[2023-06-07 19:05:01,910] [INFO] DFAST_QC pipeline started.
[2023-06-07 19:05:01,913] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 19:05:01,913] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc8f24d1-09af-42c7-917c-e4a6d0bc8369/dqc_reference
[2023-06-07 19:05:03,277] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 19:05:03,278] [INFO] Task started: Prodigal
[2023-06-07 19:05:03,278] [INFO] Running command: gunzip -c /var/lib/cwl/stgf82edf16-a42c-4520-9c6f-011d377ae144/GCA_947595345.1_Lapin-008_bin17_genomic.fna.gz | prodigal -d GCA_947595345.1_Lapin-008_bin17_genomic.fna/cds.fna -a GCA_947595345.1_Lapin-008_bin17_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 19:05:04,732] [INFO] Task succeeded: Prodigal
[2023-06-07 19:05:04,732] [INFO] Task started: HMMsearch
[2023-06-07 19:05:04,733] [INFO] Running command: hmmsearch --tblout GCA_947595345.1_Lapin-008_bin17_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc8f24d1-09af-42c7-917c-e4a6d0bc8369/dqc_reference/reference_markers.hmm GCA_947595345.1_Lapin-008_bin17_genomic.fna/protein.faa > /dev/null
[2023-06-07 19:05:04,958] [INFO] Task succeeded: HMMsearch
[2023-06-07 19:05:04,959] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf82edf16-a42c-4520-9c6f-011d377ae144/GCA_947595345.1_Lapin-008_bin17_genomic.fna.gz]
[2023-06-07 19:05:04,984] [INFO] Query marker FASTA was written to GCA_947595345.1_Lapin-008_bin17_genomic.fna/markers.fasta
[2023-06-07 19:05:04,984] [INFO] Task started: Blastn
[2023-06-07 19:05:04,984] [INFO] Running command: blastn -query GCA_947595345.1_Lapin-008_bin17_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc8f24d1-09af-42c7-917c-e4a6d0bc8369/dqc_reference/reference_markers.fasta -out GCA_947595345.1_Lapin-008_bin17_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 19:05:06,569] [INFO] Task succeeded: Blastn
[2023-06-07 19:05:06,576] [INFO] Selected 29 target genomes.
[2023-06-07 19:05:06,577] [INFO] Target genome list was writen to GCA_947595345.1_Lapin-008_bin17_genomic.fna/target_genomes.txt
[2023-06-07 19:05:06,579] [INFO] Task started: fastANI
[2023-06-07 19:05:06,579] [INFO] Running command: fastANI --query /var/lib/cwl/stgf82edf16-a42c-4520-9c6f-011d377ae144/GCA_947595345.1_Lapin-008_bin17_genomic.fna.gz --refList GCA_947595345.1_Lapin-008_bin17_genomic.fna/target_genomes.txt --output GCA_947595345.1_Lapin-008_bin17_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 19:05:18,322] [INFO] Task succeeded: fastANI
[2023-06-07 19:05:18,323] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc8f24d1-09af-42c7-917c-e4a6d0bc8369/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 19:05:18,324] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc8f24d1-09af-42c7-917c-e4a6d0bc8369/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 19:05:18,326] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 19:05:18,326] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 19:05:18,326] [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
--------------------------------------------------------------------------------
[2023-06-07 19:05:18,329] [INFO] DFAST Taxonomy check result was written to GCA_947595345.1_Lapin-008_bin17_genomic.fna/tc_result.tsv
[2023-06-07 19:05:18,329] [INFO] ===== Taxonomy check completed =====
[2023-06-07 19:05:18,330] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 19:05:18,330] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc8f24d1-09af-42c7-917c-e4a6d0bc8369/dqc_reference/checkm_data
[2023-06-07 19:05:18,334] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 19:05:18,354] [INFO] Task started: CheckM
[2023-06-07 19:05:18,354] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947595345.1_Lapin-008_bin17_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947595345.1_Lapin-008_bin17_genomic.fna/checkm_input GCA_947595345.1_Lapin-008_bin17_genomic.fna/checkm_result
[2023-06-07 19:05:31,637] [INFO] Task succeeded: CheckM
[2023-06-07 19:05:31,638] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 19:05:31,657] [INFO] ===== Completeness check finished =====
[2023-06-07 19:05:31,658] [INFO] ===== Start GTDB Search =====
[2023-06-07 19:05:31,658] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947595345.1_Lapin-008_bin17_genomic.fna/markers.fasta)
[2023-06-07 19:05:31,659] [INFO] Task started: Blastn
[2023-06-07 19:05:31,659] [INFO] Running command: blastn -query GCA_947595345.1_Lapin-008_bin17_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc8f24d1-09af-42c7-917c-e4a6d0bc8369/dqc_reference/reference_markers_gtdb.fasta -out GCA_947595345.1_Lapin-008_bin17_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 19:05:32,458] [INFO] Task succeeded: Blastn
[2023-06-07 19:05:32,463] [INFO] Selected 23 target genomes.
[2023-06-07 19:05:32,463] [INFO] Target genome list was writen to GCA_947595345.1_Lapin-008_bin17_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 19:05:32,469] [INFO] Task started: fastANI
[2023-06-07 19:05:32,469] [INFO] Running command: fastANI --query /var/lib/cwl/stgf82edf16-a42c-4520-9c6f-011d377ae144/GCA_947595345.1_Lapin-008_bin17_genomic.fna.gz --refList GCA_947595345.1_Lapin-008_bin17_genomic.fna/target_genomes_gtdb.txt --output GCA_947595345.1_Lapin-008_bin17_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 19:05:37,272] [INFO] Task succeeded: fastANI
[2023-06-07 19:05:37,286] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-07 19:05:37,286] [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_017472015.1	s__RUG591 sp017472015	79.2885	171	351	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG591	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017528315.1	s__RUG591 sp017528315	78.4102	141	351	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG591	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017460745.1	s__RUG591 sp017460745	78.1209	138	351	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG591	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900320425.1	s__RUG591 sp900320425	77.7083	127	351	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG591	95.0	99.39	98.77	0.92	0.86	3	-
GCA_902782915.1	s__RUG591 sp902782915	77.4667	114	351	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG591	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902782535.1	s__RUG12783 sp902782535	75.9041	59	351	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG12783	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 19:05:37,288] [INFO] GTDB search result was written to GCA_947595345.1_Lapin-008_bin17_genomic.fna/result_gtdb.tsv
[2023-06-07 19:05:37,289] [INFO] ===== GTDB Search completed =====
[2023-06-07 19:05:37,292] [INFO] DFAST_QC result json was written to GCA_947595345.1_Lapin-008_bin17_genomic.fna/dqc_result.json
[2023-06-07 19:05:37,292] [INFO] DFAST_QC completed!
[2023-06-07 19:05:37,292] [INFO] Total running time: 0h0m35s