[2023-06-05 19:01:13,609] [INFO] DFAST_QC pipeline started.
[2023-06-05 19:01:13,612] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 19:01:13,612] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb7da490-d94f-4a88-852a-de3ddc02f7c4/dqc_reference
[2023-06-05 19:01:14,832] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 19:01:14,832] [INFO] Task started: Prodigal
[2023-06-05 19:01:14,833] [INFO] Running command: gunzip -c /var/lib/cwl/stgce7245a0-1ed7-465c-bafd-6de6c003494d/GCA_004211145.1_ASM421114v1_genomic.fna.gz | prodigal -d GCA_004211145.1_ASM421114v1_genomic.fna/cds.fna -a GCA_004211145.1_ASM421114v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 19:01:37,257] [INFO] Task succeeded: Prodigal
[2023-06-05 19:01:37,258] [INFO] Task started: HMMsearch
[2023-06-05 19:01:37,258] [INFO] Running command: hmmsearch --tblout GCA_004211145.1_ASM421114v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb7da490-d94f-4a88-852a-de3ddc02f7c4/dqc_reference/reference_markers.hmm GCA_004211145.1_ASM421114v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 19:01:37,533] [INFO] Task succeeded: HMMsearch
[2023-06-05 19:01:37,534] [INFO] Found 6/6 markers.
[2023-06-05 19:01:37,569] [INFO] Query marker FASTA was written to GCA_004211145.1_ASM421114v1_genomic.fna/markers.fasta
[2023-06-05 19:01:37,570] [INFO] Task started: Blastn
[2023-06-05 19:01:37,570] [INFO] Running command: blastn -query GCA_004211145.1_ASM421114v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb7da490-d94f-4a88-852a-de3ddc02f7c4/dqc_reference/reference_markers.fasta -out GCA_004211145.1_ASM421114v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 19:01:38,170] [INFO] Task succeeded: Blastn
[2023-06-05 19:01:38,175] [INFO] Selected 16 target genomes.
[2023-06-05 19:01:38,176] [INFO] Target genome list was writen to GCA_004211145.1_ASM421114v1_genomic.fna/target_genomes.txt
[2023-06-05 19:01:38,179] [INFO] Task started: fastANI
[2023-06-05 19:01:38,180] [INFO] Running command: fastANI --query /var/lib/cwl/stgce7245a0-1ed7-465c-bafd-6de6c003494d/GCA_004211145.1_ASM421114v1_genomic.fna.gz --refList GCA_004211145.1_ASM421114v1_genomic.fna/target_genomes.txt --output GCA_004211145.1_ASM421114v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 19:01:47,816] [INFO] Task succeeded: fastANI
[2023-06-05 19:01:47,817] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb7da490-d94f-4a88-852a-de3ddc02f7c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 19:01:47,818] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb7da490-d94f-4a88-852a-de3ddc02f7c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 19:01:47,839] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 19:01:47,840] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 19:01:47,840] [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 agri	strain=MAH-1	GCA_013401995.1	2743471	2743471	type	True	79.5052	657	1299	95	below_threshold
Flavobacterium agri	strain=MAH-1	GCA_013366395.1	2743471	2743471	type	True	79.4987	653	1299	95	below_threshold
Flavobacterium silvaticum	strain=SE-s28	GCA_012911565.1	1852020	1852020	type	True	77.2723	293	1299	95	below_threshold
Flavobacterium caeni	strain=CGMCC 1.7031	GCA_900101895.1	490189	490189	type	True	77.1776	265	1299	95	below_threshold
Flavobacterium noncentrifugens	strain=CGMCC 1.10076	GCA_900100375.1	1128970	1128970	type	True	76.5108	204	1299	95	below_threshold
Flavobacterium noncentrifugens	strain=NBRC 108844	GCA_007992475.1	1128970	1128970	type	True	76.4961	207	1299	95	below_threshold
Flavobacterium lotistagni	strain=CYK-4	GCA_011392125.1	2709660	2709660	type	True	76.3717	122	1299	95	below_threshold
Flavobacterium cauense	strain=R2A-7	GCA_000498475.1	510946	510946	type	True	76.3638	77	1299	95	below_threshold
Flavobacterium cauense	strain=CGMCC 1.7270	GCA_007830385.1	510946	510946	type	True	76.3239	76	1299	95	below_threshold
Flavobacterium magnum	strain=HYN0048	GCA_003055625.1	2162713	2162713	type	True	76.1997	110	1299	95	below_threshold
Flavobacterium album	strain=HYN0059	GCA_003096035.1	2175091	2175091	type	True	76.191	70	1299	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	75.6917	50	1299	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 19:01:47,842] [INFO] DFAST Taxonomy check result was written to GCA_004211145.1_ASM421114v1_genomic.fna/tc_result.tsv
[2023-06-05 19:01:47,843] [INFO] ===== Taxonomy check completed =====
[2023-06-05 19:01:47,843] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 19:01:47,843] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb7da490-d94f-4a88-852a-de3ddc02f7c4/dqc_reference/checkm_data
[2023-06-05 19:01:47,844] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 19:01:47,886] [INFO] Task started: CheckM
[2023-06-05 19:01:47,886] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004211145.1_ASM421114v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004211145.1_ASM421114v1_genomic.fna/checkm_input GCA_004211145.1_ASM421114v1_genomic.fna/checkm_result
[2023-06-05 19:02:51,142] [INFO] Task succeeded: CheckM
[2023-06-05 19:02:51,144] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 19:02:51,166] [INFO] ===== Completeness check finished =====
[2023-06-05 19:02:51,167] [INFO] ===== Start GTDB Search =====
[2023-06-05 19:02:51,168] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004211145.1_ASM421114v1_genomic.fna/markers.fasta)
[2023-06-05 19:02:51,168] [INFO] Task started: Blastn
[2023-06-05 19:02:51,169] [INFO] Running command: blastn -query GCA_004211145.1_ASM421114v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb7da490-d94f-4a88-852a-de3ddc02f7c4/dqc_reference/reference_markers_gtdb.fasta -out GCA_004211145.1_ASM421114v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 19:02:51,993] [INFO] Task succeeded: Blastn
[2023-06-05 19:02:51,999] [INFO] Selected 11 target genomes.
[2023-06-05 19:02:51,999] [INFO] Target genome list was writen to GCA_004211145.1_ASM421114v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 19:02:52,012] [INFO] Task started: fastANI
[2023-06-05 19:02:52,012] [INFO] Running command: fastANI --query /var/lib/cwl/stgce7245a0-1ed7-465c-bafd-6de6c003494d/GCA_004211145.1_ASM421114v1_genomic.fna.gz --refList GCA_004211145.1_ASM421114v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004211145.1_ASM421114v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 19:03:00,080] [INFO] Task succeeded: fastANI
[2023-06-05 19:03:00,095] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 19:03:00,095] [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
GCA_004211145.1	s__Flavobacterium sp004211145	100.0	1296	1299	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_013401995.1	s__Flavobacterium agri	79.5088	657	1299	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_004295795.1	s__Flavobacterium sp004295795	78.7966	642	1299	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014748335.1	s__Flavobacterium sp014748335	78.3691	502	1299	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911565.1	s__Flavobacterium sp012911565	77.2723	293	1299	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101895.1	s__Flavobacterium caeni	77.1832	263	1299	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483285.1	s__Flavobacterium sp002483285	76.5938	177	1299	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100375.1	s__Flavobacterium noncentrifugens	76.5217	203	1299	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_015478765.1	s__Flavobacterium sp015478765	76.3841	78	1299	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015234525.1	s__Flavobacterium sp015234525	76.2893	88	1299	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096035.1	s__Flavobacterium album	76.224	71	1299	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 19:03:00,098] [INFO] GTDB search result was written to GCA_004211145.1_ASM421114v1_genomic.fna/result_gtdb.tsv
[2023-06-05 19:03:00,098] [INFO] ===== GTDB Search completed =====
[2023-06-05 19:03:00,106] [INFO] DFAST_QC result json was written to GCA_004211145.1_ASM421114v1_genomic.fna/dqc_result.json
[2023-06-05 19:03:00,107] [INFO] DFAST_QC completed!
[2023-06-05 19:03:00,107] [INFO] Total running time: 0h1m46s