[2024-01-24 13:40:34,588] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:34,590] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:34,590] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d6b635c-06f0-46f0-ab89-bf7892730c40/dqc_reference
[2024-01-24 13:40:36,134] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:36,134] [INFO] Task started: Prodigal
[2024-01-24 13:40:36,135] [INFO] Running command: gunzip -c /var/lib/cwl/stgd8bbd410-e8ec-42d4-a665-b45e8ed798b7/GCF_005860765.1_ASM586076v1_genomic.fna.gz | prodigal -d GCF_005860765.1_ASM586076v1_genomic.fna/cds.fna -a GCF_005860765.1_ASM586076v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:07,404] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:07,405] [INFO] Task started: HMMsearch
[2024-01-24 13:41:07,405] [INFO] Running command: hmmsearch --tblout GCF_005860765.1_ASM586076v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d6b635c-06f0-46f0-ab89-bf7892730c40/dqc_reference/reference_markers.hmm GCF_005860765.1_ASM586076v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:07,815] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:07,816] [INFO] Found 6/6 markers.
[2024-01-24 13:41:07,870] [INFO] Query marker FASTA was written to GCF_005860765.1_ASM586076v1_genomic.fna/markers.fasta
[2024-01-24 13:41:07,870] [INFO] Task started: Blastn
[2024-01-24 13:41:07,870] [INFO] Running command: blastn -query GCF_005860765.1_ASM586076v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d6b635c-06f0-46f0-ab89-bf7892730c40/dqc_reference/reference_markers.fasta -out GCF_005860765.1_ASM586076v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:08,525] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:08,529] [INFO] Selected 14 target genomes.
[2024-01-24 13:41:08,529] [INFO] Target genome list was writen to GCF_005860765.1_ASM586076v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:08,540] [INFO] Task started: fastANI
[2024-01-24 13:41:08,540] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8bbd410-e8ec-42d4-a665-b45e8ed798b7/GCF_005860765.1_ASM586076v1_genomic.fna.gz --refList GCF_005860765.1_ASM586076v1_genomic.fna/target_genomes.txt --output GCF_005860765.1_ASM586076v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:25,378] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:25,378] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d6b635c-06f0-46f0-ab89-bf7892730c40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:25,379] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d6b635c-06f0-46f0-ab89-bf7892730c40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:25,388] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:25,388] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:25,388] [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 sediminis	strain=Z12	GCA_005860765.1	1493691	1493691	type	True	100.0	2050	2050	95	conclusive
Dyadobacter sediminis	strain=CGMCC 1.12895	GCA_014640015.1	1493691	1493691	type	True	99.9962	2035	2050	95	conclusive
Dyadobacter flavalbus	strain=NS28	GCA_006149045.1	2579942	2579942	type	True	90.7036	1779	2050	95	below_threshold
Dyadobacter bucti	strain=QTA69	GCA_005869225.1	2572203	2572203	type	True	78.9265	632	2050	95	below_threshold
Dyadobacter alkalitolerans	strain=DSM 23607	GCA_000428845.1	492736	492736	type	True	78.2265	591	2050	95	below_threshold
Dyadobacter crusticola	strain=DSM 16708	GCA_000701505.1	292407	292407	type	True	77.8982	470	2050	95	below_threshold
Dyadobacter luticola	strain=T17	GCA_005860805.1	1979387	1979387	type	True	77.8135	525	2050	95	below_threshold
Dyadobacter sandarakinus	strain=Q3-56	GCA_016894445.1	2747268	2747268	type	True	77.6484	526	2050	95	below_threshold
Dyadobacter soli	strain=DSM 25329	GCA_900101885.1	659014	659014	type	True	77.3396	474	2050	95	below_threshold
Dyadobacter subterraneus	strain=UP-52	GCA_015221875.1	2773304	2773304	type	True	77.1511	362	2050	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:25,390] [INFO] DFAST Taxonomy check result was written to GCF_005860765.1_ASM586076v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:25,390] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:25,391] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:25,391] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d6b635c-06f0-46f0-ab89-bf7892730c40/dqc_reference/checkm_data
[2024-01-24 13:41:25,393] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:25,475] [INFO] Task started: CheckM
[2024-01-24 13:41:25,476] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005860765.1_ASM586076v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005860765.1_ASM586076v1_genomic.fna/checkm_input GCF_005860765.1_ASM586076v1_genomic.fna/checkm_result
[2024-01-24 13:42:51,950] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:51,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:51,980] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:51,981] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:51,981] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005860765.1_ASM586076v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:51,982] [INFO] Task started: Blastn
[2024-01-24 13:42:51,982] [INFO] Running command: blastn -query GCF_005860765.1_ASM586076v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d6b635c-06f0-46f0-ab89-bf7892730c40/dqc_reference/reference_markers_gtdb.fasta -out GCF_005860765.1_ASM586076v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:52,771] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:52,776] [INFO] Selected 18 target genomes.
[2024-01-24 13:42:52,776] [INFO] Target genome list was writen to GCF_005860765.1_ASM586076v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:52,847] [INFO] Task started: fastANI
[2024-01-24 13:42:52,847] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8bbd410-e8ec-42d4-a665-b45e8ed798b7/GCF_005860765.1_ASM586076v1_genomic.fna.gz --refList GCF_005860765.1_ASM586076v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005860765.1_ASM586076v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:12,148] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:12,163] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:12,164] [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_005860765.1	s__Dyadobacter sediminis	100.0	2050	2050	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_006149045.1	s__Dyadobacter flavalbus	90.7126	1778	2050	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167945.1	s__Dyadobacter psychrophilus	79.6024	623	2050	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	78.9176	632	2050	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	78.2285	591	2050	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	77.8835	470	2050	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	77.8135	525	2050	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	77.7944	475	2050	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016894445.1	s__Dyadobacter sp016894445	77.638	527	2050	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898145.1	s__Dyadobacter sp001898145	77.6257	477	2050	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	99.32	99.32	0.98	0.98	2	-
GCF_001424405.1	s__Dyadobacter sp001424405	77.5552	502	2050	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	77.5239	450	2050	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	77.3465	472	2050	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	77.1511	362	2050	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 13:43:12,165] [INFO] GTDB search result was written to GCF_005860765.1_ASM586076v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:12,166] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:12,169] [INFO] DFAST_QC result json was written to GCF_005860765.1_ASM586076v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:12,169] [INFO] DFAST_QC completed!
[2024-01-24 13:43:12,169] [INFO] Total running time: 0h2m38s