[2024-01-24 13:27:58,764] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:58,766] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:58,766] [INFO] DQC Reference Directory: /var/lib/cwl/stg019303eb-a631-477e-aec3-2b7e2e434605/dqc_reference
[2024-01-24 13:27:59,977] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:59,978] [INFO] Task started: Prodigal
[2024-01-24 13:27:59,978] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d5132b7-0074-4b2c-a992-04b87c0a5ff6/GCF_000621625.1_ASM62162v1_genomic.fna.gz | prodigal -d GCF_000621625.1_ASM62162v1_genomic.fna/cds.fna -a GCF_000621625.1_ASM62162v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:15,807] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:15,807] [INFO] Task started: HMMsearch
[2024-01-24 13:28:15,807] [INFO] Running command: hmmsearch --tblout GCF_000621625.1_ASM62162v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg019303eb-a631-477e-aec3-2b7e2e434605/dqc_reference/reference_markers.hmm GCF_000621625.1_ASM62162v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:16,127] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:16,128] [INFO] Found 6/6 markers.
[2024-01-24 13:28:16,167] [INFO] Query marker FASTA was written to GCF_000621625.1_ASM62162v1_genomic.fna/markers.fasta
[2024-01-24 13:28:16,168] [INFO] Task started: Blastn
[2024-01-24 13:28:16,168] [INFO] Running command: blastn -query GCF_000621625.1_ASM62162v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg019303eb-a631-477e-aec3-2b7e2e434605/dqc_reference/reference_markers.fasta -out GCF_000621625.1_ASM62162v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:16,828] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:16,832] [INFO] Selected 26 target genomes.
[2024-01-24 13:28:16,833] [INFO] Target genome list was writen to GCF_000621625.1_ASM62162v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:16,856] [INFO] Task started: fastANI
[2024-01-24 13:28:16,857] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d5132b7-0074-4b2c-a992-04b87c0a5ff6/GCF_000621625.1_ASM62162v1_genomic.fna.gz --refList GCF_000621625.1_ASM62162v1_genomic.fna/target_genomes.txt --output GCF_000621625.1_ASM62162v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:33,806] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:33,807] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg019303eb-a631-477e-aec3-2b7e2e434605/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:33,807] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg019303eb-a631-477e-aec3-2b7e2e434605/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:33,818] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:33,818] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:33,818] [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
Crocinitomix catalasitica	strain=ATCC 23190	GCA_000621625.1	184607	184607	type	True	100.0	1502	1506	95	conclusive
Crocinitomix algicola	strain=0182	GCA_001661595.2	1740263	1740263	type	True	76.8453	170	1506	95	below_threshold
Putridiphycobacter roseus	strain=SM1701	GCA_003234935.1	2219161	2219161	type	True	76.7118	121	1506	95	below_threshold
Brumimicrobium aurantiacum	strain=N62	GCA_003402975.1	1737063	1737063	type	True	76.3467	66	1506	95	below_threshold
Brumimicrobium mesophilum	strain=JCM 14063	GCA_003025005.1	392717	392717	type	True	76.287	64	1506	95	below_threshold
Brumimicrobium glaciale	strain=IC156	GCA_004152935.1	200475	200475	type	True	75.8519	59	1506	95	below_threshold
Aureibaculum flavum	strain=A20	GCA_016406085.1	2795986	2795986	type	True	75.6635	51	1506	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	75.5863	52	1506	95	below_threshold
Aureibaculum luteum	strain=SM1352	GCA_003449015.1	1548456	1548456	type	True	75.5544	52	1506	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	75.4619	55	1506	95	below_threshold
Flavobacterium jejuense	strain=EC11	GCA_006491595.2	1544455	1544455	type	True	75.4049	51	1506	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:33,822] [INFO] DFAST Taxonomy check result was written to GCF_000621625.1_ASM62162v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:33,822] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:33,823] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:33,823] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg019303eb-a631-477e-aec3-2b7e2e434605/dqc_reference/checkm_data
[2024-01-24 13:28:33,824] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:33,872] [INFO] Task started: CheckM
[2024-01-24 13:28:33,872] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000621625.1_ASM62162v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000621625.1_ASM62162v1_genomic.fna/checkm_input GCF_000621625.1_ASM62162v1_genomic.fna/checkm_result
[2024-01-24 13:29:23,511] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:23,513] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:23,530] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:23,531] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:23,531] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000621625.1_ASM62162v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:23,532] [INFO] Task started: Blastn
[2024-01-24 13:29:23,532] [INFO] Running command: blastn -query GCF_000621625.1_ASM62162v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg019303eb-a631-477e-aec3-2b7e2e434605/dqc_reference/reference_markers_gtdb.fasta -out GCF_000621625.1_ASM62162v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:24,393] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:24,399] [INFO] Selected 22 target genomes.
[2024-01-24 13:29:24,400] [INFO] Target genome list was writen to GCF_000621625.1_ASM62162v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:24,450] [INFO] Task started: fastANI
[2024-01-24 13:29:24,451] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d5132b7-0074-4b2c-a992-04b87c0a5ff6/GCF_000621625.1_ASM62162v1_genomic.fna.gz --refList GCF_000621625.1_ASM62162v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000621625.1_ASM62162v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:37,876] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:37,884] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:37,884] [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_000621625.1	s__Crocinitomix catalasitica	100.0	1502	1506	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Crocinitomix	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013138735.1	s__Crocinitomix sp013138735	77.1087	188	1506	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Crocinitomix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478225.1	s__Crocinitomix sp905478225	76.9304	178	1506	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Crocinitomix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001661595.2	s__Crocinitomix algicola	76.8315	171	1506	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Crocinitomix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003234935.1	s__Putridiphycobacter roseus	76.7276	120	1506	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Putridiphycobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003402975.1	s__Brumimicrobium aurantiacum	76.3467	66	1506	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004152935.1	s__Brumimicrobium glaciale	75.8519	59	1506	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015319355.1	s__Psychroserpens luteus	75.6777	52	1506	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:37,886] [INFO] GTDB search result was written to GCF_000621625.1_ASM62162v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:37,887] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:37,890] [INFO] DFAST_QC result json was written to GCF_000621625.1_ASM62162v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:37,890] [INFO] DFAST_QC completed!
[2024-01-24 13:29:37,890] [INFO] Total running time: 0h1m39s