[2024-01-25 18:40:21,076] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:40:21,080] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:40:21,080] [INFO] DQC Reference Directory: /var/lib/cwl/stg65ddee2a-e802-4caa-b910-e6a2f34f1cda/dqc_reference
[2024-01-25 18:40:22,267] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:40:22,268] [INFO] Task started: Prodigal
[2024-01-25 18:40:22,268] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d3fde3f-1bb4-4863-8a10-5f0916765ab8/GCF_009741375.1_ASM974137v1_genomic.fna.gz | prodigal -d GCF_009741375.1_ASM974137v1_genomic.fna/cds.fna -a GCF_009741375.1_ASM974137v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:40:33,250] [INFO] Task succeeded: Prodigal
[2024-01-25 18:40:33,250] [INFO] Task started: HMMsearch
[2024-01-25 18:40:33,250] [INFO] Running command: hmmsearch --tblout GCF_009741375.1_ASM974137v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg65ddee2a-e802-4caa-b910-e6a2f34f1cda/dqc_reference/reference_markers.hmm GCF_009741375.1_ASM974137v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:40:33,483] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:40:33,484] [INFO] Found 6/6 markers.
[2024-01-25 18:40:33,520] [INFO] Query marker FASTA was written to GCF_009741375.1_ASM974137v1_genomic.fna/markers.fasta
[2024-01-25 18:40:33,520] [INFO] Task started: Blastn
[2024-01-25 18:40:33,520] [INFO] Running command: blastn -query GCF_009741375.1_ASM974137v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65ddee2a-e802-4caa-b910-e6a2f34f1cda/dqc_reference/reference_markers.fasta -out GCF_009741375.1_ASM974137v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:34,166] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:34,169] [INFO] Selected 15 target genomes.
[2024-01-25 18:40:34,170] [INFO] Target genome list was writen to GCF_009741375.1_ASM974137v1_genomic.fna/target_genomes.txt
[2024-01-25 18:40:34,176] [INFO] Task started: fastANI
[2024-01-25 18:40:34,176] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d3fde3f-1bb4-4863-8a10-5f0916765ab8/GCF_009741375.1_ASM974137v1_genomic.fna.gz --refList GCF_009741375.1_ASM974137v1_genomic.fna/target_genomes.txt --output GCF_009741375.1_ASM974137v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:40:44,725] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:44,726] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg65ddee2a-e802-4caa-b910-e6a2f34f1cda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:40:44,726] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg65ddee2a-e802-4caa-b910-e6a2f34f1cda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:40:44,736] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:40:44,736] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:40:44,736] [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 rakeshii	strain=JCM 17928	GCA_009741375.1	1038845	1038845	type	True	100.0	1264	1266	95	conclusive
Flavobacterium beibuense	strain=F44-8	GCA_000769915.1	657326	657326	type	True	93.8673	1061	1266	95	below_threshold
Flavobacterium alkalisoli	strain=XS-5	GCA_008000935.1	2602769	2602769	type	True	82.449	853	1266	95	below_threshold
Flavobacterium cerinum	strain=1E403	GCA_004028155.1	2502784	2502784	type	True	78.2706	371	1266	95	below_threshold
Flavobacterium subsaxonicum	strain=DSM 21790	GCA_000422725.1	426226	426226	type	True	77.9366	300	1266	95	below_threshold
Flavobacterium arcticum	strain=KCTC 42668	GCA_004634185.1	1784713	1784713	type	True	77.8828	294	1266	95	below_threshold
Flavobacterium salilacus subsp. altitudinum	strain=LaA7.5	GCA_010078225.1	2691899	2898423	type	True	77.7553	323	1266	95	below_threshold
Flavobacterium coralii	strain=D11R37	GCA_019891545.1	2838017	2838017	type	True	77.6873	286	1266	95	below_threshold
Flavobacterium zepuense	strain=ZT4R6	GCA_007097145.1	2593302	2593302	type	True	77.5868	321	1266	95	below_threshold
Flavobacterium litorale	strain=WSW3-B6	GCA_019613795.1	2856519	2856519	type	True	77.5569	239	1266	95	below_threshold
Flavobacterium microcysteis	strain=MaA-Y11	GCA_006385255.1	2596891	2596891	type	True	77.1787	149	1266	95	below_threshold
Flavobacterium akiainvivens	strain=IK-1	GCA_001278115.1	1202724	1202724	type	True	77.1037	268	1266	95	below_threshold
Flavobacterium akiainvivens	strain=DSM 25510	GCA_900115875.1	1202724	1202724	type	True	77.0857	265	1266	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	76.4224	103	1266	95	below_threshold
Abyssalbus ytuae	strain=MT3330	GCA_022807975.1	2926907	2926907	type	True	75.9917	66	1266	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:40:44,739] [INFO] DFAST Taxonomy check result was written to GCF_009741375.1_ASM974137v1_genomic.fna/tc_result.tsv
[2024-01-25 18:40:44,739] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:40:44,739] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:40:44,740] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg65ddee2a-e802-4caa-b910-e6a2f34f1cda/dqc_reference/checkm_data
[2024-01-25 18:40:44,740] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:40:44,780] [INFO] Task started: CheckM
[2024-01-25 18:40:44,780] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009741375.1_ASM974137v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009741375.1_ASM974137v1_genomic.fna/checkm_input GCF_009741375.1_ASM974137v1_genomic.fna/checkm_result
[2024-01-25 18:41:19,323] [INFO] Task succeeded: CheckM
[2024-01-25 18:41:19,324] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:41:19,352] [INFO] ===== Completeness check finished =====
[2024-01-25 18:41:19,353] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:41:19,353] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009741375.1_ASM974137v1_genomic.fna/markers.fasta)
[2024-01-25 18:41:19,353] [INFO] Task started: Blastn
[2024-01-25 18:41:19,353] [INFO] Running command: blastn -query GCF_009741375.1_ASM974137v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65ddee2a-e802-4caa-b910-e6a2f34f1cda/dqc_reference/reference_markers_gtdb.fasta -out GCF_009741375.1_ASM974137v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:20,266] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:20,269] [INFO] Selected 11 target genomes.
[2024-01-25 18:41:20,269] [INFO] Target genome list was writen to GCF_009741375.1_ASM974137v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:41:20,276] [INFO] Task started: fastANI
[2024-01-25 18:41:20,276] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d3fde3f-1bb4-4863-8a10-5f0916765ab8/GCF_009741375.1_ASM974137v1_genomic.fna.gz --refList GCF_009741375.1_ASM974137v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009741375.1_ASM974137v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:41:28,921] [INFO] Task succeeded: fastANI
[2024-01-25 18:41:28,928] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:41:28,929] [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_009741375.1	s__Flavobacterium rakeshii	100.0	1264	1266	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000769915.1	s__Flavobacterium beibuense	93.8644	1062	1266	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	82.4394	854	1266	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	82.4354	835	1266	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	78.6399	368	1266	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	78.4353	390	1266	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004028155.1	s__Flavobacterium cerinum	78.2602	371	1266	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001708385.1	s__Flavobacterium psychrophilum_A	78.2456	392	1266	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003344925.1	s__Flavobacterium arcticum	77.8653	296	1266	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002714575.1	s__Flavobacterium sp002714575	77.733	299	1266	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097145.1	s__Flavobacterium sp007097145	77.5895	320	1266	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:41:28,930] [INFO] GTDB search result was written to GCF_009741375.1_ASM974137v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:41:28,931] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:41:28,934] [INFO] DFAST_QC result json was written to GCF_009741375.1_ASM974137v1_genomic.fna/dqc_result.json
[2024-01-25 18:41:28,934] [INFO] DFAST_QC completed!
[2024-01-25 18:41:28,934] [INFO] Total running time: 0h1m8s