[2023-06-08 19:15:55,891] [INFO] DFAST_QC pipeline started.
[2023-06-08 19:15:55,893] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 19:15:55,893] [INFO] DQC Reference Directory: /var/lib/cwl/stg99e51165-7fd5-4031-a34f-e2da237a839e/dqc_reference
[2023-06-08 19:15:58,293] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 19:15:58,294] [INFO] Task started: Prodigal
[2023-06-08 19:15:58,294] [INFO] Running command: gunzip -c /var/lib/cwl/stg836d7567-e06f-4329-8955-49ca40d2d559/GCA_947486855.1_ZE-13oct10-55_genomic.fna.gz | prodigal -d GCA_947486855.1_ZE-13oct10-55_genomic.fna/cds.fna -a GCA_947486855.1_ZE-13oct10-55_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 19:16:10,773] [INFO] Task succeeded: Prodigal
[2023-06-08 19:16:10,773] [INFO] Task started: HMMsearch
[2023-06-08 19:16:10,773] [INFO] Running command: hmmsearch --tblout GCA_947486855.1_ZE-13oct10-55_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99e51165-7fd5-4031-a34f-e2da237a839e/dqc_reference/reference_markers.hmm GCA_947486855.1_ZE-13oct10-55_genomic.fna/protein.faa > /dev/null
[2023-06-08 19:16:11,018] [INFO] Task succeeded: HMMsearch
[2023-06-08 19:16:11,019] [INFO] Found 6/6 markers.
[2023-06-08 19:16:11,053] [INFO] Query marker FASTA was written to GCA_947486855.1_ZE-13oct10-55_genomic.fna/markers.fasta
[2023-06-08 19:16:11,054] [INFO] Task started: Blastn
[2023-06-08 19:16:11,054] [INFO] Running command: blastn -query GCA_947486855.1_ZE-13oct10-55_genomic.fna/markers.fasta -db /var/lib/cwl/stg99e51165-7fd5-4031-a34f-e2da237a839e/dqc_reference/reference_markers.fasta -out GCA_947486855.1_ZE-13oct10-55_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 19:16:11,626] [INFO] Task succeeded: Blastn
[2023-06-08 19:16:11,631] [INFO] Selected 27 target genomes.
[2023-06-08 19:16:11,631] [INFO] Target genome list was writen to GCA_947486855.1_ZE-13oct10-55_genomic.fna/target_genomes.txt
[2023-06-08 19:16:11,638] [INFO] Task started: fastANI
[2023-06-08 19:16:11,638] [INFO] Running command: fastANI --query /var/lib/cwl/stg836d7567-e06f-4329-8955-49ca40d2d559/GCA_947486855.1_ZE-13oct10-55_genomic.fna.gz --refList GCA_947486855.1_ZE-13oct10-55_genomic.fna/target_genomes.txt --output GCA_947486855.1_ZE-13oct10-55_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 19:16:33,203] [INFO] Task succeeded: fastANI
[2023-06-08 19:16:33,203] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99e51165-7fd5-4031-a34f-e2da237a839e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 19:16:33,204] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99e51165-7fd5-4031-a34f-e2da237a839e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 19:16:33,206] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 19:16:33,207] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 19:16:33,207] [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
--------------------------------------------------------------------------------
[2023-06-08 19:16:33,209] [INFO] DFAST Taxonomy check result was written to GCA_947486855.1_ZE-13oct10-55_genomic.fna/tc_result.tsv
[2023-06-08 19:16:33,210] [INFO] ===== Taxonomy check completed =====
[2023-06-08 19:16:33,210] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 19:16:33,211] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99e51165-7fd5-4031-a34f-e2da237a839e/dqc_reference/checkm_data
[2023-06-08 19:16:33,214] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 19:16:33,239] [INFO] Task started: CheckM
[2023-06-08 19:16:33,239] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947486855.1_ZE-13oct10-55_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947486855.1_ZE-13oct10-55_genomic.fna/checkm_input GCA_947486855.1_ZE-13oct10-55_genomic.fna/checkm_result
[2023-06-08 19:17:14,294] [INFO] Task succeeded: CheckM
[2023-06-08 19:17:14,296] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.81%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 19:17:14,316] [INFO] ===== Completeness check finished =====
[2023-06-08 19:17:14,316] [INFO] ===== Start GTDB Search =====
[2023-06-08 19:17:14,316] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947486855.1_ZE-13oct10-55_genomic.fna/markers.fasta)
[2023-06-08 19:17:14,317] [INFO] Task started: Blastn
[2023-06-08 19:17:14,317] [INFO] Running command: blastn -query GCA_947486855.1_ZE-13oct10-55_genomic.fna/markers.fasta -db /var/lib/cwl/stg99e51165-7fd5-4031-a34f-e2da237a839e/dqc_reference/reference_markers_gtdb.fasta -out GCA_947486855.1_ZE-13oct10-55_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 19:17:15,087] [INFO] Task succeeded: Blastn
[2023-06-08 19:17:15,092] [INFO] Selected 13 target genomes.
[2023-06-08 19:17:15,092] [INFO] Target genome list was writen to GCA_947486855.1_ZE-13oct10-55_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 19:17:15,099] [INFO] Task started: fastANI
[2023-06-08 19:17:15,099] [INFO] Running command: fastANI --query /var/lib/cwl/stg836d7567-e06f-4329-8955-49ca40d2d559/GCA_947486855.1_ZE-13oct10-55_genomic.fna.gz --refList GCA_947486855.1_ZE-13oct10-55_genomic.fna/target_genomes_gtdb.txt --output GCA_947486855.1_ZE-13oct10-55_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 19:17:21,872] [INFO] Task succeeded: fastANI
[2023-06-08 19:17:21,885] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 19:17:21,885] [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_903834825.1	s__SXYR01 sp903834825	98.1984	522	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__SXYR01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903894575.1	s__SXYR01 sp903894575	86.5625	476	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__SXYR01	95.0	99.30	99.27	0.86	0.85	4	-
GCA_009922495.1	s__SXYR01 sp009922495	77.3215	124	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__SXYR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903920455.1	s__SXYR01 sp903920455	77.0009	95	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__SXYR01	95.0	99.79	99.77	0.93	0.92	3	-
GCA_903951405.1	s__SXYR01 sp903951405	76.9052	56	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__SXYR01	95.0	99.45	99.45	0.84	0.84	3	-
GCA_017853575.1	s__SXYR01 sp009919185	76.8331	90	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__SXYR01	95.0	99.01	98.05	0.94	0.93	3	-
GCA_016868855.1	s__SXYR01 sp016868855	76.6049	80	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__SXYR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005788265.1	s__SXYR01 sp005788265	76.2368	80	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__SXYR01	95.0	98.83	98.83	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-06-08 19:17:21,887] [INFO] GTDB search result was written to GCA_947486855.1_ZE-13oct10-55_genomic.fna/result_gtdb.tsv
[2023-06-08 19:17:21,887] [INFO] ===== GTDB Search completed =====
[2023-06-08 19:17:21,890] [INFO] DFAST_QC result json was written to GCA_947486855.1_ZE-13oct10-55_genomic.fna/dqc_result.json
[2023-06-08 19:17:21,890] [INFO] DFAST_QC completed!
[2023-06-08 19:17:21,890] [INFO] Total running time: 0h1m26s