[2023-06-13 11:03:34,282] [INFO] DFAST_QC pipeline started.
[2023-06-13 11:03:34,286] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 11:03:34,286] [INFO] DQC Reference Directory: /var/lib/cwl/stg055dd8cf-b560-4201-8ae0-9744cc3bb57e/dqc_reference
[2023-06-13 11:03:35,977] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 11:03:35,978] [INFO] Task started: Prodigal
[2023-06-13 11:03:35,978] [INFO] Running command: gunzip -c /var/lib/cwl/stgcfc8f39e-73f8-4998-a3ee-ca5fc69a29ed/GCA_947460545.1_RE-23may17-536_genomic.fna.gz | prodigal -d GCA_947460545.1_RE-23may17-536_genomic.fna/cds.fna -a GCA_947460545.1_RE-23may17-536_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 11:03:47,837] [INFO] Task succeeded: Prodigal
[2023-06-13 11:03:47,837] [INFO] Task started: HMMsearch
[2023-06-13 11:03:47,837] [INFO] Running command: hmmsearch --tblout GCA_947460545.1_RE-23may17-536_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg055dd8cf-b560-4201-8ae0-9744cc3bb57e/dqc_reference/reference_markers.hmm GCA_947460545.1_RE-23may17-536_genomic.fna/protein.faa > /dev/null
[2023-06-13 11:03:48,217] [INFO] Task succeeded: HMMsearch
[2023-06-13 11:03:48,218] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgcfc8f39e-73f8-4998-a3ee-ca5fc69a29ed/GCA_947460545.1_RE-23may17-536_genomic.fna.gz]
[2023-06-13 11:03:48,257] [INFO] Query marker FASTA was written to GCA_947460545.1_RE-23may17-536_genomic.fna/markers.fasta
[2023-06-13 11:03:48,258] [INFO] Task started: Blastn
[2023-06-13 11:03:48,258] [INFO] Running command: blastn -query GCA_947460545.1_RE-23may17-536_genomic.fna/markers.fasta -db /var/lib/cwl/stg055dd8cf-b560-4201-8ae0-9744cc3bb57e/dqc_reference/reference_markers.fasta -out GCA_947460545.1_RE-23may17-536_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:03:49,153] [INFO] Task succeeded: Blastn
[2023-06-13 11:03:49,158] [INFO] Selected 26 target genomes.
[2023-06-13 11:03:49,158] [INFO] Target genome list was writen to GCA_947460545.1_RE-23may17-536_genomic.fna/target_genomes.txt
[2023-06-13 11:03:49,163] [INFO] Task started: fastANI
[2023-06-13 11:03:49,164] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfc8f39e-73f8-4998-a3ee-ca5fc69a29ed/GCA_947460545.1_RE-23may17-536_genomic.fna.gz --refList GCA_947460545.1_RE-23may17-536_genomic.fna/target_genomes.txt --output GCA_947460545.1_RE-23may17-536_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 11:04:06,857] [INFO] Task succeeded: fastANI
[2023-06-13 11:04:06,858] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg055dd8cf-b560-4201-8ae0-9744cc3bb57e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 11:04:06,858] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg055dd8cf-b560-4201-8ae0-9744cc3bb57e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 11:04:06,860] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 11:04:06,860] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 11:04:06,860] [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 11:04:06,862] [INFO] DFAST Taxonomy check result was written to GCA_947460545.1_RE-23may17-536_genomic.fna/tc_result.tsv
[2023-06-13 11:04:06,862] [INFO] ===== Taxonomy check completed =====
[2023-06-13 11:04:06,863] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 11:04:06,863] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg055dd8cf-b560-4201-8ae0-9744cc3bb57e/dqc_reference/checkm_data
[2023-06-13 11:04:06,866] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 11:04:06,899] [INFO] Task started: CheckM
[2023-06-13 11:04:06,899] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947460545.1_RE-23may17-536_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947460545.1_RE-23may17-536_genomic.fna/checkm_input GCA_947460545.1_RE-23may17-536_genomic.fna/checkm_result
[2023-06-13 11:04:46,893] [INFO] Task succeeded: CheckM
[2023-06-13 11:04:46,895] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.08%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 11:04:46,917] [INFO] ===== Completeness check finished =====
[2023-06-13 11:04:46,918] [INFO] ===== Start GTDB Search =====
[2023-06-13 11:04:46,918] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947460545.1_RE-23may17-536_genomic.fna/markers.fasta)
[2023-06-13 11:04:46,918] [INFO] Task started: Blastn
[2023-06-13 11:04:46,919] [INFO] Running command: blastn -query GCA_947460545.1_RE-23may17-536_genomic.fna/markers.fasta -db /var/lib/cwl/stg055dd8cf-b560-4201-8ae0-9744cc3bb57e/dqc_reference/reference_markers_gtdb.fasta -out GCA_947460545.1_RE-23may17-536_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:04:47,629] [INFO] Task succeeded: Blastn
[2023-06-13 11:04:47,635] [INFO] Selected 28 target genomes.
[2023-06-13 11:04:47,635] [INFO] Target genome list was writen to GCA_947460545.1_RE-23may17-536_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 11:04:47,653] [INFO] Task started: fastANI
[2023-06-13 11:04:47,653] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfc8f39e-73f8-4998-a3ee-ca5fc69a29ed/GCA_947460545.1_RE-23may17-536_genomic.fna.gz --refList GCA_947460545.1_RE-23may17-536_genomic.fna/target_genomes_gtdb.txt --output GCA_947460545.1_RE-23may17-536_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 11:05:02,057] [INFO] Task succeeded: fastANI
[2023-06-13 11:05:02,069] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 11:05:02,069] [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_903873915.1	s__M0103 sp903873915	84.1105	466	627	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	99.96	99.96	0.94	0.94	3	-
GCA_903945495.1	s__M0103 sp903945495	76.4095	78	627	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	99.87	99.80	0.95	0.92	6	-
GCA_017984635.1	s__M0103 sp017984635	75.9915	50	627	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 11:05:02,071] [INFO] GTDB search result was written to GCA_947460545.1_RE-23may17-536_genomic.fna/result_gtdb.tsv
[2023-06-13 11:05:02,072] [INFO] ===== GTDB Search completed =====
[2023-06-13 11:05:02,074] [INFO] DFAST_QC result json was written to GCA_947460545.1_RE-23may17-536_genomic.fna/dqc_result.json
[2023-06-13 11:05:02,075] [INFO] DFAST_QC completed!
[2023-06-13 11:05:02,075] [INFO] Total running time: 0h1m28s