[2024-01-24 14:39:45,823] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:45,825] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:45,825] [INFO] DQC Reference Directory: /var/lib/cwl/stgc19f80a7-900d-49eb-bc8a-a76e7fe4829a/dqc_reference
[2024-01-24 14:39:48,364] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:48,365] [INFO] Task started: Prodigal
[2024-01-24 14:39:48,365] [INFO] Running command: gunzip -c /var/lib/cwl/stg44d099f9-700a-412c-bfae-1d84d7b5634e/GCF_900447045.1_52087_F01_genomic.fna.gz | prodigal -d GCF_900447045.1_52087_F01_genomic.fna/cds.fna -a GCF_900447045.1_52087_F01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:53,891] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:53,891] [INFO] Task started: HMMsearch
[2024-01-24 14:39:53,891] [INFO] Running command: hmmsearch --tblout GCF_900447045.1_52087_F01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc19f80a7-900d-49eb-bc8a-a76e7fe4829a/dqc_reference/reference_markers.hmm GCF_900447045.1_52087_F01_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:54,220] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:54,222] [INFO] Found 6/6 markers.
[2024-01-24 14:39:54,257] [INFO] Query marker FASTA was written to GCF_900447045.1_52087_F01_genomic.fna/markers.fasta
[2024-01-24 14:39:54,258] [INFO] Task started: Blastn
[2024-01-24 14:39:54,258] [INFO] Running command: blastn -query GCF_900447045.1_52087_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stgc19f80a7-900d-49eb-bc8a-a76e7fe4829a/dqc_reference/reference_markers.fasta -out GCF_900447045.1_52087_F01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:54,915] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:54,921] [INFO] Selected 27 target genomes.
[2024-01-24 14:39:54,922] [INFO] Target genome list was writen to GCF_900447045.1_52087_F01_genomic.fna/target_genomes.txt
[2024-01-24 14:39:54,940] [INFO] Task started: fastANI
[2024-01-24 14:39:54,940] [INFO] Running command: fastANI --query /var/lib/cwl/stg44d099f9-700a-412c-bfae-1d84d7b5634e/GCF_900447045.1_52087_F01_genomic.fna.gz --refList GCF_900447045.1_52087_F01_genomic.fna/target_genomes.txt --output GCF_900447045.1_52087_F01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:13,903] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:13,904] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc19f80a7-900d-49eb-bc8a-a76e7fe4829a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:13,905] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc19f80a7-900d-49eb-bc8a-a76e7fe4829a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:13,935] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:40:13,935] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:13,936] [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 paraputrificum	strain=NCTC11833	GCA_900447045.1	29363	29363	type	True	100.0	1201	1202	95	conclusive
Clostridium chauvoei	strain=DSM 7528	GCA_002327185.1	46867	46867	type	True	78.5211	261	1202	95	below_threshold
Clostridium cibarium	strain=Sa3CVN1	GCA_014836335.1	2762247	2762247	type	True	78.4942	300	1202	95	below_threshold
Clostridium septicum	strain=FDAARGOS_1551	GCA_020736665.1	1504	1504	type	True	78.4785	259	1202	95	below_threshold
Clostridium isatidis	strain=DSM 15098	GCA_002285495.1	182773	182773	type	True	78.3428	202	1202	95	below_threshold
Clostridium perfringens	strain=ATCC 13124	GCA_000013285.1	1502	1502	type	True	78.3227	205	1202	95	below_threshold
Clostridium neonatale	strain=LCDC 99A005	GCA_002553615.1	137838	137838	type	True	78.262	269	1202	95	below_threshold
Clostridium saccharoperbutylacetonicum	strain=N1-4(HMT)	GCA_000340885.1	36745	36745	type	True	78.2176	236	1202	95	below_threshold
Clostridium tertium	strain=DSM 2485	GCA_017873245.1	1559	1559	type	True	77.9155	311	1202	95	below_threshold
Clostridium saudiense	strain=JCC	GCA_000577815.1	1414720	1414720	type	True	77.8619	258	1202	95	below_threshold
Clostridium thermobutyricum	strain=DSM 4928	GCA_002050515.1	29372	29372	type	True	77.8318	266	1202	95	below_threshold
Clostridium celatum	strain=DSM 1785	GCA_000320405.1	36834	36834	type	True	77.8112	256	1202	95	below_threshold
Clostridium uliginosum	strain=DSM 12992	GCA_900112485.1	119641	119641	type	True	77.7818	240	1202	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	77.7374	272	1202	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	77.7249	251	1202	95	below_threshold
Clostridium vincentii	strain=DSM 10228	GCA_002995745.1	52704	52704	type	True	77.6339	257	1202	95	below_threshold
Clostridium autoethanogenum	strain=DSM 10061	GCA_000484505.2	84023	84023	suspected-type	True	77.4515	76	1202	95	below_threshold
Clostridium saccharoperbutylacetonicum	strain=ATCC 27021	GCA_000334435.1	36745	36745	type	True	77.3807	228	1202	95	below_threshold
Clostridium chrysemydis	strain=PT	GCA_015234215.1	2665504	2665504	type	True	77.2768	224	1202	95	below_threshold
Clostridium puniceum	strain=DSM 2619	GCA_002006345.1	29367	29367	type	True	77.2355	254	1202	95	below_threshold
Clostridium zeae	strain=CSC2	GCA_017312485.1	2759022	2759022	type	True	77.1205	166	1202	95	below_threshold
Clostridium tarantellae	strain=DSM 3997	GCA_009295725.1	39493	39493	type	True	77.1101	187	1202	95	below_threshold
Clostridium intestinale	strain=DSM 6191	GCA_900130055.1	36845	36845	type	True	77.0652	183	1202	95	below_threshold
Clostridium massiliodielmoense	strain=MT26	GCA_900176615.1	1776385	1776385	type	True	76.708	112	1202	95	below_threshold
Clostridium simiarum	strain=MSJ-4	GCA_018919175.1	2841506	2841506	type	True	76.5815	115	1202	95	below_threshold
Clostridium thailandense	strain=PL3	GCA_019207025.1	2794346	2794346	type	True	75.8051	114	1202	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:13,938] [INFO] DFAST Taxonomy check result was written to GCF_900447045.1_52087_F01_genomic.fna/tc_result.tsv
[2024-01-24 14:40:13,939] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:13,939] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:13,939] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc19f80a7-900d-49eb-bc8a-a76e7fe4829a/dqc_reference/checkm_data
[2024-01-24 14:40:13,941] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:13,988] [INFO] Task started: CheckM
[2024-01-24 14:40:13,989] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900447045.1_52087_F01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900447045.1_52087_F01_genomic.fna/checkm_input GCF_900447045.1_52087_F01_genomic.fna/checkm_result
[2024-01-24 14:40:37,875] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:37,876] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:37,898] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:37,899] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:37,899] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900447045.1_52087_F01_genomic.fna/markers.fasta)
[2024-01-24 14:40:37,900] [INFO] Task started: Blastn
[2024-01-24 14:40:37,900] [INFO] Running command: blastn -query GCF_900447045.1_52087_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stgc19f80a7-900d-49eb-bc8a-a76e7fe4829a/dqc_reference/reference_markers_gtdb.fasta -out GCF_900447045.1_52087_F01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:38,702] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:38,705] [INFO] Selected 21 target genomes.
[2024-01-24 14:40:38,705] [INFO] Target genome list was writen to GCF_900447045.1_52087_F01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:38,723] [INFO] Task started: fastANI
[2024-01-24 14:40:38,723] [INFO] Running command: fastANI --query /var/lib/cwl/stg44d099f9-700a-412c-bfae-1d84d7b5634e/GCF_900447045.1_52087_F01_genomic.fna.gz --refList GCF_900447045.1_52087_F01_genomic.fna/target_genomes_gtdb.txt --output GCF_900447045.1_52087_F01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:52,179] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:52,204] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:52,204] [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_900447045.1	s__Clostridium paraputrificum	100.0	1201	1202	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.58	95.42	0.89	0.83	29	conclusive
GCA_018372875.1	s__Clostridium sp018372875	94.473	915	1202	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.91	98.91	0.87	0.87	2	-
GCF_002327185.1	s__Clostridium chauvoei	78.5462	262	1202	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.96	99.88	0.99	0.99	5	-
GCA_015058405.1	s__Clostridium sp015058405	78.5382	311	1202	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_003606265.1	s__Clostridium septicum	78.445	272	1202	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.65	99.48	0.94	0.92	5	-
GCF_900116755.1	s__Clostridium sp900116755	78.4411	285	1202	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	78.4301	291	1202	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.75	97.60	0.86	0.82	5	-
GCA_900539375.1	s__Clostridium sp900539375	78.4185	293	1202	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.09	99.02	0.89	0.86	4	-
GCF_007115085.1	s__Clostridium sp007115085	78.3419	309	1202	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	78.3258	264	1202	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_001405015.1	s__Clostridium disporicum	78.1835	235	1202	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.24	98.87	0.93	0.88	4	-
GCA_015058375.1	s__Clostridium sp015058375	78.0828	230	1202	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_003129525.1	s__Clostridium beijerinckii_D	78.0434	252	1202	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_902785295.1	s__Clostridium sp902785295	78.0093	251	1202	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_015555905.1	s__Clostridium sp015555905	77.9976	264	1202	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.95	98.95	0.73	0.73	2	-
GCA_015058525.1	s__Clostridium butyricum_A	77.8924	182	1202	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_900112485.1	s__Clostridium uliginosum	77.7798	241	1202	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_012519845.1	s__Clostridium sp012519845	77.6823	240	1202	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_002995745.1	s__Clostridium vincentii	77.628	260	1202	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_009295725.1	s__Clostridium_P tarantellae	77.0949	188	1202	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	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:52,206] [INFO] GTDB search result was written to GCF_900447045.1_52087_F01_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:52,207] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:52,215] [INFO] DFAST_QC result json was written to GCF_900447045.1_52087_F01_genomic.fna/dqc_result.json
[2024-01-24 14:40:52,216] [INFO] DFAST_QC completed!
[2024-01-24 14:40:52,216] [INFO] Total running time: 0h1m6s