[2023-06-05 09:56:17,898] [INFO] DFAST_QC pipeline started.
[2023-06-05 09:56:17,903] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 09:56:17,903] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc536032-9021-4a17-8c17-afc609452921/dqc_reference
[2023-06-05 09:56:19,706] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 09:56:19,710] [INFO] Task started: Prodigal
[2023-06-05 09:56:19,711] [INFO] Running command: gunzip -c /var/lib/cwl/stge42bd51e-b98a-4994-853d-28353ea333f5/GCA_004294245.1_ASM429424v1_genomic.fna.gz | prodigal -d GCA_004294245.1_ASM429424v1_genomic.fna/cds.fna -a GCA_004294245.1_ASM429424v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 09:56:29,402] [INFO] Task succeeded: Prodigal
[2023-06-05 09:56:29,402] [INFO] Task started: HMMsearch
[2023-06-05 09:56:29,402] [INFO] Running command: hmmsearch --tblout GCA_004294245.1_ASM429424v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc536032-9021-4a17-8c17-afc609452921/dqc_reference/reference_markers.hmm GCA_004294245.1_ASM429424v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 09:56:29,633] [INFO] Task succeeded: HMMsearch
[2023-06-05 09:56:29,634] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge42bd51e-b98a-4994-853d-28353ea333f5/GCA_004294245.1_ASM429424v1_genomic.fna.gz]
[2023-06-05 09:56:29,658] [INFO] Query marker FASTA was written to GCA_004294245.1_ASM429424v1_genomic.fna/markers.fasta
[2023-06-05 09:56:29,659] [INFO] Task started: Blastn
[2023-06-05 09:56:29,659] [INFO] Running command: blastn -query GCA_004294245.1_ASM429424v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc536032-9021-4a17-8c17-afc609452921/dqc_reference/reference_markers.fasta -out GCA_004294245.1_ASM429424v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:56:30,248] [INFO] Task succeeded: Blastn
[2023-06-05 09:56:30,267] [INFO] Selected 31 target genomes.
[2023-06-05 09:56:30,267] [INFO] Target genome list was writen to GCA_004294245.1_ASM429424v1_genomic.fna/target_genomes.txt
[2023-06-05 09:56:30,276] [INFO] Task started: fastANI
[2023-06-05 09:56:30,276] [INFO] Running command: fastANI --query /var/lib/cwl/stge42bd51e-b98a-4994-853d-28353ea333f5/GCA_004294245.1_ASM429424v1_genomic.fna.gz --refList GCA_004294245.1_ASM429424v1_genomic.fna/target_genomes.txt --output GCA_004294245.1_ASM429424v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 09:56:52,521] [INFO] Task succeeded: fastANI
[2023-06-05 09:56:52,522] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc536032-9021-4a17-8c17-afc609452921/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 09:56:52,522] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc536032-9021-4a17-8c17-afc609452921/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 09:56:52,524] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 09:56:52,524] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 09:56:52,524] [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
--------------------------------------------------------------------------------
[2023-06-05 09:56:52,526] [INFO] DFAST Taxonomy check result was written to GCA_004294245.1_ASM429424v1_genomic.fna/tc_result.tsv
[2023-06-05 09:56:52,526] [INFO] ===== Taxonomy check completed =====
[2023-06-05 09:56:52,527] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 09:56:52,527] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc536032-9021-4a17-8c17-afc609452921/dqc_reference/checkm_data
[2023-06-05 09:56:52,529] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 09:56:52,559] [INFO] Task started: CheckM
[2023-06-05 09:56:52,560] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004294245.1_ASM429424v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004294245.1_ASM429424v1_genomic.fna/checkm_input GCA_004294245.1_ASM429424v1_genomic.fna/checkm_result
[2023-06-05 09:57:23,447] [INFO] Task succeeded: CheckM
[2023-06-05 09:57:23,448] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 09:57:23,468] [INFO] ===== Completeness check finished =====
[2023-06-05 09:57:23,468] [INFO] ===== Start GTDB Search =====
[2023-06-05 09:57:23,469] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004294245.1_ASM429424v1_genomic.fna/markers.fasta)
[2023-06-05 09:57:23,469] [INFO] Task started: Blastn
[2023-06-05 09:57:23,469] [INFO] Running command: blastn -query GCA_004294245.1_ASM429424v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc536032-9021-4a17-8c17-afc609452921/dqc_reference/reference_markers_gtdb.fasta -out GCA_004294245.1_ASM429424v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:57:24,204] [INFO] Task succeeded: Blastn
[2023-06-05 09:57:24,207] [INFO] Selected 18 target genomes.
[2023-06-05 09:57:24,207] [INFO] Target genome list was writen to GCA_004294245.1_ASM429424v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 09:57:24,242] [INFO] Task started: fastANI
[2023-06-05 09:57:24,243] [INFO] Running command: fastANI --query /var/lib/cwl/stge42bd51e-b98a-4994-853d-28353ea333f5/GCA_004294245.1_ASM429424v1_genomic.fna.gz --refList GCA_004294245.1_ASM429424v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004294245.1_ASM429424v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 09:57:36,208] [INFO] Task succeeded: fastANI
[2023-06-05 09:57:36,214] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 09:57:36,214] [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_004294005.1	s__RDXZ01 sp004294005	99.54	643	768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Microscillaceae;g__RDXZ01	95.0	98.45	97.30	0.78	0.73	3	conclusive
GCA_004293265.1	s__RDXZ01 sp004293265	81.2965	516	768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Microscillaceae;g__RDXZ01	95.0	99.68	99.68	0.88	0.88	2	-
GCA_013298075.1	s__RDXZ01 sp013298075	80.485	547	768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Microscillaceae;g__RDXZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013297825.1	s__JAAFIN01 sp013297825	75.6171	193	768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Microscillaceae;g__JAAFIN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004292785.1	s__RDXG01 sp004292785	75.3035	65	768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Bernardetiaceae;g__RDXG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 09:57:36,216] [INFO] GTDB search result was written to GCA_004294245.1_ASM429424v1_genomic.fna/result_gtdb.tsv
[2023-06-05 09:57:36,216] [INFO] ===== GTDB Search completed =====
[2023-06-05 09:57:36,219] [INFO] DFAST_QC result json was written to GCA_004294245.1_ASM429424v1_genomic.fna/dqc_result.json
[2023-06-05 09:57:36,219] [INFO] DFAST_QC completed!
[2023-06-05 09:57:36,219] [INFO] Total running time: 0h1m18s