[2024-01-24 11:05:03,927] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:03,929] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:03,929] [INFO] DQC Reference Directory: /var/lib/cwl/stga060d12f-d71b-4961-bd72-90f5caf93170/dqc_reference
[2024-01-24 11:05:05,761] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:05,764] [INFO] Task started: Prodigal
[2024-01-24 11:05:05,765] [INFO] Running command: gunzip -c /var/lib/cwl/stg633c694b-a318-44fe-b2e2-bcbd413abeff/GCF_004028155.1_ASM402815v1_genomic.fna.gz | prodigal -d GCF_004028155.1_ASM402815v1_genomic.fna/cds.fna -a GCF_004028155.1_ASM402815v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:18,063] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:18,064] [INFO] Task started: HMMsearch
[2024-01-24 11:05:18,064] [INFO] Running command: hmmsearch --tblout GCF_004028155.1_ASM402815v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga060d12f-d71b-4961-bd72-90f5caf93170/dqc_reference/reference_markers.hmm GCF_004028155.1_ASM402815v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:18,344] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:18,345] [INFO] Found 6/6 markers.
[2024-01-24 11:05:18,382] [INFO] Query marker FASTA was written to GCF_004028155.1_ASM402815v1_genomic.fna/markers.fasta
[2024-01-24 11:05:18,382] [INFO] Task started: Blastn
[2024-01-24 11:05:18,382] [INFO] Running command: blastn -query GCF_004028155.1_ASM402815v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga060d12f-d71b-4961-bd72-90f5caf93170/dqc_reference/reference_markers.fasta -out GCF_004028155.1_ASM402815v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:19,024] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:19,026] [INFO] Selected 17 target genomes.
[2024-01-24 11:05:19,027] [INFO] Target genome list was writen to GCF_004028155.1_ASM402815v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:19,031] [INFO] Task started: fastANI
[2024-01-24 11:05:19,032] [INFO] Running command: fastANI --query /var/lib/cwl/stg633c694b-a318-44fe-b2e2-bcbd413abeff/GCF_004028155.1_ASM402815v1_genomic.fna.gz --refList GCF_004028155.1_ASM402815v1_genomic.fna/target_genomes.txt --output GCF_004028155.1_ASM402815v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:30,382] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:30,382] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga060d12f-d71b-4961-bd72-90f5caf93170/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:30,382] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga060d12f-d71b-4961-bd72-90f5caf93170/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:30,392] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:05:30,392] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:30,393] [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
Flavobacterium cerinum	strain=1E403	GCA_004028155.1	2502784	2502784	type	True	100.0	1357	1358	95	conclusive
Flavobacterium alkalisoli	strain=XS-5	GCA_008000935.1	2602769	2602769	type	True	78.5519	408	1358	95	below_threshold
Flavobacterium subsaxonicum	strain=WB 4.1-42	GCA_000769935.1	426226	426226	type	True	78.3137	348	1358	95	below_threshold
Flavobacterium subsaxonicum	strain=DSM 21790	GCA_000422725.1	426226	426226	type	True	78.2841	351	1358	95	below_threshold
Flavobacterium zepuense	strain=ZT4R6	GCA_007097145.1	2593302	2593302	type	True	78.2381	344	1358	95	below_threshold
Flavobacterium rakeshii	strain=JCM 17928	GCA_009741375.1	1038845	1038845	type	True	78.1922	387	1358	95	below_threshold
Flavobacterium beibuense	strain=F44-8	GCA_000769915.1	657326	657326	type	True	78.1722	363	1358	95	below_threshold
Flavobacterium rivuli	strain=WB 3.3-2	GCA_000769825.1	498301	498301	type	True	77.9387	345	1358	95	below_threshold
Flavobacterium rivuli	strain=DSM 21788	GCA_000378485.1	498301	498301	type	True	77.9119	344	1358	95	below_threshold
Flavobacterium album	strain=HYN0059	GCA_003096035.1	2175091	2175091	type	True	77.8884	291	1358	95	below_threshold
Flavobacterium litorale	strain=WSW3-B6	GCA_019613795.1	2856519	2856519	type	True	77.8378	213	1358	95	below_threshold
Flavobacterium salilacus subsp. altitudinum	strain=LaA7.5	GCA_010078225.1	2691899	2898423	type	True	77.7671	298	1358	95	below_threshold
Flavobacterium salilacus subsp. salilacus	strain=SaA2.12	GCA_004634195.1	2545633	2898423	type	True	77.7359	298	1358	95	below_threshold
Flavobacterium filum	strain=DSM 17961	GCA_000425465.1	370974	370974	type	True	76.8173	104	1358	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.0317	58	1358	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:30,397] [INFO] DFAST Taxonomy check result was written to GCF_004028155.1_ASM402815v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:30,398] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:30,398] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:30,398] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga060d12f-d71b-4961-bd72-90f5caf93170/dqc_reference/checkm_data
[2024-01-24 11:05:30,399] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:30,458] [INFO] Task started: CheckM
[2024-01-24 11:05:30,458] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004028155.1_ASM402815v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004028155.1_ASM402815v1_genomic.fna/checkm_input GCF_004028155.1_ASM402815v1_genomic.fna/checkm_result
[2024-01-24 11:06:06,039] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:06,040] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:06,056] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:06,056] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:06,057] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004028155.1_ASM402815v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:06,057] [INFO] Task started: Blastn
[2024-01-24 11:06:06,057] [INFO] Running command: blastn -query GCF_004028155.1_ASM402815v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga060d12f-d71b-4961-bd72-90f5caf93170/dqc_reference/reference_markers_gtdb.fasta -out GCF_004028155.1_ASM402815v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:06,989] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:06,991] [INFO] Selected 11 target genomes.
[2024-01-24 11:06:06,992] [INFO] Target genome list was writen to GCF_004028155.1_ASM402815v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:06,997] [INFO] Task started: fastANI
[2024-01-24 11:06:06,997] [INFO] Running command: fastANI --query /var/lib/cwl/stg633c694b-a318-44fe-b2e2-bcbd413abeff/GCF_004028155.1_ASM402815v1_genomic.fna.gz --refList GCF_004028155.1_ASM402815v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004028155.1_ASM402815v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:15,794] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:15,801] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:15,801] [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_004028155.1	s__Flavobacterium cerinum	100.0	1357	1358	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001708385.1	s__Flavobacterium psychrophilum_A	79.6784	558	1358	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003243255.1	s__Flavobacterium psychrophilum_B	79.184	494	1358	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350375.1	s__Flavobacterium sp003350375	79.1265	504	1358	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932585.1	s__Flavobacterium sp012932585	79.004	512	1358	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004151245.1	s__Flavobacterium beibuense_A	78.5872	392	1358	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008000935.1	s__Flavobacterium alkalisoli	78.5519	408	1358	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422725.1	s__Flavobacterium subsaxonicum	78.2841	351	1358	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007097145.1	s__Flavobacterium sp007097145	78.239	344	1358	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378485.1	s__Flavobacterium rivuli	77.9194	345	1358	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004634195.1	s__Flavobacterium sp004634195	77.7359	298	1358	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.56	97.13	0.95	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:15,803] [INFO] GTDB search result was written to GCF_004028155.1_ASM402815v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:15,803] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:15,806] [INFO] DFAST_QC result json was written to GCF_004028155.1_ASM402815v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:15,806] [INFO] DFAST_QC completed!
[2024-01-24 11:06:15,806] [INFO] Total running time: 0h1m12s