[2024-01-25 18:09:35,638] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:09:35,639] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:09:35,639] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c7f7129-0316-4738-898e-bd150b9a0379/dqc_reference
[2024-01-25 18:09:36,836] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:09:36,837] [INFO] Task started: Prodigal
[2024-01-25 18:09:36,837] [INFO] Running command: gunzip -c /var/lib/cwl/stgf7457df6-8ff6-4827-b0fc-43a09fdacb2e/GCF_016786255.1_ASM1678625v1_genomic.fna.gz | prodigal -d GCF_016786255.1_ASM1678625v1_genomic.fna/cds.fna -a GCF_016786255.1_ASM1678625v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:09:50,403] [INFO] Task succeeded: Prodigal
[2024-01-25 18:09:50,403] [INFO] Task started: HMMsearch
[2024-01-25 18:09:50,403] [INFO] Running command: hmmsearch --tblout GCF_016786255.1_ASM1678625v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c7f7129-0316-4738-898e-bd150b9a0379/dqc_reference/reference_markers.hmm GCF_016786255.1_ASM1678625v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:09:50,676] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:09:50,677] [INFO] Found 6/6 markers.
[2024-01-25 18:09:50,711] [INFO] Query marker FASTA was written to GCF_016786255.1_ASM1678625v1_genomic.fna/markers.fasta
[2024-01-25 18:09:50,711] [INFO] Task started: Blastn
[2024-01-25 18:09:50,711] [INFO] Running command: blastn -query GCF_016786255.1_ASM1678625v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c7f7129-0316-4738-898e-bd150b9a0379/dqc_reference/reference_markers.fasta -out GCF_016786255.1_ASM1678625v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:51,336] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:51,339] [INFO] Selected 16 target genomes.
[2024-01-25 18:09:51,340] [INFO] Target genome list was writen to GCF_016786255.1_ASM1678625v1_genomic.fna/target_genomes.txt
[2024-01-25 18:09:51,347] [INFO] Task started: fastANI
[2024-01-25 18:09:51,348] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7457df6-8ff6-4827-b0fc-43a09fdacb2e/GCF_016786255.1_ASM1678625v1_genomic.fna.gz --refList GCF_016786255.1_ASM1678625v1_genomic.fna/target_genomes.txt --output GCF_016786255.1_ASM1678625v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:10:01,443] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:01,443] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c7f7129-0316-4738-898e-bd150b9a0379/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:10:01,444] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c7f7129-0316-4738-898e-bd150b9a0379/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:10:01,452] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:10:01,452] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:10:01,452] [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
Robertkochia sediminum	strain=1368	GCA_016786255.1	2785326	2785326	type	True	100.0	1154	1157	95	conclusive
Robertkochia marina	strain=CC-AMO-30D	GCA_004799345.1	1227945	1227945	type	True	78.9867	384	1157	95	below_threshold
Robertkochia marina	strain=CC-AMO-30D	GCA_007279605.1	1227945	1227945	type	True	78.9593	386	1157	95	below_threshold
Robertkochia solimangrovi	strain=CL23	GCA_007279655.1	2213046	2213046	type	True	77.6092	158	1157	95	below_threshold
Leptobacterium flavescens	strain=KCTC 22160	GCA_010671605.1	472055	472055	type	True	77.0216	123	1157	95	below_threshold
Sinomicrobium oceani	strain=CGMCC 1.12145	GCA_900119185.1	1150368	1150368	type	True	77.0017	75	1157	95	below_threshold
Sinomicrobium weinanense	strain=FJxs	GCA_018863395.1	2842200	2842200	type	True	76.6491	81	1157	95	below_threshold
Sinomicrobium kalidii	strain=HD2P242	GCA_021183825.1	2900738	2900738	type	True	76.5225	83	1157	95	below_threshold
Sinomicrobium weinanense	strain=FJxs	GCA_014518365.1	2842200	2842200	type	True	76.5133	79	1157	95	below_threshold
Muricauda amoyensis	strain=GCL-11	GCA_003058265.1	2169401	2169401	type	True	76.4287	53	1157	95	below_threshold
Gramella gaetbulicola	strain=DSM 23082	GCA_003054225.1	703340	703340	type	True	76.3644	72	1157	95	below_threshold
Salegentibacter tibetensis	strain=JZCK2	GCA_020164485.1	2873600	2873600	type	True	76.3174	54	1157	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:10:01,453] [INFO] DFAST Taxonomy check result was written to GCF_016786255.1_ASM1678625v1_genomic.fna/tc_result.tsv
[2024-01-25 18:10:01,454] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:10:01,454] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:10:01,454] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c7f7129-0316-4738-898e-bd150b9a0379/dqc_reference/checkm_data
[2024-01-25 18:10:01,455] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:10:01,492] [INFO] Task started: CheckM
[2024-01-25 18:10:01,492] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016786255.1_ASM1678625v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016786255.1_ASM1678625v1_genomic.fna/checkm_input GCF_016786255.1_ASM1678625v1_genomic.fna/checkm_result
[2024-01-25 18:10:41,310] [INFO] Task succeeded: CheckM
[2024-01-25 18:10:41,311] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:10:41,331] [INFO] ===== Completeness check finished =====
[2024-01-25 18:10:41,331] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:10:41,332] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016786255.1_ASM1678625v1_genomic.fna/markers.fasta)
[2024-01-25 18:10:41,332] [INFO] Task started: Blastn
[2024-01-25 18:10:41,332] [INFO] Running command: blastn -query GCF_016786255.1_ASM1678625v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c7f7129-0316-4738-898e-bd150b9a0379/dqc_reference/reference_markers_gtdb.fasta -out GCF_016786255.1_ASM1678625v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:42,210] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:42,213] [INFO] Selected 19 target genomes.
[2024-01-25 18:10:42,213] [INFO] Target genome list was writen to GCF_016786255.1_ASM1678625v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:10:42,235] [INFO] Task started: fastANI
[2024-01-25 18:10:42,235] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7457df6-8ff6-4827-b0fc-43a09fdacb2e/GCF_016786255.1_ASM1678625v1_genomic.fna.gz --refList GCF_016786255.1_ASM1678625v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016786255.1_ASM1678625v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:10:54,753] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:54,761] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:10:54,761] [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_016786255.1	s__Robertkochia sp016786255	100.0	1154	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robertkochia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004799345.1	s__Robertkochia marina	78.9866	385	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robertkochia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013391805.1	s__Galbibacter_A sp013391805	77.7166	87	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Galbibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007279655.1	s__Robertkochia solimangrovi	77.6013	157	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robertkochia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163875.1	s__Gilvibacter sp002163875	77.5597	54	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gilvibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016734785.1	s__Galbibacter_A mesophilus	77.2633	88	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Galbibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010671605.1	s__Leptobacterium flavescens	77.021	122	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leptobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119185.1	s__Sinomicrobium oceani	77.0017	75	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Sinomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102915.1	s__Salinimicrobium catena	76.8638	66	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018863395.1	s__Sinomicrobium sp014518365	76.6437	80	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Sinomicrobium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003058265.1	s__Muricauda sp003058265	76.4218	51	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054225.1	s__Gramella gaetbulicola	76.3836	71	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009901585.1	s__R33 sp009901585	76.1592	51	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__R33	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:10:54,763] [INFO] GTDB search result was written to GCF_016786255.1_ASM1678625v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:10:54,763] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:10:54,766] [INFO] DFAST_QC result json was written to GCF_016786255.1_ASM1678625v1_genomic.fna/dqc_result.json
[2024-01-25 18:10:54,766] [INFO] DFAST_QC completed!
[2024-01-25 18:10:54,766] [INFO] Total running time: 0h1m19s