[2023-06-13 16:35:32,585] [INFO] DFAST_QC pipeline started.
[2023-06-13 16:35:32,587] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 16:35:32,587] [INFO] DQC Reference Directory: /var/lib/cwl/stg89da4d80-718e-4c84-80ed-273c8e9e2b59/dqc_reference
[2023-06-13 16:35:33,836] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 16:35:33,837] [INFO] Task started: Prodigal
[2023-06-13 16:35:33,837] [INFO] Running command: gunzip -c /var/lib/cwl/stg74212144-5ee0-46d9-ad93-62e7a0e3b238/GCA_947448565.1_Jr-12mar18-41_genomic.fna.gz | prodigal -d GCA_947448565.1_Jr-12mar18-41_genomic.fna/cds.fna -a GCA_947448565.1_Jr-12mar18-41_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 16:35:40,195] [INFO] Task succeeded: Prodigal
[2023-06-13 16:35:40,196] [INFO] Task started: HMMsearch
[2023-06-13 16:35:40,196] [INFO] Running command: hmmsearch --tblout GCA_947448565.1_Jr-12mar18-41_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89da4d80-718e-4c84-80ed-273c8e9e2b59/dqc_reference/reference_markers.hmm GCA_947448565.1_Jr-12mar18-41_genomic.fna/protein.faa > /dev/null
[2023-06-13 16:35:40,392] [INFO] Task succeeded: HMMsearch
[2023-06-13 16:35:40,393] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg74212144-5ee0-46d9-ad93-62e7a0e3b238/GCA_947448565.1_Jr-12mar18-41_genomic.fna.gz]
[2023-06-13 16:35:40,414] [INFO] Query marker FASTA was written to GCA_947448565.1_Jr-12mar18-41_genomic.fna/markers.fasta
[2023-06-13 16:35:40,415] [INFO] Task started: Blastn
[2023-06-13 16:35:40,415] [INFO] Running command: blastn -query GCA_947448565.1_Jr-12mar18-41_genomic.fna/markers.fasta -db /var/lib/cwl/stg89da4d80-718e-4c84-80ed-273c8e9e2b59/dqc_reference/reference_markers.fasta -out GCA_947448565.1_Jr-12mar18-41_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 16:35:40,986] [INFO] Task succeeded: Blastn
[2023-06-13 16:35:40,989] [INFO] Selected 23 target genomes.
[2023-06-13 16:35:40,989] [INFO] Target genome list was writen to GCA_947448565.1_Jr-12mar18-41_genomic.fna/target_genomes.txt
[2023-06-13 16:35:40,991] [INFO] Task started: fastANI
[2023-06-13 16:35:40,991] [INFO] Running command: fastANI --query /var/lib/cwl/stg74212144-5ee0-46d9-ad93-62e7a0e3b238/GCA_947448565.1_Jr-12mar18-41_genomic.fna.gz --refList GCA_947448565.1_Jr-12mar18-41_genomic.fna/target_genomes.txt --output GCA_947448565.1_Jr-12mar18-41_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 16:35:54,901] [INFO] Task succeeded: fastANI
[2023-06-13 16:35:54,902] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89da4d80-718e-4c84-80ed-273c8e9e2b59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 16:35:54,902] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89da4d80-718e-4c84-80ed-273c8e9e2b59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 16:35:54,916] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 16:35:54,916] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 16:35:54,916] [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 aquatile	strain=ATCC 11947	GCA_002217235.1	245	245	type	True	79.4743	277	617	95	below_threshold
Flavobacterium aquatile	strain=NBRC 15052	GCA_006539785.1	245	245	type	True	79.4636	273	617	95	below_threshold
Flavobacterium aquatile	strain=LMG 4008	GCA_000757385.1	245	245	type	True	79.4546	280	617	95	below_threshold
Flavobacterium dankookense	strain=DSM 25687	GCA_004362665.1	706186	706186	type	True	78.4242	207	617	95	below_threshold
Flavobacterium solisilvae	strain=SE-s27	GCA_012911605.1	1852019	1852019	type	True	78.2056	197	617	95	below_threshold
Flavobacterium macrobrachii	strain=an-8	GCA_014486675.1	591204	591204	type	True	77.9598	218	617	95	below_threshold
Flavobacterium macrobrachii	strain=LMG 25203	GCA_014385475.2	591204	591204	type	True	77.9386	220	617	95	below_threshold
Flavobacterium sangjuense	strain=GS03	GCA_004797125.1	2518177	2518177	type	True	77.8769	181	617	95	below_threshold
Flavobacterium swingsii	strain=DSM 21789	GCA_900111965.1	498292	498292	type	True	77.562	150	617	95	below_threshold
Flavobacterium fluviale	strain=HYN0086	GCA_003312915.1	2249356	2249356	type	True	77.5265	116	617	95	below_threshold
Flavobacterium luteum	strain=NBRC 112527	GCA_008806775.1	2026654	2026654	type	True	77.3944	153	617	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	77.2674	149	617	95	below_threshold
Flavobacterium degerlachei	strain=DSM 15718	GCA_900106645.1	229203	229203	type	True	77.1448	119	617	95	below_threshold
Flavobacterium geliluteum	strain=P7388	GCA_017948595.1	2816120	2816120	type	True	77.0124	108	617	95	below_threshold
Flavobacterium filum	strain=DSM 17961	GCA_000425465.1	370974	370974	type	True	76.946	121	617	95	below_threshold
Flavobacterium faecale	strain=WV33	GCA_003076455.1	1355330	1355330	type	True	76.8443	96	617	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	76.8354	129	617	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	76.7725	131	617	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	76.7575	94	617	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_006491645.1	1774945	1774945	type	True	76.6069	120	617	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_009753805.1	1774945	1774945	type	True	76.6069	120	617	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	76.5719	123	617	95	below_threshold
Flavobacterium stagni	strain=WWJ-16	GCA_004122105.1	2506421	2506421	type	True	76.3121	103	617	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 16:35:54,918] [INFO] DFAST Taxonomy check result was written to GCA_947448565.1_Jr-12mar18-41_genomic.fna/tc_result.tsv
[2023-06-13 16:35:54,919] [INFO] ===== Taxonomy check completed =====
[2023-06-13 16:35:54,919] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 16:35:54,919] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89da4d80-718e-4c84-80ed-273c8e9e2b59/dqc_reference/checkm_data
[2023-06-13 16:35:54,920] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 16:35:54,946] [INFO] Task started: CheckM
[2023-06-13 16:35:54,947] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947448565.1_Jr-12mar18-41_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947448565.1_Jr-12mar18-41_genomic.fna/checkm_input GCA_947448565.1_Jr-12mar18-41_genomic.fna/checkm_result
[2023-06-13 16:36:18,320] [INFO] Task succeeded: CheckM
[2023-06-13 16:36:18,321] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 39.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 16:36:18,336] [INFO] ===== Completeness check finished =====
[2023-06-13 16:36:18,336] [INFO] ===== Start GTDB Search =====
[2023-06-13 16:36:18,336] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947448565.1_Jr-12mar18-41_genomic.fna/markers.fasta)
[2023-06-13 16:36:18,337] [INFO] Task started: Blastn
[2023-06-13 16:36:18,337] [INFO] Running command: blastn -query GCA_947448565.1_Jr-12mar18-41_genomic.fna/markers.fasta -db /var/lib/cwl/stg89da4d80-718e-4c84-80ed-273c8e9e2b59/dqc_reference/reference_markers_gtdb.fasta -out GCA_947448565.1_Jr-12mar18-41_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 16:36:19,097] [INFO] Task succeeded: Blastn
[2023-06-13 16:36:19,100] [INFO] Selected 11 target genomes.
[2023-06-13 16:36:19,100] [INFO] Target genome list was writen to GCA_947448565.1_Jr-12mar18-41_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 16:36:19,103] [INFO] Task started: fastANI
[2023-06-13 16:36:19,103] [INFO] Running command: fastANI --query /var/lib/cwl/stg74212144-5ee0-46d9-ad93-62e7a0e3b238/GCA_947448565.1_Jr-12mar18-41_genomic.fna.gz --refList GCA_947448565.1_Jr-12mar18-41_genomic.fna/target_genomes_gtdb.txt --output GCA_947448565.1_Jr-12mar18-41_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 16:36:25,675] [INFO] Task succeeded: fastANI
[2023-06-13 16:36:25,682] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 16:36:25,683] [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_903879645.1	s__Flavobacterium sp903879645	95.5092	425	617	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_903913315.1	s__Flavobacterium sp903913315	91.3298	475	617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.66	99.66	0.86	0.86	2	-
GCA_903888655.1	s__Flavobacterium sp903888655	81.4871	296	617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464475.1	s__Flavobacterium sp001464475	80.227	325	617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298525.1	s__Flavobacterium sp013298525	79.8344	298	617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003525665.1	s__Flavobacterium sp003525665	79.7261	263	617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000757385.1	s__Flavobacterium aquatile	79.4368	281	617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	99.99	1.00	1.00	3	-
GCA_903842575.1	s__Flavobacterium sp903842575	77.8947	185	617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004797125.1	s__Flavobacterium sangjuense	77.8769	181	617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017948595.1	s__Flavobacterium sp017948595	77.0124	108	617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425465.1	s__Flavobacterium filum	76.964	120	617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 16:36:25,684] [INFO] GTDB search result was written to GCA_947448565.1_Jr-12mar18-41_genomic.fna/result_gtdb.tsv
[2023-06-13 16:36:25,685] [INFO] ===== GTDB Search completed =====
[2023-06-13 16:36:25,688] [INFO] DFAST_QC result json was written to GCA_947448565.1_Jr-12mar18-41_genomic.fna/dqc_result.json
[2023-06-13 16:36:25,688] [INFO] DFAST_QC completed!
[2023-06-13 16:36:25,688] [INFO] Total running time: 0h0m53s