[2024-01-24 13:27:41,472] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:41,474] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:41,474] [INFO] DQC Reference Directory: /var/lib/cwl/stg3643da92-6126-463c-bb10-eb98dc11592f/dqc_reference
[2024-01-24 13:27:42,670] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:42,671] [INFO] Task started: Prodigal
[2024-01-24 13:27:42,671] [INFO] Running command: gunzip -c /var/lib/cwl/stg448e13f2-e5bb-4628-aa48-cf661ef62248/GCF_000334435.1_CloSac1.0_genomic.fna.gz | prodigal -d GCF_000334435.1_CloSac1.0_genomic.fna/cds.fna -a GCF_000334435.1_CloSac1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:27:52,638] [INFO] Task succeeded: Prodigal
[2024-01-24 13:27:52,638] [INFO] Task started: HMMsearch
[2024-01-24 13:27:52,638] [INFO] Running command: hmmsearch --tblout GCF_000334435.1_CloSac1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3643da92-6126-463c-bb10-eb98dc11592f/dqc_reference/reference_markers.hmm GCF_000334435.1_CloSac1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:27:52,994] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:27:52,995] [INFO] Found 6/6 markers.
[2024-01-24 13:27:53,048] [INFO] Query marker FASTA was written to GCF_000334435.1_CloSac1.0_genomic.fna/markers.fasta
[2024-01-24 13:27:53,048] [INFO] Task started: Blastn
[2024-01-24 13:27:53,048] [INFO] Running command: blastn -query GCF_000334435.1_CloSac1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg3643da92-6126-463c-bb10-eb98dc11592f/dqc_reference/reference_markers.fasta -out GCF_000334435.1_CloSac1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:53,643] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:53,646] [INFO] Selected 17 target genomes.
[2024-01-24 13:27:53,647] [INFO] Target genome list was writen to GCF_000334435.1_CloSac1.0_genomic.fna/target_genomes.txt
[2024-01-24 13:27:53,700] [INFO] Task started: fastANI
[2024-01-24 13:27:53,700] [INFO] Running command: fastANI --query /var/lib/cwl/stg448e13f2-e5bb-4628-aa48-cf661ef62248/GCF_000334435.1_CloSac1.0_genomic.fna.gz --refList GCF_000334435.1_CloSac1.0_genomic.fna/target_genomes.txt --output GCF_000334435.1_CloSac1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:16,073] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:16,073] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3643da92-6126-463c-bb10-eb98dc11592f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:16,074] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3643da92-6126-463c-bb10-eb98dc11592f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:16,089] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:28:16,089] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:16,089] [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 saccharoperbutylacetonicum	strain=ATCC 27021	GCA_000334435.1	36745	36745	type	True	100.0	2085	2097	95	conclusive
Clostridium saccharoperbutylacetonicum	strain=N1-4(HMT)	GCA_000340885.1	36745	36745	type	True	99.9929	2096	2097	95	conclusive
Clostridium puniceum	strain=DSM 2619	GCA_002006345.1	29367	29367	type	True	81.0016	968	2097	95	below_threshold
Clostridium gelidum	strain=C5S11	GCA_019977655.1	704125	704125	type	True	80.8277	923	2097	95	below_threshold
Clostridium diolis	strain=DSM 15410	GCA_008705175.1	223919	223919	suspected-type	True	80.7972	918	2097	95	below_threshold
Clostridium beijerinckii	strain=NCTC13035	GCA_900447025.1	1520	1520	suspected-type	True	80.7225	894	2097	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_018223745.1	1520	1520	suspected-type	True	80.6825	898	2097	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_002006445.1	1520	1520	suspected-type	True	80.6806	860	2097	95	below_threshold
Clostridium chromiireducens	strain=DSM 23318	GCA_002029255.1	225345	225345	type	True	80.6617	830	2097	95	below_threshold
Clostridium saccharobutylicum	strain=DSM 13864	GCA_000473995.1	169679	169679	type	True	80.0771	730	2097	95	below_threshold
Clostridium saccharobutylicum	strain=DSM 13864	GCA_001657435.1	169679	169679	type	True	80.0588	674	2097	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	78.7241	495	2097	95	below_threshold
Clostridium zeae	strain=CSC2	GCA_017312485.1	2759022	2759022	type	True	76.8062	253	2097	95	below_threshold
Clostridium mobile	strain=MSJ-11	GCA_018918285.1	2841512	2841512	type	True	75.9253	132	2097	95	below_threshold
Anaerovirgula multivorans	strain=SCA	GCA_900188145.1	312168	312168	type	True	75.0872	62	2097	95	below_threshold
Malaciobacter canalis	strain=F138-33	GCA_002723485.1	1912871	1912871	type	True	74.6274	67	2097	95	below_threshold
Malaciobacter canalis	strain=LMG 29148	GCA_008000835.1	1912871	1912871	type	True	74.6227	68	2097	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:16,091] [INFO] DFAST Taxonomy check result was written to GCF_000334435.1_CloSac1.0_genomic.fna/tc_result.tsv
[2024-01-24 13:28:16,091] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:16,091] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:16,092] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3643da92-6126-463c-bb10-eb98dc11592f/dqc_reference/checkm_data
[2024-01-24 13:28:16,092] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:16,157] [INFO] Task started: CheckM
[2024-01-24 13:28:16,157] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000334435.1_CloSac1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000334435.1_CloSac1.0_genomic.fna/checkm_input GCF_000334435.1_CloSac1.0_genomic.fna/checkm_result
[2024-01-24 13:28:50,477] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:50,479] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:50,504] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:50,505] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:50,505] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000334435.1_CloSac1.0_genomic.fna/markers.fasta)
[2024-01-24 13:28:50,506] [INFO] Task started: Blastn
[2024-01-24 13:28:50,506] [INFO] Running command: blastn -query GCF_000334435.1_CloSac1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg3643da92-6126-463c-bb10-eb98dc11592f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000334435.1_CloSac1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:51,248] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:51,253] [INFO] Selected 16 target genomes.
[2024-01-24 13:28:51,253] [INFO] Target genome list was writen to GCF_000334435.1_CloSac1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:51,345] [INFO] Task started: fastANI
[2024-01-24 13:28:51,345] [INFO] Running command: fastANI --query /var/lib/cwl/stg448e13f2-e5bb-4628-aa48-cf661ef62248/GCF_000334435.1_CloSac1.0_genomic.fna.gz --refList GCF_000334435.1_CloSac1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000334435.1_CloSac1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:15,101] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:15,117] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:15,117] [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_000340885.1	s__Clostridium saccharoperbutylacetonicum	99.9929	2096	2097	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.35	98.00	0.96	0.89	7	conclusive
GCF_009928485.1	s__Clostridium sp009928485	81.1241	949	2097	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_002006345.1	s__Clostridium puniceum	80.9928	969	2097	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_000621745.1	s__Clostridium beijerinckii_A	80.9266	873	2097	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	80.7796	709	2097	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_000230835.1	s__Clostridium sp000230835	80.7654	942	2097	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_018223745.1	s__Clostridium beijerinckii	80.69	899	2097	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_002029255.1	s__Clostridium chromiireducens	80.6774	827	2097	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.07	97.40	0.90	0.87	3	-
GCF_002760435.1	s__Clostridium sp002760435	80.4977	844	2097	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_000473995.1	s__Clostridium saccharobutylicum	80.116	724	2097	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.89	95.82	0.99	0.83	65	-
GCF_012843905.1	s__Clostridium sp012843905	78.5069	387	2097	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_003539755.1	s__Clostridium sp003539755	77.9892	307	2097	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_900129365.1	s__Clostridium_AH fallax	76.7876	198	2097	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AH	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018918285.1	s__MSJ-11 sp018918285	75.9253	132	2097	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__MSJ-11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188145.1	s__Anaerovirgula multivorans	75.0872	62	2097	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Anaerovirgula	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:15,119] [INFO] GTDB search result was written to GCF_000334435.1_CloSac1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:15,120] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:15,123] [INFO] DFAST_QC result json was written to GCF_000334435.1_CloSac1.0_genomic.fna/dqc_result.json
[2024-01-24 13:29:15,124] [INFO] DFAST_QC completed!
[2024-01-24 13:29:15,124] [INFO] Total running time: 0h1m34s