --refList GCF_021432385.1_ASM2143238v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021432385.1_ASM2143238v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:23:29,451] [INFO] Task succeeded: fastANI
[2024-01-25 20:23:29,466] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:23:29,466] [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_001270375.1	s__Clostridium_S sp001270375	80.0924	619	1832	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_S	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001705235.1	s__Clostridium_S pasteurianum_A	79.1611	487	1832	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_S	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000008765.1	s__Clostridium_S acetobutylicum	78.3769	311	1832	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_S	95.0	99.88	98.04	0.99	0.94	19	-
GCF_002006355.1	s__Clostridium_S felsineum	77.7399	369	1832	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_S	95.0	98.29	98.24	0.88	0.87	4	-
GCF_001038625.1	s__Clostridium_AM carboxidivorans	77.6164	290	1832	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	95.0	99.97	99.96	1.00	0.99	3	-
GCF_000389635.1	s__Clostridium_I pasteurianum_A	77.2206	219	1832	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000807255.1	s__Clostridium_I pasteurianum	77.1926	208	1832	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_I	95.0	99.98	99.90	1.00	0.99	7	-
GCF_000230835.1	s__Clostridium sp000230835	76.9175	249	1832	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_000744935.1	s__Haloimpatiens sp000744935	76.9005	158	1832	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Haloimpatiens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000633595.2	s__Clostridium_AM drakei	76.6594	274	1832	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	-
GCF_000246895.1	s__Clostridium_I arbusti	76.6039	202	1832	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901447495.1	s__Haloimpatiens lingqiaonensis	76.3863	137	1832	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Haloimpatiens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765615.1	s__Clostridium_T sp016765615	76.2867	144	1832	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_T	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012843905.1	s__Clostridium sp012843905	76.2015	134	1832	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_002934235.1	s__Clostridium_L algidicarnis	76.1674	105	1832	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_L	95.0	97.66	96.15	0.89	0.86	14	-
GCA_902363375.1	s__Clostridium_J sp902363375	76.0186	107	1832	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141845.1	s__Clostridium_AG cavendishii	76.0182	200	1832	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AG	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167505.1	s__F0540 sp900167505	75.9185	187	1832	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__F0540	95.0	98.87	98.87	0.90	0.90	2	-
GCF_000498355.1	s__Clostridium sp000498355	75.9083	168	1832	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_000612845.1	s__Clostridium_J ihumii	75.8123	172	1832	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	100.00	100.00	0.99	0.99	2	-
GCF_015234215.1	s__Clostridium sp015234215	75.8028	122	1832	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_004794105.1	s__Clostridium sartagoforme_B	75.751	135	1832	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.58	98.58	0.90	0.90	2	-
GCF_014836835.1	s__Clostridium_J sp900547625	75.7478	151	1832	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	99.59	99.59	0.89	0.87	3	-
GCF_900130005.1	s__Clostridium_D collagenovorans	75.6988	107	1832	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018372555.1	s__Clostridium sp018372555	75.4425	104	1832	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_001915995.1	s__CAG-269 sp001915995	74.9601	54	1832	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003525075.1	s__CAG-269 sp003525075	74.835	63	1832	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	99.02	98.89	0.90	0.88	5	-
--------------------------------------------------------------------------------
[2024-01-25 20:23:29,468] [INFO] GTDB search result was written to GCF_021432385.1_ASM2143238v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:23:29,468] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:23:29,472] [INFO] DFAST_QC result json was written to GCF_021432385.1_ASM2143238v1_genomic.fna/dqc_result.json
[2024-01-25 20:23:29,472] [INFO] DFAST_QC completed!
[2024-01-25 20:23:29,472] [INFO] Total running time: 0h1m24s