[2024-01-24 12:07:06,787] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:07:06,790] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:07:06,790] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d4285f1-7ed5-409f-bc7a-bec55292ae31/dqc_reference
[2024-01-24 12:07:08,082] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:07:08,083] [INFO] Task started: Prodigal
[2024-01-24 12:07:08,083] [INFO] Running command: gunzip -c /var/lib/cwl/stg6450fc4b-b6f9-4afc-8c9a-e430fea352fc/GCF_004005965.1_ASM400596v1_genomic.fna.gz | prodigal -d GCF_004005965.1_ASM400596v1_genomic.fna/cds.fna -a GCF_004005965.1_ASM400596v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:19,220] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:19,221] [INFO] Task started: HMMsearch
[2024-01-24 12:07:19,221] [INFO] Running command: hmmsearch --tblout GCF_004005965.1_ASM400596v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d4285f1-7ed5-409f-bc7a-bec55292ae31/dqc_reference/reference_markers.hmm GCF_004005965.1_ASM400596v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:19,522] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:19,524] [INFO] Found 6/6 markers.
[2024-01-24 12:07:19,549] [INFO] Query marker FASTA was written to GCF_004005965.1_ASM400596v1_genomic.fna/markers.fasta
[2024-01-24 12:07:19,549] [INFO] Task started: Blastn
[2024-01-24 12:07:19,549] [INFO] Running command: blastn -query GCF_004005965.1_ASM400596v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d4285f1-7ed5-409f-bc7a-bec55292ae31/dqc_reference/reference_markers.fasta -out GCF_004005965.1_ASM400596v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:20,137] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:20,141] [INFO] Selected 17 target genomes.
[2024-01-24 12:07:20,141] [INFO] Target genome list was writen to GCF_004005965.1_ASM400596v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:20,148] [INFO] Task started: fastANI
[2024-01-24 12:07:20,148] [INFO] Running command: fastANI --query /var/lib/cwl/stg6450fc4b-b6f9-4afc-8c9a-e430fea352fc/GCF_004005965.1_ASM400596v1_genomic.fna.gz --refList GCF_004005965.1_ASM400596v1_genomic.fna/target_genomes.txt --output GCF_004005965.1_ASM400596v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:28,684] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:28,685] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d4285f1-7ed5-409f-bc7a-bec55292ae31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:28,686] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d4285f1-7ed5-409f-bc7a-bec55292ae31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:28,697] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:28,698] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:28,698] [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
Sandaracinomonas limnophila	strain=FSY-15	GCA_004005965.1	1862386	1862386	type	True	100.0	891	891	95	conclusive
Aquirufa lenticrescens	strain=9H-EGSE	GCA_019916085.1	2696560	2696560	type	True	77.6658	122	891	95	below_threshold
Aquirufa aurantiipilula	strain=15D-MOB	GCA_019923745.1	2696561	2696561	type	True	77.6275	185	891	95	below_threshold
Aquirufa nivalisilvae	strain=59G-WUEMPEL	GCA_004307455.1	2516557	2516557	type	True	77.2658	187	891	95	below_threshold
Aquirufa antheringensis	strain=30S-ANTBAC	GCA_004307425.1	2516559	2516559	type	True	77.1961	127	891	95	below_threshold
Aquirufa beregesia	strain=50C-KIRBA	GCA_011090385.1	2516556	2516556	type	True	77.0397	155	891	95	below_threshold
Aquirufa rosea	strain=CAR-16	GCA_004118285.1	2509241	2509241	type	True	77.0301	159	891	95	below_threshold
Aquirufa ecclesiirivi	strain=50A-KIRBA	GCA_011250515.1	2715124	2715124	type	True	76.8566	169	891	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:28,700] [INFO] DFAST Taxonomy check result was written to GCF_004005965.1_ASM400596v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:28,700] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:28,701] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:28,701] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d4285f1-7ed5-409f-bc7a-bec55292ae31/dqc_reference/checkm_data
[2024-01-24 12:07:28,703] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:28,732] [INFO] Task started: CheckM
[2024-01-24 12:07:28,732] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004005965.1_ASM400596v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004005965.1_ASM400596v1_genomic.fna/checkm_input GCF_004005965.1_ASM400596v1_genomic.fna/checkm_result
[2024-01-24 12:08:06,064] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:06,066] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:06,088] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:06,089] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:06,089] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004005965.1_ASM400596v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:06,089] [INFO] Task started: Blastn
[2024-01-24 12:08:06,090] [INFO] Running command: blastn -query GCF_004005965.1_ASM400596v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d4285f1-7ed5-409f-bc7a-bec55292ae31/dqc_reference/reference_markers_gtdb.fasta -out GCF_004005965.1_ASM400596v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:06,835] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:06,840] [INFO] Selected 22 target genomes.
[2024-01-24 12:08:06,840] [INFO] Target genome list was writen to GCF_004005965.1_ASM400596v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:06,870] [INFO] Task started: fastANI
[2024-01-24 12:08:06,870] [INFO] Running command: fastANI --query /var/lib/cwl/stg6450fc4b-b6f9-4afc-8c9a-e430fea352fc/GCF_004005965.1_ASM400596v1_genomic.fna.gz --refList GCF_004005965.1_ASM400596v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004005965.1_ASM400596v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:19,433] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:19,449] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:19,450] [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
GCA_004005965.1	s__UBA6715 sp004005965	100.0	891	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__UBA6715	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903898715.1	s__Aquirufa sp903898715	77.4375	104	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Aquirufa	95.0	99.63	99.56	0.90	0.88	3	-
GCA_004307455.1	s__Allopseudarcicella nivalisilvae	77.2658	187	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Allopseudarcicella	95.0	97.41	97.41	0.94	0.94	2	-
GCA_903907915.1	s__Aquirufa sp903907915	77.2396	81	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Aquirufa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017984215.1	s__Aquirufa sp017984215	77.2322	142	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Aquirufa	95.0	99.80	99.80	0.94	0.94	2	-
GCA_002479785.1	s__Aquirufa sp002479785	77.1975	100	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Aquirufa	95.0	99.96	99.96	0.93	0.93	2	-
GCF_004307425.1	s__Aquirufa antheringensis	77.1923	128	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Aquirufa	95.0	97.17	97.17	0.93	0.93	2	-
GCA_002454335.1	s__Aquirufa sp002454335	77.1031	139	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Aquirufa	95.0	99.80	99.80	0.91	0.91	2	-
GCF_011090385.1	s__Allopseudarcicella beregesia	77.0397	155	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Allopseudarcicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004118285.1	s__Allopseudarcicella rosea	77.0301	159	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Allopseudarcicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011250515.1	s__Allopseudarcicella ecclesiirivi	76.8566	169	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Allopseudarcicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005791165.1	s__Aquirufa sp005791165	76.5528	113	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Aquirufa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204325.1	s__Arcicella rosea	76.4433	77	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Arcicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298805.1	s__Arcicella sp013298805	76.1897	64	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Arcicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903837305.1	s__Aquirufa sp903837305	75.7502	71	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Aquirufa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014376355.1	s__Arcicella sp014376355	75.4948	57	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Arcicella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:19,451] [INFO] GTDB search result was written to GCF_004005965.1_ASM400596v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:19,452] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:19,455] [INFO] DFAST_QC result json was written to GCF_004005965.1_ASM400596v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:19,456] [INFO] DFAST_QC completed!
[2024-01-24 12:08:19,456] [INFO] Total running time: 0h1m13s