[2024-01-24 14:12:35,988] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:35,990] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:35,990] [INFO] DQC Reference Directory: /var/lib/cwl/stg2bf808b5-7ab7-4854-a8cb-5d8c3f964c58/dqc_reference
[2024-01-24 14:12:37,348] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:37,349] [INFO] Task started: Prodigal
[2024-01-24 14:12:37,350] [INFO] Running command: gunzip -c /var/lib/cwl/stgb53b650d-64c3-4223-8145-4c6c78d91572/GCF_000428845.1_ASM42884v1_genomic.fna.gz | prodigal -d GCF_000428845.1_ASM42884v1_genomic.fna/cds.fna -a GCF_000428845.1_ASM42884v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:10,008] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:10,009] [INFO] Task started: HMMsearch
[2024-01-24 14:13:10,009] [INFO] Running command: hmmsearch --tblout GCF_000428845.1_ASM42884v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2bf808b5-7ab7-4854-a8cb-5d8c3f964c58/dqc_reference/reference_markers.hmm GCF_000428845.1_ASM42884v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:10,348] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:10,350] [INFO] Found 6/6 markers.
[2024-01-24 14:13:10,403] [INFO] Query marker FASTA was written to GCF_000428845.1_ASM42884v1_genomic.fna/markers.fasta
[2024-01-24 14:13:10,404] [INFO] Task started: Blastn
[2024-01-24 14:13:10,404] [INFO] Running command: blastn -query GCF_000428845.1_ASM42884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bf808b5-7ab7-4854-a8cb-5d8c3f964c58/dqc_reference/reference_markers.fasta -out GCF_000428845.1_ASM42884v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:11,011] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:11,015] [INFO] Selected 15 target genomes.
[2024-01-24 14:13:11,015] [INFO] Target genome list was writen to GCF_000428845.1_ASM42884v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:11,024] [INFO] Task started: fastANI
[2024-01-24 14:13:11,024] [INFO] Running command: fastANI --query /var/lib/cwl/stgb53b650d-64c3-4223-8145-4c6c78d91572/GCF_000428845.1_ASM42884v1_genomic.fna.gz --refList GCF_000428845.1_ASM42884v1_genomic.fna/target_genomes.txt --output GCF_000428845.1_ASM42884v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:28,092] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:28,093] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2bf808b5-7ab7-4854-a8cb-5d8c3f964c58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:28,094] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2bf808b5-7ab7-4854-a8cb-5d8c3f964c58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:28,107] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:13:28,107] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:28,107] [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 alkalitolerans	strain=DSM 23607	GCA_000428845.1	492736	492736	type	True	100.0	2070	2073	95	conclusive
Dyadobacter psychrophilus	strain=DSM 22270	GCA_900167945.1	651661	651661	type	True	83.1935	1437	2073	95	below_threshold
Dyadobacter bucti	strain=QTA69	GCA_005869225.1	2572203	2572203	type	True	78.6982	617	2073	95	below_threshold
Dyadobacter luticola	strain=T17	GCA_005860805.1	1979387	1979387	type	True	78.3796	670	2073	95	below_threshold
Dyadobacter crusticola	strain=DSM 16708	GCA_000701505.1	292407	292407	type	True	78.3534	623	2073	95	below_threshold
Dyadobacter sediminis	strain=CGMCC 1.12895	GCA_014640015.1	1493691	1493691	type	True	78.2372	595	2073	95	below_threshold
Dyadobacter sediminis	strain=Z12	GCA_005860765.1	1493691	1493691	type	True	78.2283	604	2073	95	below_threshold
Dyadobacter flavalbus	strain=NS28	GCA_006149045.1	2579942	2579942	type	True	78.223	620	2073	95	below_threshold
Dyadobacter arcticus	strain=DSM 102865	GCA_011762185.1	1078754	1078754	type	True	78.165	542	2073	95	below_threshold
Dyadobacter fermentans	strain=DSM 18053	GCA_000023125.1	94254	94254	type	True	78.0086	596	2073	95	below_threshold
Dyadobacter psychrotolerans	strain=AR-3-6	GCA_004349265.1	2541721	2541721	type	True	77.8776	382	2073	95	below_threshold
Dyadobacter frigoris	strain=AR-3-8	GCA_005280585.1	2576211	2576211	type	True	77.5434	334	2073	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:28,109] [INFO] DFAST Taxonomy check result was written to GCF_000428845.1_ASM42884v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:28,109] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:28,110] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:28,110] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2bf808b5-7ab7-4854-a8cb-5d8c3f964c58/dqc_reference/checkm_data
[2024-01-24 14:13:28,111] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:28,166] [INFO] Task started: CheckM
[2024-01-24 14:13:28,167] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000428845.1_ASM42884v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000428845.1_ASM42884v1_genomic.fna/checkm_input GCF_000428845.1_ASM42884v1_genomic.fna/checkm_result
[2024-01-24 14:14:55,612] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:55,614] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:55,636] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:55,637] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:55,637] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000428845.1_ASM42884v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:55,638] [INFO] Task started: Blastn
[2024-01-24 14:14:55,638] [INFO] Running command: blastn -query GCF_000428845.1_ASM42884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bf808b5-7ab7-4854-a8cb-5d8c3f964c58/dqc_reference/reference_markers_gtdb.fasta -out GCF_000428845.1_ASM42884v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:56,493] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:56,497] [INFO] Selected 14 target genomes.
[2024-01-24 14:14:56,498] [INFO] Target genome list was writen to GCF_000428845.1_ASM42884v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:56,559] [INFO] Task started: fastANI
[2024-01-24 14:14:56,559] [INFO] Running command: fastANI --query /var/lib/cwl/stgb53b650d-64c3-4223-8145-4c6c78d91572/GCF_000428845.1_ASM42884v1_genomic.fna.gz --refList GCF_000428845.1_ASM42884v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000428845.1_ASM42884v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:15,258] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:15,275] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:15,276] [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_000428845.1	s__Dyadobacter alkalitolerans	100.0	2070	2073	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_900167945.1	s__Dyadobacter psychrophilus	83.1939	1437	2073	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	78.7121	615	2073	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_907165045.1	s__Dyadobacter sp907165045	78.672	626	2073	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005860805.1	s__Dyadobacter luticola	78.391	668	2073	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701505.1	s__Dyadobacter crusticola	78.3615	621	2073	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424405.1	s__Dyadobacter sp001424405	78.2674	590	2073	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005860765.1	s__Dyadobacter sediminis	78.2288	604	2073	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006149045.1	s__Dyadobacter flavalbus	78.2159	620	2073	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762185.1	s__Dyadobacter arcticus	78.1582	543	2073	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008369915.1	s__Dyadobacter sp008369915	78.1554	568	2073	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023125.1	s__Dyadobacter fermentans	78.0145	595	2073	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	77.8775	382	2073	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005280585.1	s__Dyadobacter frigoris	77.5434	334	2073	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:15,277] [INFO] GTDB search result was written to GCF_000428845.1_ASM42884v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:15,278] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:15,282] [INFO] DFAST_QC result json was written to GCF_000428845.1_ASM42884v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:15,283] [INFO] DFAST_QC completed!
[2024-01-24 14:15:15,283] [INFO] Total running time: 0h2m39s