[2024-01-24 13:49:30,731] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:30,733] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:30,733] [INFO] DQC Reference Directory: /var/lib/cwl/stgff85ad7b-73a4-46f0-a4aa-e625b09745c8/dqc_reference
[2024-01-24 13:49:32,034] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:32,034] [INFO] Task started: Prodigal
[2024-01-24 13:49:32,035] [INFO] Running command: gunzip -c /var/lib/cwl/stgaea878c3-7a9a-42ca-8e01-23737082416e/GCF_005280585.1_ASM528058v1_genomic.fna.gz | prodigal -d GCF_005280585.1_ASM528058v1_genomic.fna/cds.fna -a GCF_005280585.1_ASM528058v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:09,315] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:09,316] [INFO] Task started: HMMsearch
[2024-01-24 13:50:09,316] [INFO] Running command: hmmsearch --tblout GCF_005280585.1_ASM528058v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff85ad7b-73a4-46f0-a4aa-e625b09745c8/dqc_reference/reference_markers.hmm GCF_005280585.1_ASM528058v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:09,812] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:09,814] [INFO] Found 6/6 markers.
[2024-01-24 13:50:09,892] [INFO] Query marker FASTA was written to GCF_005280585.1_ASM528058v1_genomic.fna/markers.fasta
[2024-01-24 13:50:09,892] [INFO] Task started: Blastn
[2024-01-24 13:50:09,893] [INFO] Running command: blastn -query GCF_005280585.1_ASM528058v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff85ad7b-73a4-46f0-a4aa-e625b09745c8/dqc_reference/reference_markers.fasta -out GCF_005280585.1_ASM528058v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:10,501] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:10,504] [INFO] Selected 14 target genomes.
[2024-01-24 13:50:10,504] [INFO] Target genome list was writen to GCF_005280585.1_ASM528058v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:10,510] [INFO] Task started: fastANI
[2024-01-24 13:50:10,510] [INFO] Running command: fastANI --query /var/lib/cwl/stgaea878c3-7a9a-42ca-8e01-23737082416e/GCF_005280585.1_ASM528058v1_genomic.fna.gz --refList GCF_005280585.1_ASM528058v1_genomic.fna/target_genomes.txt --output GCF_005280585.1_ASM528058v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:27,402] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:27,403] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff85ad7b-73a4-46f0-a4aa-e625b09745c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:27,404] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff85ad7b-73a4-46f0-a4aa-e625b09745c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:27,416] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:27,416] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:27,417] [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
Dyadobacter frigoris	strain=AR-3-8	GCA_005280585.1	2576211	2576211	type	True	100.0	2741	2746	95	conclusive
Dyadobacter subterraneus	strain=UP-52	GCA_015221875.1	2773304	2773304	type	True	85.4637	1845	2746	95	below_threshold
Dyadobacter koreensis	strain=DSM 19938	GCA_900108855.1	408657	408657	type	True	80.8875	1025	2746	95	below_threshold
Dyadobacter psychrotolerans	strain=AR-3-6	GCA_004349265.1	2541721	2541721	type	True	78.7099	542	2746	95	below_threshold
Dyadobacter luteus	strain=RS19	GCA_003383615.1	2259619	2259619	type	True	77.6636	319	2746	95	below_threshold
Dyadobacter psychrophilus	strain=DSM 22270	GCA_900167945.1	651661	651661	type	True	77.6464	353	2746	95	below_threshold
Dyadobacter sediminis	strain=CGMCC 1.12895	GCA_014640015.1	1493691	1493691	type	True	77.4552	365	2746	95	below_threshold
Dyadobacter alkalitolerans	strain=DSM 23607	GCA_000428845.1	492736	492736	type	True	77.3829	331	2746	95	below_threshold
Dyadobacter flavalbus	strain=NS28	GCA_006149045.1	2579942	2579942	type	True	77.3422	365	2746	95	below_threshold
Dyadobacter beijingensis	strain=CGMCC 1.6375	GCA_014645155.1	365489	365489	type	True	76.9782	201	2746	95	below_threshold
Dyadobacter beijingensis	strain=DSM 21582	GCA_000382205.1	365489	365489	type	True	76.8472	202	2746	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:27,418] [INFO] DFAST Taxonomy check result was written to GCF_005280585.1_ASM528058v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:27,419] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:27,419] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:27,419] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff85ad7b-73a4-46f0-a4aa-e625b09745c8/dqc_reference/checkm_data
[2024-01-24 13:50:27,420] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:27,495] [INFO] Task started: CheckM
[2024-01-24 13:50:27,495] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005280585.1_ASM528058v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005280585.1_ASM528058v1_genomic.fna/checkm_input GCF_005280585.1_ASM528058v1_genomic.fna/checkm_result
[2024-01-24 13:52:04,914] [INFO] Task succeeded: CheckM
[2024-01-24 13:52:04,916] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:52:04,941] [INFO] ===== Completeness check finished =====
[2024-01-24 13:52:04,942] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:52:04,942] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005280585.1_ASM528058v1_genomic.fna/markers.fasta)
[2024-01-24 13:52:04,942] [INFO] Task started: Blastn
[2024-01-24 13:52:04,943] [INFO] Running command: blastn -query GCF_005280585.1_ASM528058v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff85ad7b-73a4-46f0-a4aa-e625b09745c8/dqc_reference/reference_markers_gtdb.fasta -out GCF_005280585.1_ASM528058v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:52:05,684] [INFO] Task succeeded: Blastn
[2024-01-24 13:52:05,688] [INFO] Selected 9 target genomes.
[2024-01-24 13:52:05,689] [INFO] Target genome list was writen to GCF_005280585.1_ASM528058v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:52:05,712] [INFO] Task started: fastANI
[2024-01-24 13:52:05,712] [INFO] Running command: fastANI --query /var/lib/cwl/stgaea878c3-7a9a-42ca-8e01-23737082416e/GCF_005280585.1_ASM528058v1_genomic.fna.gz --refList GCF_005280585.1_ASM528058v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005280585.1_ASM528058v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:52:19,192] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:19,204] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:52:19,205] [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_005280585.1	s__Dyadobacter frigoris	100.0	2741	2746	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009801115.1	s__Dyadobacter sp009801115	85.6455	1833	2746	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015221875.1	s__Dyadobacter sp015221875	85.4767	1842	2746	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108855.1	s__Dyadobacter koreensis	80.8751	1027	2746	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349265.1	s__Dyadobacter psychrotolerans	78.7036	543	2746	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005869225.1	s__Dyadobacter bucti	77.6068	344	2746	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428845.1	s__Dyadobacter alkalitolerans	77.3829	331	2746	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006149045.1	s__Dyadobacter flavalbus	77.3422	365	2746	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382205.1	s__Dyadobacter beijingensis	76.8472	202	2746	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:52:19,210] [INFO] GTDB search result was written to GCF_005280585.1_ASM528058v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:52:19,210] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:52:19,213] [INFO] DFAST_QC result json was written to GCF_005280585.1_ASM528058v1_genomic.fna/dqc_result.json
[2024-01-24 13:52:19,213] [INFO] DFAST_QC completed!
[2024-01-24 13:52:19,213] [INFO] Total running time: 0h2m48s