[2024-01-25 18:58:35,592] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:58:35,594] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:58:35,594] [INFO] DQC Reference Directory: /var/lib/cwl/stgffa6371d-22f8-488a-9afa-fe427c681cb3/dqc_reference
[2024-01-25 18:58:36,721] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:58:36,722] [INFO] Task started: Prodigal
[2024-01-25 18:58:36,722] [INFO] Running command: gunzip -c /var/lib/cwl/stg75b825f1-77de-4ad5-81a5-b8d870c9f357/GCF_030409795.1_ASM3040979v1_genomic.fna.gz | prodigal -d GCF_030409795.1_ASM3040979v1_genomic.fna/cds.fna -a GCF_030409795.1_ASM3040979v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:58:47,829] [INFO] Task succeeded: Prodigal
[2024-01-25 18:58:47,829] [INFO] Task started: HMMsearch
[2024-01-25 18:58:47,829] [INFO] Running command: hmmsearch --tblout GCF_030409795.1_ASM3040979v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgffa6371d-22f8-488a-9afa-fe427c681cb3/dqc_reference/reference_markers.hmm GCF_030409795.1_ASM3040979v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:58:48,046] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:58:48,047] [INFO] Found 6/6 markers.
[2024-01-25 18:58:48,075] [INFO] Query marker FASTA was written to GCF_030409795.1_ASM3040979v1_genomic.fna/markers.fasta
[2024-01-25 18:58:48,075] [INFO] Task started: Blastn
[2024-01-25 18:58:48,075] [INFO] Running command: blastn -query GCF_030409795.1_ASM3040979v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgffa6371d-22f8-488a-9afa-fe427c681cb3/dqc_reference/reference_markers.fasta -out GCF_030409795.1_ASM3040979v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:48,726] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:48,729] [INFO] Selected 22 target genomes.
[2024-01-25 18:58:48,729] [INFO] Target genome list was writen to GCF_030409795.1_ASM3040979v1_genomic.fna/target_genomes.txt
[2024-01-25 18:58:48,749] [INFO] Task started: fastANI
[2024-01-25 18:58:48,749] [INFO] Running command: fastANI --query /var/lib/cwl/stg75b825f1-77de-4ad5-81a5-b8d870c9f357/GCF_030409795.1_ASM3040979v1_genomic.fna.gz --refList GCF_030409795.1_ASM3040979v1_genomic.fna/target_genomes.txt --output GCF_030409795.1_ASM3040979v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:59:02,213] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:02,213] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgffa6371d-22f8-488a-9afa-fe427c681cb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:59:02,214] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgffa6371d-22f8-488a-9afa-fe427c681cb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:59:02,227] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:59:02,227] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:59:02,228] [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 sangjuense	strain=GS03	GCA_004797125.1	2518177	2518177	type	True	84.4456	726	1204	95	below_threshold
Flavobacterium phycosphaerae	strain=MK012	GCA_010119235.1	2697515	2697515	type	True	79.5304	505	1204	95	below_threshold
Flavobacterium dankookense	strain=DSM 25687	GCA_004362665.1	706186	706186	type	True	79.2205	441	1204	95	below_threshold
Flavobacterium solisilvae	strain=SE-s27	GCA_012911605.1	1852019	1852019	type	True	79.09	433	1204	95	below_threshold
Flavobacterium macrobrachii	strain=LMG 25203	GCA_014385475.2	591204	591204	type	True	78.9063	434	1204	95	below_threshold
Flavobacterium macrobrachii	strain=an-8	GCA_014486675.1	591204	591204	type	True	78.8668	438	1204	95	below_threshold
Flavobacterium silvisoli	strain=RD-2-33	GCA_004329815.1	2529433	2529433	type	True	78.8054	382	1204	95	below_threshold
Flavobacterium aquatile	strain=LMG 4008	GCA_000757385.1	245	245	type	True	78.6749	393	1204	95	below_threshold
Flavobacterium aquatile	strain=ATCC 11947	GCA_002217235.1	245	245	type	True	78.6585	384	1204	95	below_threshold
Flavobacterium cheniae	strain=DSM 22462	GCA_004363695.1	295428	295428	type	True	78.0072	249	1204	95	below_threshold
Flavobacterium cheniae	strain=CGMCC 1.6844	GCA_007830415.1	295428	295428	type	True	77.9462	247	1204	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	77.9258	273	1204	95	below_threshold
Flavobacterium psychrolimnae	strain=LMG 22018	GCA_003312425.1	249351	249351	type	True	77.8332	257	1204	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	77.7738	240	1204	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	77.7601	245	1204	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	77.7546	173	1204	95	below_threshold
Flavobacterium xinjiangense	strain=CGMCC 1.2749	GCA_900142885.1	178356	178356	type	True	77.7466	253	1204	95	below_threshold
Flavobacterium xueshanense	strain=CGMCC 1.9227	GCA_900112975.1	935223	935223	type	True	77.7077	234	1204	95	below_threshold
Flavobacterium laiguense	strain=LB2P30	GCA_003097655.1	2169409	2169409	type	True	77.7046	226	1204	95	below_threshold
Flavobacterium gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	77.6599	281	1204	95	below_threshold
Flavobacterium filum	strain=DSM 17961	GCA_000425465.1	370974	370974	type	True	77.5678	256	1204	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	77.4448	164	1204	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:59:02,229] [INFO] DFAST Taxonomy check result was written to GCF_030409795.1_ASM3040979v1_genomic.fna/tc_result.tsv
[2024-01-25 18:59:02,229] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:59:02,230] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:59:02,230] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgffa6371d-22f8-488a-9afa-fe427c681cb3/dqc_reference/checkm_data
[2024-01-25 18:59:02,231] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:59:02,273] [INFO] Task started: CheckM
[2024-01-25 18:59:02,273] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030409795.1_ASM3040979v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030409795.1_ASM3040979v1_genomic.fna/checkm_input GCF_030409795.1_ASM3040979v1_genomic.fna/checkm_result
[2024-01-25 18:59:37,402] [INFO] Task succeeded: CheckM
[2024-01-25 18:59:37,403] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:59:37,423] [INFO] ===== Completeness check finished =====
[2024-01-25 18:59:37,424] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:59:37,424] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030409795.1_ASM3040979v1_genomic.fna/markers.fasta)
[2024-01-25 18:59:37,424] [INFO] Task started: Blastn
[2024-01-25 18:59:37,424] [INFO] Running command: blastn -query GCF_030409795.1_ASM3040979v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgffa6371d-22f8-488a-9afa-fe427c681cb3/dqc_reference/reference_markers_gtdb.fasta -out GCF_030409795.1_ASM3040979v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:38,369] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:38,372] [INFO] Selected 18 target genomes.
[2024-01-25 18:59:38,372] [INFO] Target genome list was writen to GCF_030409795.1_ASM3040979v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:59:38,385] [INFO] Task started: fastANI
[2024-01-25 18:59:38,385] [INFO] Running command: fastANI --query /var/lib/cwl/stg75b825f1-77de-4ad5-81a5-b8d870c9f357/GCF_030409795.1_ASM3040979v1_genomic.fna.gz --refList GCF_030409795.1_ASM3040979v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030409795.1_ASM3040979v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:59:49,136] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:49,151] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:59:49,151] [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_004797125.1	s__Flavobacterium sangjuense	84.4456	726	1204	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002296885.1	s__Flavobacterium sp002296885	80.1037	399	1204	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634615.1	s__Flavobacterium sp002482945	79.8982	530	1204	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.37	98.37	0.85	0.85	2	-
GCF_014486695.1	s__Flavobacterium buctense	79.799	494	1204	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010119235.1	s__Flavobacterium phycosphaerae	79.5429	508	1204	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011742145.1	s__Flavobacterium sp011742145	79.5407	469	1204	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013072765.1	s__Flavobacterium sp013072765	79.3366	478	1204	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362665.1	s__Flavobacterium dankookense	79.2082	441	1204	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911605.1	s__Flavobacterium sp012911605	79.1061	431	1204	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014486675.1	s__Flavobacterium macrobrachii	78.8665	438	1204	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.85	97.73	0.92	0.87	3	-
GCA_001464475.1	s__Flavobacterium sp001464475	78.5478	389	1204	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903842575.1	s__Flavobacterium sp903842575	78.5367	369	1204	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	78.3929	361	1204	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634825.1	s__Flavobacterium sp003634825	78.2137	246	1204	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903888655.1	s__Flavobacterium sp903888655	78.1191	225	1204	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002001005.1	s__Flavobacterium sp002001005	78.0159	224	1204	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014379405.1	s__Flavobacterium sp014379405	77.8741	221	1204	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009693635.1	s__Flavobacterium sp009693635	77.2724	186	1204	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 18:59:49,153] [INFO] GTDB search result was written to GCF_030409795.1_ASM3040979v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:59:49,154] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:59:49,158] [INFO] DFAST_QC result json was written to GCF_030409795.1_ASM3040979v1_genomic.fna/dqc_result.json
[2024-01-25 18:59:49,158] [INFO] DFAST_QC completed!
[2024-01-25 18:59:49,158] [INFO] Total running time: 0h1m14s