[2024-01-24 12:53:41,663] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:41,666] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:41,666] [INFO] DQC Reference Directory: /var/lib/cwl/stga9df6ece-3f65-416e-802b-450426f8c13c/dqc_reference
[2024-01-24 12:53:43,031] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:43,032] [INFO] Task started: Prodigal
[2024-01-24 12:53:43,032] [INFO] Running command: gunzip -c /var/lib/cwl/stgfab3be12-8d6b-4b86-82a9-4e98012a0824/GCF_002843175.1_ASM284317v1_genomic.fna.gz | prodigal -d GCF_002843175.1_ASM284317v1_genomic.fna/cds.fna -a GCF_002843175.1_ASM284317v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:58,707] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:58,707] [INFO] Task started: HMMsearch
[2024-01-24 12:53:58,707] [INFO] Running command: hmmsearch --tblout GCF_002843175.1_ASM284317v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga9df6ece-3f65-416e-802b-450426f8c13c/dqc_reference/reference_markers.hmm GCF_002843175.1_ASM284317v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:59,024] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:59,025] [INFO] Found 6/6 markers.
[2024-01-24 12:53:59,067] [INFO] Query marker FASTA was written to GCF_002843175.1_ASM284317v1_genomic.fna/markers.fasta
[2024-01-24 12:53:59,068] [INFO] Task started: Blastn
[2024-01-24 12:53:59,068] [INFO] Running command: blastn -query GCF_002843175.1_ASM284317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9df6ece-3f65-416e-802b-450426f8c13c/dqc_reference/reference_markers.fasta -out GCF_002843175.1_ASM284317v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:00,214] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:00,217] [INFO] Selected 12 target genomes.
[2024-01-24 12:54:00,218] [INFO] Target genome list was writen to GCF_002843175.1_ASM284317v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:00,224] [INFO] Task started: fastANI
[2024-01-24 12:54:00,225] [INFO] Running command: fastANI --query /var/lib/cwl/stgfab3be12-8d6b-4b86-82a9-4e98012a0824/GCF_002843175.1_ASM284317v1_genomic.fna.gz --refList GCF_002843175.1_ASM284317v1_genomic.fna/target_genomes.txt --output GCF_002843175.1_ASM284317v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:10,370] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:10,370] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga9df6ece-3f65-416e-802b-450426f8c13c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:10,371] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga9df6ece-3f65-416e-802b-450426f8c13c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:10,382] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:10,382] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:10,382] [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
Confluentibacter flavum	strain=3B	GCA_002843175.1	1909700	1909700	type	True	100.0	1343	1351	95	conclusive
Confluentibacter citreus	strain=XJNY	GCA_002807055.1	2007307	2007307	type	True	88.0496	945	1351	95	below_threshold
Confluentibacter lentus	strain=HJM-3	GCA_002806995.1	1699412	1699412	type	True	86.2381	885	1351	95	below_threshold
Confluentibacter sediminis	strain=DSL-48	GCA_003258355.1	2219045	2219045	type	True	82.0037	733	1351	95	below_threshold
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	78.7207	483	1351	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	78.644	478	1351	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	77.83	327	1351	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.7419	312	1351	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	77.4609	256	1351	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.2353	202	1351	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	77.1523	185	1351	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	76.9184	203	1351	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:10,384] [INFO] DFAST Taxonomy check result was written to GCF_002843175.1_ASM284317v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:10,385] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:10,385] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:10,385] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga9df6ece-3f65-416e-802b-450426f8c13c/dqc_reference/checkm_data
[2024-01-24 12:54:10,387] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:10,435] [INFO] Task started: CheckM
[2024-01-24 12:54:10,435] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002843175.1_ASM284317v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002843175.1_ASM284317v1_genomic.fna/checkm_input GCF_002843175.1_ASM284317v1_genomic.fna/checkm_result
[2024-01-24 12:54:57,416] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:57,418] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:57,441] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:57,442] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:57,442] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002843175.1_ASM284317v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:57,443] [INFO] Task started: Blastn
[2024-01-24 12:54:57,443] [INFO] Running command: blastn -query GCF_002843175.1_ASM284317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9df6ece-3f65-416e-802b-450426f8c13c/dqc_reference/reference_markers_gtdb.fasta -out GCF_002843175.1_ASM284317v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:58,476] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:58,480] [INFO] Selected 9 target genomes.
[2024-01-24 12:54:58,480] [INFO] Target genome list was writen to GCF_002843175.1_ASM284317v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:58,490] [INFO] Task started: fastANI
[2024-01-24 12:54:58,490] [INFO] Running command: fastANI --query /var/lib/cwl/stgfab3be12-8d6b-4b86-82a9-4e98012a0824/GCF_002843175.1_ASM284317v1_genomic.fna.gz --refList GCF_002843175.1_ASM284317v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002843175.1_ASM284317v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:06,712] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:06,764] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:06,764] [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_002843175.1	s__Confluentibacter flavum	100.0	1343	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002807055.1	s__Confluentibacter citreus	88.0496	945	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002806995.1	s__Confluentibacter lentus	86.2526	883	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280395.1	s__Confluentibacter sp002280395	85.1344	501	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003258355.1	s__Confluentibacter sp003258355	81.9835	735	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341235.1	s__Mariniflexile fucanivorans	78.6535	476	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002784145.1	s__Yeosuana sp002784145	78.5064	361	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	99.75	99.57	0.88	0.85	11	-
GCF_900114265.1	s__Flaviramulus basaltis	78.3739	439	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141715.1	s__Arenitalea lutea	77.8198	328	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenitalea	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:06,766] [INFO] GTDB search result was written to GCF_002843175.1_ASM284317v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:06,766] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:06,770] [INFO] DFAST_QC result json was written to GCF_002843175.1_ASM284317v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:06,770] [INFO] DFAST_QC completed!
[2024-01-24 12:55:06,770] [INFO] Total running time: 0h1m25s