[2024-01-24 11:51:37,320] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:37,323] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:37,324] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf331ba8-861b-4011-a68f-48fad67f607b/dqc_reference
[2024-01-24 11:51:38,578] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:38,579] [INFO] Task started: Prodigal
[2024-01-24 11:51:38,579] [INFO] Running command: gunzip -c /var/lib/cwl/stg95636f70-8349-41fd-9f03-5005581d9ad1/GCF_021172165.1_ASM2117216v1_genomic.fna.gz | prodigal -d GCF_021172165.1_ASM2117216v1_genomic.fna/cds.fna -a GCF_021172165.1_ASM2117216v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:47,880] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:47,880] [INFO] Task started: HMMsearch
[2024-01-24 11:51:47,881] [INFO] Running command: hmmsearch --tblout GCF_021172165.1_ASM2117216v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf331ba8-861b-4011-a68f-48fad67f607b/dqc_reference/reference_markers.hmm GCF_021172165.1_ASM2117216v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:48,125] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:48,127] [INFO] Found 6/6 markers.
[2024-01-24 11:51:48,155] [INFO] Query marker FASTA was written to GCF_021172165.1_ASM2117216v1_genomic.fna/markers.fasta
[2024-01-24 11:51:48,156] [INFO] Task started: Blastn
[2024-01-24 11:51:48,156] [INFO] Running command: blastn -query GCF_021172165.1_ASM2117216v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf331ba8-861b-4011-a68f-48fad67f607b/dqc_reference/reference_markers.fasta -out GCF_021172165.1_ASM2117216v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:48,838] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:48,841] [INFO] Selected 10 target genomes.
[2024-01-24 11:51:48,841] [INFO] Target genome list was writen to GCF_021172165.1_ASM2117216v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:48,846] [INFO] Task started: fastANI
[2024-01-24 11:51:48,846] [INFO] Running command: fastANI --query /var/lib/cwl/stg95636f70-8349-41fd-9f03-5005581d9ad1/GCF_021172165.1_ASM2117216v1_genomic.fna.gz --refList GCF_021172165.1_ASM2117216v1_genomic.fna/target_genomes.txt --output GCF_021172165.1_ASM2117216v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:55,451] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:55,451] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf331ba8-861b-4011-a68f-48fad67f607b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:55,452] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf331ba8-861b-4011-a68f-48fad67f607b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:55,461] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:55,461] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:55,461] [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 channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	100.0	936	936	95	conclusive
Flavobacterium sasangense	strain=DSM 21067	GCA_000686885.1	503361	503361	type	True	86.2163	711	936	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	85.6916	679	936	95	below_threshold
Flavobacterium aquaticum	strain=CGMCC 1.12398	GCA_003259835.1	1236486	1236486	type	True	85.6557	705	936	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	85.4626	712	936	95	below_threshold
Flavobacterium cheniae	strain=CGMCC 1.6844	GCA_007830415.1	295428	295428	type	True	85.0393	693	936	95	below_threshold
Flavobacterium cheniae	strain=DSM 22462	GCA_004363695.1	295428	295428	type	True	85.007	698	936	95	below_threshold
Flavobacterium celericrescens	strain=TWA-26	GCA_011392075.1	2709780	2709780	type	True	83.1856	588	936	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	78.5033	375	936	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	77.1443	138	936	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:55,463] [INFO] DFAST Taxonomy check result was written to GCF_021172165.1_ASM2117216v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:55,464] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:55,464] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:55,464] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf331ba8-861b-4011-a68f-48fad67f607b/dqc_reference/checkm_data
[2024-01-24 11:51:55,465] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:55,503] [INFO] Task started: CheckM
[2024-01-24 11:51:55,504] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021172165.1_ASM2117216v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021172165.1_ASM2117216v1_genomic.fna/checkm_input GCF_021172165.1_ASM2117216v1_genomic.fna/checkm_result
[2024-01-24 11:52:27,526] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:27,527] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:27,545] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:27,545] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:27,546] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021172165.1_ASM2117216v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:27,546] [INFO] Task started: Blastn
[2024-01-24 11:52:27,546] [INFO] Running command: blastn -query GCF_021172165.1_ASM2117216v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf331ba8-861b-4011-a68f-48fad67f607b/dqc_reference/reference_markers_gtdb.fasta -out GCF_021172165.1_ASM2117216v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:28,563] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:28,567] [INFO] Selected 12 target genomes.
[2024-01-24 11:52:28,567] [INFO] Target genome list was writen to GCF_021172165.1_ASM2117216v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:28,578] [INFO] Task started: fastANI
[2024-01-24 11:52:28,579] [INFO] Running command: fastANI --query /var/lib/cwl/stg95636f70-8349-41fd-9f03-5005581d9ad1/GCF_021172165.1_ASM2117216v1_genomic.fna.gz --refList GCF_021172165.1_ASM2117216v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021172165.1_ASM2117216v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:35,243] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:35,258] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:52:35,259] [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_000686885.1	s__Flavobacterium sasangense	86.1827	712	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015223105.1	s__Flavobacterium aquaticum_A	85.6879	678	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259835.1	s__Flavobacterium aquaticum	85.6557	705	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422095.1	s__Flavobacterium sp002422095	85.2891	544	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963025.1	s__Flavobacterium sp003963025	85.2491	456	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002421645.1	s__Flavobacterium sp002421645	85.1673	323	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363695.1	s__Flavobacterium cheniae	85.0222	697	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003497625.1	s__Flavobacterium sp003497625	84.9429	672	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	0.98	0.98	2	-
GCA_019105125.1	s__Flavobacterium sp019105125	84.6477	364	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009495755.1	s__Flavobacterium sp009495755	84.6349	651	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000169355.1	s__Flavobacterium sp000169355	83.7359	650	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.75	96.74	0.84	0.84	3	-
GCF_011392075.1	s__Flavobacterium celericrescens	83.1856	588	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:35,262] [INFO] GTDB search result was written to GCF_021172165.1_ASM2117216v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:35,262] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:35,265] [INFO] DFAST_QC result json was written to GCF_021172165.1_ASM2117216v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:35,265] [INFO] DFAST_QC completed!
[2024-01-24 11:52:35,265] [INFO] Total running time: 0h0m58s