[2024-01-25 17:39:05,792] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:39:05,794] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:39:05,794] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c4959dc-8940-438d-b695-377e5fa1f1d5/dqc_reference
[2024-01-25 17:39:06,949] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:39:06,950] [INFO] Task started: Prodigal
[2024-01-25 17:39:06,950] [INFO] Running command: gunzip -c /var/lib/cwl/stg8f17012c-8bfb-41fe-8ccb-d0d1ac929419/GCF_023822005.2_ASM2382200v2_genomic.fna.gz | prodigal -d GCF_023822005.2_ASM2382200v2_genomic.fna/cds.fna -a GCF_023822005.2_ASM2382200v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:39:34,257] [INFO] Task succeeded: Prodigal
[2024-01-25 17:39:34,257] [INFO] Task started: HMMsearch
[2024-01-25 17:39:34,258] [INFO] Running command: hmmsearch --tblout GCF_023822005.2_ASM2382200v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c4959dc-8940-438d-b695-377e5fa1f1d5/dqc_reference/reference_markers.hmm GCF_023822005.2_ASM2382200v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:39:34,586] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:39:34,587] [INFO] Found 6/6 markers.
[2024-01-25 17:39:34,636] [INFO] Query marker FASTA was written to GCF_023822005.2_ASM2382200v2_genomic.fna/markers.fasta
[2024-01-25 17:39:34,637] [INFO] Task started: Blastn
[2024-01-25 17:39:34,637] [INFO] Running command: blastn -query GCF_023822005.2_ASM2382200v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c4959dc-8940-438d-b695-377e5fa1f1d5/dqc_reference/reference_markers.fasta -out GCF_023822005.2_ASM2382200v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:35,209] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:35,213] [INFO] Selected 18 target genomes.
[2024-01-25 17:39:35,213] [INFO] Target genome list was writen to GCF_023822005.2_ASM2382200v2_genomic.fna/target_genomes.txt
[2024-01-25 17:39:35,258] [INFO] Task started: fastANI
[2024-01-25 17:39:35,259] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f17012c-8bfb-41fe-8ccb-d0d1ac929419/GCF_023822005.2_ASM2382200v2_genomic.fna.gz --refList GCF_023822005.2_ASM2382200v2_genomic.fna/target_genomes.txt --output GCF_023822005.2_ASM2382200v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:39:56,493] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:56,493] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c4959dc-8940-438d-b695-377e5fa1f1d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:39:56,494] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c4959dc-8940-438d-b695-377e5fa1f1d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:39:56,503] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:39:56,503] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:39:56,503] [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 psychrophilus	strain=DSM 22270	GCA_900167945.1	651661	651661	type	True	86.2669	1761	2090	95	below_threshold
Dyadobacter alkalitolerans	strain=DSM 23607	GCA_000428845.1	492736	492736	type	True	83.5277	1434	2090	95	below_threshold
Dyadobacter bucti	strain=QTA69	GCA_005869225.1	2572203	2572203	type	True	78.7192	644	2090	95	below_threshold
Dyadobacter flavalbus	strain=NS28	GCA_006149045.1	2579942	2579942	type	True	78.4137	595	2090	95	below_threshold
Dyadobacter luticola	strain=T17	GCA_005860805.1	1979387	1979387	type	True	78.3947	673	2090	95	below_threshold
Dyadobacter sediminis	strain=CGMCC 1.12895	GCA_014640015.1	1493691	1493691	type	True	78.3284	589	2090	95	below_threshold
Dyadobacter sediminis	strain=Z12	GCA_005860765.1	1493691	1493691	type	True	78.2902	595	2090	95	below_threshold
Dyadobacter arcticus	strain=DSM 102865	GCA_011762185.1	1078754	1078754	type	True	78.2824	588	2090	95	below_threshold
Dyadobacter crusticola	strain=DSM 16708	GCA_000701505.1	292407	292407	type	True	78.1578	575	2090	95	below_threshold
Dyadobacter endophyticus	strain=CGMCC 1.15288	GCA_014641595.1	1749036	1749036	type	True	78.0617	564	2090	95	below_threshold
Dyadobacter fermentans	strain=DSM 18053	GCA_000023125.1	94254	94254	type	True	77.9496	613	2090	95	below_threshold
Dyadobacter soli	strain=DSM 25329	GCA_900101885.1	659014	659014	type	True	77.9464	598	2090	95	below_threshold
Dyadobacter psychrotolerans	strain=AR-3-6	GCA_004349265.1	2541721	2541721	type	True	77.7916	398	2090	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:39:56,505] [INFO] DFAST Taxonomy check result was written to GCF_023822005.2_ASM2382200v2_genomic.fna/tc_result.tsv
[2024-01-25 17:39:56,505] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:39:56,505] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:39:56,506] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c4959dc-8940-438d-b695-377e5fa1f1d5/dqc_reference/checkm_data
[2024-01-25 17:39:56,506] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:39:56,565] [INFO] Task started: CheckM
[2024-01-25 17:39:56,565] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023822005.2_ASM2382200v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023822005.2_ASM2382200v2_genomic.fna/checkm_input GCF_023822005.2_ASM2382200v2_genomic.fna/checkm_result
[2024-01-25 17:41:12,062] [INFO] Task succeeded: CheckM
[2024-01-25 17:41:12,064] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:41:12,084] [INFO] ===== Completeness check finished =====
[2024-01-25 17:41:12,085] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:41:12,086] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023822005.2_ASM2382200v2_genomic.fna/markers.fasta)
[2024-01-25 17:41:12,086] [INFO] Task started: Blastn
[2024-01-25 17:41:12,086] [INFO] Running command: blastn -query GCF_023822005.2_ASM2382200v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c4959dc-8940-438d-b695-377e5fa1f1d5/dqc_reference/reference_markers_gtdb.fasta -out GCF_023822005.2_ASM2382200v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:13,015] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:13,017] [INFO] Selected 16 target genomes.
[2024-01-25 17:41:13,017] [INFO] Target genome list was writen to GCF_023822005.2_ASM2382200v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:41:13,030] [INFO] Task started: fastANI
[2024-01-25 17:41:13,030] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f17012c-8bfb-41fe-8ccb-d0d1ac929419/GCF_023822005.2_ASM2382200v2_genomic.fna.gz --refList GCF_023822005.2_ASM2382200v2_genomic.fna/target_genomes_gtdb.txt --output GCF_023822005.2_ASM2382200v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:41:33,997] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:34,007] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:41:34,007] [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_900167945.1	s__Dyadobacter psychrophilus	86.2612	1762	2090	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	83.5279	1434	2090	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	78.7235	642	2090	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	78.5566	669	2090	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	78.4137	595	2090	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	78.3949	673	2090	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	78.3017	614	2090	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	78.2968	594	2090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011762185.1	s__Dyadobacter arcticus	78.2888	587	2090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641595.1	s__Dyadobacter endophyticus	78.0656	564	2090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101885.1	s__Dyadobacter soli	77.9402	595	2090	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	77.895	611	2090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109045.1	s__Dyadobacter sp900109045	77.8098	593	2090	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	77.789	397	2090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009801115.1	s__Dyadobacter sp009801115	77.5542	350	2090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:41:34,011] [INFO] GTDB search result was written to GCF_023822005.2_ASM2382200v2_genomic.fna/result_gtdb.tsv
[2024-01-25 17:41:34,012] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:41:34,016] [INFO] DFAST_QC result json was written to GCF_023822005.2_ASM2382200v2_genomic.fna/dqc_result.json
[2024-01-25 17:41:34,016] [INFO] DFAST_QC completed!
[2024-01-25 17:41:34,016] [INFO] Total running time: 0h2m28s