[2023-06-13 06:33:40,357] [INFO] DFAST_QC pipeline started.
[2023-06-13 06:33:40,361] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 06:33:40,361] [INFO] DQC Reference Directory: /var/lib/cwl/stg92d9454f-44cd-47a7-8965-32c0ba112c0b/dqc_reference
[2023-06-13 06:33:44,084] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 06:33:44,086] [INFO] Task started: Prodigal
[2023-06-13 06:33:44,087] [INFO] Running command: gunzip -c /var/lib/cwl/stg398d8b15-cf6e-435d-a90f-a2b9871d5373/GCA_022708505.1_ASM2270850v1_genomic.fna.gz | prodigal -d GCA_022708505.1_ASM2270850v1_genomic.fna/cds.fna -a GCA_022708505.1_ASM2270850v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 06:33:55,187] [INFO] Task succeeded: Prodigal
[2023-06-13 06:33:55,187] [INFO] Task started: HMMsearch
[2023-06-13 06:33:55,188] [INFO] Running command: hmmsearch --tblout GCA_022708505.1_ASM2270850v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg92d9454f-44cd-47a7-8965-32c0ba112c0b/dqc_reference/reference_markers.hmm GCA_022708505.1_ASM2270850v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 06:33:55,413] [INFO] Task succeeded: HMMsearch
[2023-06-13 06:33:55,417] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg398d8b15-cf6e-435d-a90f-a2b9871d5373/GCA_022708505.1_ASM2270850v1_genomic.fna.gz]
[2023-06-13 06:33:55,448] [INFO] Query marker FASTA was written to GCA_022708505.1_ASM2270850v1_genomic.fna/markers.fasta
[2023-06-13 06:33:55,449] [INFO] Task started: Blastn
[2023-06-13 06:33:55,449] [INFO] Running command: blastn -query GCA_022708505.1_ASM2270850v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92d9454f-44cd-47a7-8965-32c0ba112c0b/dqc_reference/reference_markers.fasta -out GCA_022708505.1_ASM2270850v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 06:33:56,129] [INFO] Task succeeded: Blastn
[2023-06-13 06:33:56,133] [INFO] Selected 25 target genomes.
[2023-06-13 06:33:56,134] [INFO] Target genome list was writen to GCA_022708505.1_ASM2270850v1_genomic.fna/target_genomes.txt
[2023-06-13 06:33:56,136] [INFO] Task started: fastANI
[2023-06-13 06:33:56,137] [INFO] Running command: fastANI --query /var/lib/cwl/stg398d8b15-cf6e-435d-a90f-a2b9871d5373/GCA_022708505.1_ASM2270850v1_genomic.fna.gz --refList GCA_022708505.1_ASM2270850v1_genomic.fna/target_genomes.txt --output GCA_022708505.1_ASM2270850v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 06:34:15,947] [INFO] Task succeeded: fastANI
[2023-06-13 06:34:15,948] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg92d9454f-44cd-47a7-8965-32c0ba112c0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 06:34:15,949] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg92d9454f-44cd-47a7-8965-32c0ba112c0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 06:34:15,951] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 06:34:15,951] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 06:34:15,952] [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
--------------------------------------------------------------------------------
[2023-06-13 06:34:15,954] [INFO] DFAST Taxonomy check result was written to GCA_022708505.1_ASM2270850v1_genomic.fna/tc_result.tsv
[2023-06-13 06:34:15,955] [INFO] ===== Taxonomy check completed =====
[2023-06-13 06:34:15,955] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 06:34:15,956] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg92d9454f-44cd-47a7-8965-32c0ba112c0b/dqc_reference/checkm_data
[2023-06-13 06:34:15,962] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 06:34:15,992] [INFO] Task started: CheckM
[2023-06-13 06:34:15,992] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022708505.1_ASM2270850v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022708505.1_ASM2270850v1_genomic.fna/checkm_input GCA_022708505.1_ASM2270850v1_genomic.fna/checkm_result
[2023-06-13 06:34:53,232] [INFO] Task succeeded: CheckM
[2023-06-13 06:34:53,236] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 06:34:53,260] [INFO] ===== Completeness check finished =====
[2023-06-13 06:34:53,260] [INFO] ===== Start GTDB Search =====
[2023-06-13 06:34:53,261] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022708505.1_ASM2270850v1_genomic.fna/markers.fasta)
[2023-06-13 06:34:53,261] [INFO] Task started: Blastn
[2023-06-13 06:34:53,261] [INFO] Running command: blastn -query GCA_022708505.1_ASM2270850v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92d9454f-44cd-47a7-8965-32c0ba112c0b/dqc_reference/reference_markers_gtdb.fasta -out GCA_022708505.1_ASM2270850v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 06:34:54,123] [INFO] Task succeeded: Blastn
[2023-06-13 06:34:54,127] [INFO] Selected 23 target genomes.
[2023-06-13 06:34:54,127] [INFO] Target genome list was writen to GCA_022708505.1_ASM2270850v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 06:34:54,139] [INFO] Task started: fastANI
[2023-06-13 06:34:54,140] [INFO] Running command: fastANI --query /var/lib/cwl/stg398d8b15-cf6e-435d-a90f-a2b9871d5373/GCA_022708505.1_ASM2270850v1_genomic.fna.gz --refList GCA_022708505.1_ASM2270850v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022708505.1_ASM2270850v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 06:35:07,269] [INFO] Task succeeded: fastANI
[2023-06-13 06:35:07,278] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 06:35:07,278] [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_002070265.1	s__Paludibacter sp002070265	80.4108	112	719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009929375.1	s__Paludibacter sp009929375	77.4317	78	719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898935.1	s__Paludibacter sp001898935	77.285	92	719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002427615.1	s__Paludibacter sp002427615	77.1442	66	719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	99.75	99.75	0.80	0.80	2	-
GCA_017860345.1	s__Paludibacter sp017860345	76.9886	60	719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010365115.1	s__Paludibacter sp010365115	76.9613	51	719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882285.1	s__Paludibacter sp017882285	76.6592	64	719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903901975.1	s__Paludibacter sp903901975	76.5287	54	719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	99.91	99.88	0.94	0.92	6	-
GCA_016937795.1	s__Paludibacter sp016937795	76.4598	70	719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 06:35:07,280] [INFO] GTDB search result was written to GCA_022708505.1_ASM2270850v1_genomic.fna/result_gtdb.tsv
[2023-06-13 06:35:07,281] [INFO] ===== GTDB Search completed =====
[2023-06-13 06:35:07,284] [INFO] DFAST_QC result json was written to GCA_022708505.1_ASM2270850v1_genomic.fna/dqc_result.json
[2023-06-13 06:35:07,284] [INFO] DFAST_QC completed!
[2023-06-13 06:35:07,284] [INFO] Total running time: 0h1m27s