[2024-01-24 15:02:36,473] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:36,475] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:36,475] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c465be2-86d5-4ae6-8092-36793b27ff98/dqc_reference
[2024-01-24 15:02:38,276] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:38,277] [INFO] Task started: Prodigal
[2024-01-24 15:02:38,278] [INFO] Running command: gunzip -c /var/lib/cwl/stg7accdb3f-bd6a-47c4-b6f1-6fa8f40a981c/GCF_002217335.1_ASM221733v1_genomic.fna.gz | prodigal -d GCF_002217335.1_ASM221733v1_genomic.fna/cds.fna -a GCF_002217335.1_ASM221733v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:56,746] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:56,747] [INFO] Task started: HMMsearch
[2024-01-24 15:02:56,747] [INFO] Running command: hmmsearch --tblout GCF_002217335.1_ASM221733v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c465be2-86d5-4ae6-8092-36793b27ff98/dqc_reference/reference_markers.hmm GCF_002217335.1_ASM221733v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:57,140] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:57,141] [INFO] Found 6/6 markers.
[2024-01-24 15:02:57,206] [INFO] Query marker FASTA was written to GCF_002217335.1_ASM221733v1_genomic.fna/markers.fasta
[2024-01-24 15:02:57,206] [INFO] Task started: Blastn
[2024-01-24 15:02:57,206] [INFO] Running command: blastn -query GCF_002217335.1_ASM221733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c465be2-86d5-4ae6-8092-36793b27ff98/dqc_reference/reference_markers.fasta -out GCF_002217335.1_ASM221733v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:58,028] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:58,033] [INFO] Selected 19 target genomes.
[2024-01-24 15:02:58,033] [INFO] Target genome list was writen to GCF_002217335.1_ASM221733v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:58,042] [INFO] Task started: fastANI
[2024-01-24 15:02:58,042] [INFO] Running command: fastANI --query /var/lib/cwl/stg7accdb3f-bd6a-47c4-b6f1-6fa8f40a981c/GCF_002217335.1_ASM221733v1_genomic.fna.gz --refList GCF_002217335.1_ASM221733v1_genomic.fna/target_genomes.txt --output GCF_002217335.1_ASM221733v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:20,249] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:20,250] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c465be2-86d5-4ae6-8092-36793b27ff98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:20,250] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c465be2-86d5-4ae6-8092-36793b27ff98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:20,266] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:03:20,266] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:20,266] [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 hydatis	strain=ATCC 29551	GCA_002217335.1	991	991	type	True	100.0	1932	1934	95	conclusive
Flavobacterium hydatis	strain=DSM 2063	GCA_000737695.1	991	991	type	True	99.9659	1879	1934	95	conclusive
Flavobacterium bizetiae	strain=CIP 105534	GCA_904425415.1	2704140	2704140	type	True	81.1607	901	1934	95	below_threshold
Flavobacterium bizetiae	strain=CIP 105534	GCA_902804475.1	2704140	2704140	type	True	81.0575	896	1934	95	below_threshold
Flavobacterium araucananum	strain=DSM 24704	GCA_002222055.1	946678	946678	type	True	80.8854	865	1934	95	below_threshold
Flavobacterium hibernum	strain=DSM 12611	GCA_000832125.1	37752	37752	type	True	80.8852	876	1934	95	below_threshold
Flavobacterium hibernum	strain=ATCC 51468	GCA_002217315.1	37752	37752	type	True	80.8792	869	1934	95	below_threshold
Flavobacterium hibernum	strain=NCTC13514	GCA_900450525.1	37752	37752	type	True	80.8359	862	1934	95	below_threshold
Flavobacterium psychroterrae	strain=CCM 8827	GCA_018380615.1	2133767	2133767	type	True	80.6527	855	1934	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_001686925.1	1114874	1114874	type	True	80.5545	853	1934	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_002222045.1	1114874	1114874	type	True	80.5151	844	1934	95	below_threshold
Flavobacterium pectinovorum	strain=DSM 6368	GCA_900142715.1	29533	29533	type	True	80.463	838	1934	95	below_threshold
Flavobacterium plurextorum	strain=CCUG 60112	GCA_002217395.1	1114867	1114867	type	True	80.3268	824	1934	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	80.0756	765	1934	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	79.6463	737	1934	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	79.5938	722	1934	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	79.5882	741	1934	95	below_threshold
Flavobacterium foetidum	strain=JCM 32085	GCA_004634245.1	2026681	2026681	type	True	79.1034	615	1934	95	below_threshold
Flavobacterium oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	76.9055	173	1934	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:20,268] [INFO] DFAST Taxonomy check result was written to GCF_002217335.1_ASM221733v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:20,269] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:20,269] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:20,269] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c465be2-86d5-4ae6-8092-36793b27ff98/dqc_reference/checkm_data
[2024-01-24 15:03:20,270] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:20,328] [INFO] Task started: CheckM
[2024-01-24 15:03:20,328] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002217335.1_ASM221733v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002217335.1_ASM221733v1_genomic.fna/checkm_input GCF_002217335.1_ASM221733v1_genomic.fna/checkm_result
[2024-01-24 15:04:15,908] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:15,909] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:15,929] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:15,929] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:15,930] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002217335.1_ASM221733v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:15,930] [INFO] Task started: Blastn
[2024-01-24 15:04:15,930] [INFO] Running command: blastn -query GCF_002217335.1_ASM221733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c465be2-86d5-4ae6-8092-36793b27ff98/dqc_reference/reference_markers_gtdb.fasta -out GCF_002217335.1_ASM221733v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:16,997] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:17,001] [INFO] Selected 15 target genomes.
[2024-01-24 15:04:17,001] [INFO] Target genome list was writen to GCF_002217335.1_ASM221733v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:17,013] [INFO] Task started: fastANI
[2024-01-24 15:04:17,014] [INFO] Running command: fastANI --query /var/lib/cwl/stg7accdb3f-bd6a-47c4-b6f1-6fa8f40a981c/GCF_002217335.1_ASM221733v1_genomic.fna.gz --refList GCF_002217335.1_ASM221733v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002217335.1_ASM221733v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:37,837] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:37,859] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:37,860] [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_000737695.1	s__Flavobacterium hydatis	99.9659	1879	1934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.97	99.97	0.98	0.98	2	conclusive
GCF_000813005.1	s__Flavobacterium sp000813005	90.6162	1539	1934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.28	97.24	0.92	0.92	3	-
GCF_015594725.1	s__Flavobacterium sp015594725	86.512	1094	1934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003668995.1	s__Flavobacterium sp003668995	86.305	1227	1934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902804475.1	s__Flavobacterium bizetiae	81.048	897	1934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.96	99.94	0.99	0.99	3	-
GCF_009707955.1	s__Flavobacterium sp009707955	80.9933	874	1934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001422725.1	s__Flavobacterium sp001422725	80.7673	866	1934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975985.1	s__Flavobacterium sp001975985	80.731	839	1934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217415.1	s__Flavobacterium sp003217415	80.7293	921	1934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.56	98.67	0.98	0.94	4	-
GCF_009664855.1	s__Flavobacterium sp009664855	80.6904	861	1934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.90	98.90	0.89	0.89	2	-
GCF_001404985.1	s__Flavobacterium aquidurense_B	80.6265	822	1934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001686925.1	s__Flavobacterium piscis	80.5674	852	1934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.33	97.30	0.93	0.88	4	-
GCF_009711165.2	s__Flavobacterium sp009711165	80.2223	845	1934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017833415.1	s__Flavobacterium sp017833415	79.9993	714	1934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004634245.1	s__Flavobacterium foetidum	79.1182	613	1934	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 15:04:37,862] [INFO] GTDB search result was written to GCF_002217335.1_ASM221733v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:37,863] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:37,870] [INFO] DFAST_QC result json was written to GCF_002217335.1_ASM221733v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:37,870] [INFO] DFAST_QC completed!
[2024-01-24 15:04:37,870] [INFO] Total running time: 0h2m1s