[2024-01-24 13:01:49,665] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:49,667] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:49,667] [INFO] DQC Reference Directory: /var/lib/cwl/stg9151e089-a1e3-47dd-ad5e-2f02c700d018/dqc_reference
[2024-01-24 13:01:51,050] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:51,051] [INFO] Task started: Prodigal
[2024-01-24 13:01:51,051] [INFO] Running command: gunzip -c /var/lib/cwl/stg98880388-40a9-49bc-89e0-9101cdfc0140/GCF_002006345.1_ASM200634v1_genomic.fna.gz | prodigal -d GCF_002006345.1_ASM200634v1_genomic.fna/cds.fna -a GCF_002006345.1_ASM200634v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:00,032] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:00,032] [INFO] Task started: HMMsearch
[2024-01-24 13:02:00,032] [INFO] Running command: hmmsearch --tblout GCF_002006345.1_ASM200634v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9151e089-a1e3-47dd-ad5e-2f02c700d018/dqc_reference/reference_markers.hmm GCF_002006345.1_ASM200634v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:00,545] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:00,549] [INFO] Found 6/6 markers.
[2024-01-24 13:02:00,611] [INFO] Query marker FASTA was written to GCF_002006345.1_ASM200634v1_genomic.fna/markers.fasta
[2024-01-24 13:02:00,611] [INFO] Task started: Blastn
[2024-01-24 13:02:00,611] [INFO] Running command: blastn -query GCF_002006345.1_ASM200634v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9151e089-a1e3-47dd-ad5e-2f02c700d018/dqc_reference/reference_markers.fasta -out GCF_002006345.1_ASM200634v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:01,514] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:01,518] [INFO] Selected 20 target genomes.
[2024-01-24 13:02:01,518] [INFO] Target genome list was writen to GCF_002006345.1_ASM200634v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:01,526] [INFO] Task started: fastANI
[2024-01-24 13:02:01,526] [INFO] Running command: fastANI --query /var/lib/cwl/stg98880388-40a9-49bc-89e0-9101cdfc0140/GCF_002006345.1_ASM200634v1_genomic.fna.gz --refList GCF_002006345.1_ASM200634v1_genomic.fna/target_genomes.txt --output GCF_002006345.1_ASM200634v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:23,267] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:23,268] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9151e089-a1e3-47dd-ad5e-2f02c700d018/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:23,268] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9151e089-a1e3-47dd-ad5e-2f02c700d018/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:23,285] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:23,285] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:23,285] [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 puniceum	strain=DSM 2619	GCA_002006345.1	29367	29367	type	True	100.0	1897	1910	95	conclusive
Clostridium gelidum	strain=C5S11	GCA_019977655.1	704125	704125	type	True	83.5811	1027	1910	95	below_threshold
Clostridium chromiireducens	strain=DSM 23318	GCA_002029255.1	225345	225345	type	True	81.1991	821	1910	95	below_threshold
Clostridium saccharoperbutylacetonicum	strain=N1-4(HMT)	GCA_000340885.1	36745	36745	type	True	81.0404	995	1910	95	below_threshold
Clostridium saccharoperbutylacetonicum	strain=ATCC 27021	GCA_000334435.1	36745	36745	type	True	80.9822	961	1910	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_018223745.1	1520	1520	suspected-type	True	80.9521	842	1910	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_002006445.1	1520	1520	suspected-type	True	80.9015	812	1910	95	below_threshold
Clostridium saccharobutylicum	strain=DSM 13864	GCA_000473995.1	169679	169679	type	True	80.811	777	1910	95	below_threshold
Clostridium saccharobutylicum	strain=DSM 13864	GCA_001657435.1	169679	169679	type	True	80.7185	712	1910	95	below_threshold
Clostridium uliginosum	strain=DSM 12992	GCA_900112485.1	119641	119641	type	True	79.5237	550	1910	95	below_threshold
Clostridium butyricum	strain=NBRC 13949	GCA_007992895.1	1492	1492	type	True	78.7361	511	1910	95	below_threshold
Clostridium butyricum	strain=DSM 10702	GCA_000409755.1	1492	1492	type	True	78.6485	496	1910	95	below_threshold
Clostridium cagae	strain=Marseille-P4344	GCA_900290265.1	2080751	2080751	type	True	78.6461	455	1910	95	below_threshold
Clostridium cibarium	strain=Sa3CVN1	GCA_014836335.1	2762247	2762247	type	True	77.7769	353	1910	95	below_threshold
Clostridium thermopalmarium	strain=DSM 5974	GCA_002995795.1	29373	29373	suspected-type	True	76.272	106	1910	95	below_threshold
Clostridium thermopalmarium	strain=DSM 5974	GCA_003097175.1	29373	29373	suspected-type	True	76.2076	108	1910	95	below_threshold
Clostridium autoethanogenum	strain=DSM 10061	GCA_000484505.2	84023	84023	suspected-type	True	76.1768	126	1910	95	below_threshold
Haloimpatiens massiliensis	strain=Mt13	GCA_900184255.1	1658110	1658110	type	True	75.9577	156	1910	95	below_threshold
Clostridium fermenticellae	strain=JN500901	GCA_003600355.1	2068654	2068654	type	True	75.9485	102	1910	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	74.6146	65	1910	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:23,289] [INFO] DFAST Taxonomy check result was written to GCF_002006345.1_ASM200634v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:23,291] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:23,292] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:23,292] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9151e089-a1e3-47dd-ad5e-2f02c700d018/dqc_reference/checkm_data
[2024-01-24 13:02:23,293] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:23,359] [INFO] Task started: CheckM
[2024-01-24 13:02:23,360] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002006345.1_ASM200634v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002006345.1_ASM200634v1_genomic.fna/checkm_input GCF_002006345.1_ASM200634v1_genomic.fna/checkm_result
[2024-01-24 13:02:56,899] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:56,900] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:56,926] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:56,927] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:56,927] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002006345.1_ASM200634v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:56,928] [INFO] Task started: Blastn
[2024-01-24 13:02:56,928] [INFO] Running command: blastn -query GCF_002006345.1_ASM200634v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9151e089-a1e3-47dd-ad5e-2f02c700d018/dqc_reference/reference_markers_gtdb.fasta -out GCF_002006345.1_ASM200634v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:57,796] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:57,799] [INFO] Selected 17 target genomes.
[2024-01-24 13:02:57,800] [INFO] Target genome list was writen to GCF_002006345.1_ASM200634v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:57,815] [INFO] Task started: fastANI
[2024-01-24 13:02:57,816] [INFO] Running command: fastANI --query /var/lib/cwl/stg98880388-40a9-49bc-89e0-9101cdfc0140/GCF_002006345.1_ASM200634v1_genomic.fna.gz --refList GCF_002006345.1_ASM200634v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002006345.1_ASM200634v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:16,270] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:16,288] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:16,289] [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_002006345.1	s__Clostridium puniceum	100.0	1897	1910	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009928485.1	s__Clostridium sp009928485	83.6402	1100	1910	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	83.3562	823	1910	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_002029255.1	s__Clostridium chromiireducens	81.1796	822	1910	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_000340885.1	s__Clostridium saccharoperbutylacetonicum	81.0237	998	1910	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	80.9651	836	1910	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_002760435.1	s__Clostridium sp002760435	80.9466	840	1910	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_000230835.1	s__Clostridium sp000230835	80.8265	860	1910	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_000473995.1	s__Clostridium saccharobutylicum	80.7921	779	1910	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_000621745.1	s__Clostridium beijerinckii_A	80.6967	859	1910	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	79.4961	553	1910	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_006742065.1	s__Clostridium butyricum	78.8722	513	1910	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.58	97.46	0.89	0.80	64	-
GCF_001458595.1	s__Clostridium neonatale	78.7058	532	1910	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_900290265.1	s__Clostridium cagae	78.6752	449	1910	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	78.4856	430	1910	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_001735765.2	s__Clostridium taeniosporum	78.3428	429	1910	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_017888745.1	s__Terrisporobacter sp017888745	74.926	95	1910	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:16,290] [INFO] GTDB search result was written to GCF_002006345.1_ASM200634v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:16,291] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:16,295] [INFO] DFAST_QC result json was written to GCF_002006345.1_ASM200634v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:16,295] [INFO] DFAST_QC completed!
[2024-01-24 13:03:16,295] [INFO] Total running time: 0h1m27s