[2024-01-24 11:19:55,055] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:19:55,059] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:19:55,059] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c0b0359-abda-4ae1-8bea-0b07ded57184/dqc_reference
[2024-01-24 11:19:56,508] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:19:56,509] [INFO] Task started: Prodigal
[2024-01-24 11:19:56,509] [INFO] Running command: gunzip -c /var/lib/cwl/stg19fc02c5-b8e8-4412-bcc5-3e9a5f847962/GCF_001458595.1_Clostridium_neonatale_genomic.fna.gz | prodigal -d GCF_001458595.1_Clostridium_neonatale_genomic.fna/cds.fna -a GCF_001458595.1_Clostridium_neonatale_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:04,022] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:04,023] [INFO] Task started: HMMsearch
[2024-01-24 11:20:04,023] [INFO] Running command: hmmsearch --tblout GCF_001458595.1_Clostridium_neonatale_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c0b0359-abda-4ae1-8bea-0b07ded57184/dqc_reference/reference_markers.hmm GCF_001458595.1_Clostridium_neonatale_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:04,370] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:04,371] [INFO] Found 6/6 markers.
[2024-01-24 11:20:04,411] [INFO] Query marker FASTA was written to GCF_001458595.1_Clostridium_neonatale_genomic.fna/markers.fasta
[2024-01-24 11:20:04,411] [INFO] Task started: Blastn
[2024-01-24 11:20:04,411] [INFO] Running command: blastn -query GCF_001458595.1_Clostridium_neonatale_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c0b0359-abda-4ae1-8bea-0b07ded57184/dqc_reference/reference_markers.fasta -out GCF_001458595.1_Clostridium_neonatale_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:05,019] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:05,022] [INFO] Selected 20 target genomes.
[2024-01-24 11:20:05,022] [INFO] Target genome list was writen to GCF_001458595.1_Clostridium_neonatale_genomic.fna/target_genomes.txt
[2024-01-24 11:20:05,030] [INFO] Task started: fastANI
[2024-01-24 11:20:05,031] [INFO] Running command: fastANI --query /var/lib/cwl/stg19fc02c5-b8e8-4412-bcc5-3e9a5f847962/GCF_001458595.1_Clostridium_neonatale_genomic.fna.gz --refList GCF_001458595.1_Clostridium_neonatale_genomic.fna/target_genomes.txt --output GCF_001458595.1_Clostridium_neonatale_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:23,519] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:23,520] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c0b0359-abda-4ae1-8bea-0b07ded57184/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:23,520] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c0b0359-abda-4ae1-8bea-0b07ded57184/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:23,538] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:20:23,538] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:23,538] [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 neonatale	strain=LCDC no.99-A-005	GCA_001458595.1	137838	137838	type	True	100.0	1563	1563	95	conclusive
Clostridium neonatale	strain=LCDC 99A005	GCA_002553615.1	137838	137838	type	True	99.9873	1554	1563	95	conclusive
Clostridium butyricum	strain=NBRC 13949	GCA_006742065.1	1492	1492	type	True	79.1074	568	1563	95	below_threshold
Clostridium butyricum	strain=NBRC 13949	GCA_007992895.1	1492	1492	type	True	79.0162	545	1563	95	below_threshold
Clostridium butyricum	strain=DSM 10702	GCA_000409755.1	1492	1492	type	True	78.9598	553	1563	95	below_threshold
Clostridium saccharobutylicum	strain=DSM 13864	GCA_000473995.1	169679	169679	type	True	78.8904	496	1563	95	below_threshold
Clostridium saccharobutylicum	strain=DSM 13864	GCA_001657435.1	169679	169679	type	True	78.8704	459	1563	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_018223745.1	1520	1520	suspected-type	True	78.7798	504	1563	95	below_threshold
Clostridium chromiireducens	strain=DSM 23318	GCA_002029255.1	225345	225345	type	True	78.6254	470	1563	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_002006445.1	1520	1520	suspected-type	True	78.6214	480	1563	95	below_threshold
Clostridium puniceum	strain=DSM 2619	GCA_002006345.1	29367	29367	type	True	78.4587	543	1563	95	below_threshold
Clostridium saccharoperbutylacetonicum	strain=N1-4(HMT)	GCA_000340885.1	36745	36745	type	True	78.3706	528	1563	95	below_threshold
Clostridium saccharoperbutylacetonicum	strain=ATCC 27021	GCA_000334435.1	36745	36745	type	True	78.3671	511	1563	95	below_threshold
Clostridium uliginosum	strain=DSM 12992	GCA_900112485.1	119641	119641	type	True	78.31	405	1563	95	below_threshold
Clostridium cagae	strain=Marseille-P4344	GCA_900290265.1	2080751	2080751	type	True	78.2642	423	1563	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	78.0644	452	1563	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	77.3627	272	1563	95	below_threshold
Clostridium nigeriense	strain=Marseille-P2414	GCA_900086595.1	1805470	1805470	type	True	77.1551	276	1563	95	below_threshold
Tepidibacter thalassicus	strain=DSM 15285	GCA_900129915.1	214905	214905	type	True	75.209	99	1563	95	below_threshold
Abyssisolibacter fermentans	strain=MCWD3	GCA_001559865.1	1766203	1766203	type	True	74.8701	103	1563	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:23,540] [INFO] DFAST Taxonomy check result was written to GCF_001458595.1_Clostridium_neonatale_genomic.fna/tc_result.tsv
[2024-01-24 11:20:23,541] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:23,541] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:23,542] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c0b0359-abda-4ae1-8bea-0b07ded57184/dqc_reference/checkm_data
[2024-01-24 11:20:23,543] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:23,594] [INFO] Task started: CheckM
[2024-01-24 11:20:23,594] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001458595.1_Clostridium_neonatale_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001458595.1_Clostridium_neonatale_genomic.fna/checkm_input GCF_001458595.1_Clostridium_neonatale_genomic.fna/checkm_result
[2024-01-24 11:20:52,085] [INFO] Task succeeded: CheckM
[2024-01-24 11:20:52,087] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:20:52,111] [INFO] ===== Completeness check finished =====
[2024-01-24 11:20:52,111] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:20:52,112] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001458595.1_Clostridium_neonatale_genomic.fna/markers.fasta)
[2024-01-24 11:20:52,112] [INFO] Task started: Blastn
[2024-01-24 11:20:52,112] [INFO] Running command: blastn -query GCF_001458595.1_Clostridium_neonatale_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c0b0359-abda-4ae1-8bea-0b07ded57184/dqc_reference/reference_markers_gtdb.fasta -out GCF_001458595.1_Clostridium_neonatale_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:53,014] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:53,018] [INFO] Selected 16 target genomes.
[2024-01-24 11:20:53,018] [INFO] Target genome list was writen to GCF_001458595.1_Clostridium_neonatale_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:20:53,048] [INFO] Task started: fastANI
[2024-01-24 11:20:53,049] [INFO] Running command: fastANI --query /var/lib/cwl/stg19fc02c5-b8e8-4412-bcc5-3e9a5f847962/GCF_001458595.1_Clostridium_neonatale_genomic.fna.gz --refList GCF_001458595.1_Clostridium_neonatale_genomic.fna/target_genomes_gtdb.txt --output GCF_001458595.1_Clostridium_neonatale_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:09,229] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:09,246] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:09,246] [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_001458595.1	s__Clostridium neonatale	100.0	1563	1563	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.07	98.42	0.91	0.80	11	conclusive
GCA_015058475.1	s__Clostridium butyricum_B	84.7823	715	1563	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	79.1218	566	1563	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.58	97.46	0.89	0.80	64	-
GCA_003129525.1	s__Clostridium beijerinckii_D	78.9791	465	1563	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	78.9767	319	1563	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_012843905.1	s__Clostridium sp012843905	78.9066	418	1563	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_000473995.1	s__Clostridium saccharobutylicum	78.8849	497	1563	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_018223745.1	s__Clostridium beijerinckii	78.7525	505	1563	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	78.6453	468	1563	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.07	97.40	0.90	0.87	3	-
GCA_003539755.1	s__Clostridium sp003539755	78.5712	313	1563	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	78.4583	542	1563	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	78.3617	523	1563	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_000230835.1	s__Clostridium sp000230835	78.3236	475	1563	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_009928485.1	s__Clostridium sp009928485	78.3129	511	1563	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	78.3068	406	1563	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_002760435.1	s__Clostridium sp002760435	78.2921	479	1563	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.99	99.99	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:09,248] [INFO] GTDB search result was written to GCF_001458595.1_Clostridium_neonatale_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:09,248] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:09,255] [INFO] DFAST_QC result json was written to GCF_001458595.1_Clostridium_neonatale_genomic.fna/dqc_result.json
[2024-01-24 11:21:09,256] [INFO] DFAST_QC completed!
[2024-01-24 11:21:09,256] [INFO] Total running time: 0h1m14s