[2023-06-29 18:14:18,248] [INFO] DFAST_QC pipeline started.
[2023-06-29 18:14:18,249] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 18:14:18,250] [INFO] DQC Reference Directory: /var/lib/cwl/stg947c7f0c-ba41-45da-9227-417039b5ac94/dqc_reference
[2023-06-29 18:14:19,507] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 18:14:19,508] [INFO] Task started: Prodigal
[2023-06-29 18:14:19,508] [INFO] Running command: gunzip -c /var/lib/cwl/stg9351fc04-3dbd-401a-9a8c-2c0997fc9f66/GCA_910587465.1_MGBC157433_genomic.fna.gz | prodigal -d GCA_910587465.1_MGBC157433_genomic.fna/cds.fna -a GCA_910587465.1_MGBC157433_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 18:14:26,570] [INFO] Task succeeded: Prodigal
[2023-06-29 18:14:26,570] [INFO] Task started: HMMsearch
[2023-06-29 18:14:26,570] [INFO] Running command: hmmsearch --tblout GCA_910587465.1_MGBC157433_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg947c7f0c-ba41-45da-9227-417039b5ac94/dqc_reference/reference_markers.hmm GCA_910587465.1_MGBC157433_genomic.fna/protein.faa > /dev/null
[2023-06-29 18:14:26,785] [INFO] Task succeeded: HMMsearch
[2023-06-29 18:14:26,786] [INFO] Found 6/6 markers.
[2023-06-29 18:14:26,815] [INFO] Query marker FASTA was written to GCA_910587465.1_MGBC157433_genomic.fna/markers.fasta
[2023-06-29 18:14:26,815] [INFO] Task started: Blastn
[2023-06-29 18:14:26,815] [INFO] Running command: blastn -query GCA_910587465.1_MGBC157433_genomic.fna/markers.fasta -db /var/lib/cwl/stg947c7f0c-ba41-45da-9227-417039b5ac94/dqc_reference/reference_markers.fasta -out GCA_910587465.1_MGBC157433_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 18:14:27,430] [INFO] Task succeeded: Blastn
[2023-06-29 18:14:27,433] [INFO] Selected 17 target genomes.
[2023-06-29 18:14:27,434] [INFO] Target genome list was writen to GCA_910587465.1_MGBC157433_genomic.fna/target_genomes.txt
[2023-06-29 18:14:27,437] [INFO] Task started: fastANI
[2023-06-29 18:14:27,437] [INFO] Running command: fastANI --query /var/lib/cwl/stg9351fc04-3dbd-401a-9a8c-2c0997fc9f66/GCA_910587465.1_MGBC157433_genomic.fna.gz --refList GCA_910587465.1_MGBC157433_genomic.fna/target_genomes.txt --output GCA_910587465.1_MGBC157433_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 18:14:35,792] [INFO] Task succeeded: fastANI
[2023-06-29 18:14:35,792] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg947c7f0c-ba41-45da-9227-417039b5ac94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 18:14:35,793] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg947c7f0c-ba41-45da-9227-417039b5ac94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 18:14:35,794] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 18:14:35,795] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 18:14:35,795] [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
--------------------------------------------------------------------------------
[2023-06-29 18:14:35,797] [INFO] DFAST Taxonomy check result was written to GCA_910587465.1_MGBC157433_genomic.fna/tc_result.tsv
[2023-06-29 18:14:35,797] [INFO] ===== Taxonomy check completed =====
[2023-06-29 18:14:35,797] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 18:14:35,798] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg947c7f0c-ba41-45da-9227-417039b5ac94/dqc_reference/checkm_data
[2023-06-29 18:14:35,801] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 18:14:35,836] [INFO] Task started: CheckM
[2023-06-29 18:14:35,837] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_910587465.1_MGBC157433_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_910587465.1_MGBC157433_genomic.fna/checkm_input GCA_910587465.1_MGBC157433_genomic.fna/checkm_result
[2023-06-29 18:15:01,863] [INFO] Task succeeded: CheckM
[2023-06-29 18:15:01,864] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 18:15:01,883] [INFO] ===== Completeness check finished =====
[2023-06-29 18:15:01,883] [INFO] ===== Start GTDB Search =====
[2023-06-29 18:15:01,883] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_910587465.1_MGBC157433_genomic.fna/markers.fasta)
[2023-06-29 18:15:01,883] [INFO] Task started: Blastn
[2023-06-29 18:15:01,884] [INFO] Running command: blastn -query GCA_910587465.1_MGBC157433_genomic.fna/markers.fasta -db /var/lib/cwl/stg947c7f0c-ba41-45da-9227-417039b5ac94/dqc_reference/reference_markers_gtdb.fasta -out GCA_910587465.1_MGBC157433_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 18:15:02,920] [INFO] Task succeeded: Blastn
[2023-06-29 18:15:02,923] [INFO] Selected 12 target genomes.
[2023-06-29 18:15:02,923] [INFO] Target genome list was writen to GCA_910587465.1_MGBC157433_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 18:15:02,926] [INFO] Task started: fastANI
[2023-06-29 18:15:02,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg9351fc04-3dbd-401a-9a8c-2c0997fc9f66/GCA_910587465.1_MGBC157433_genomic.fna.gz --refList GCA_910587465.1_MGBC157433_genomic.fna/target_genomes_gtdb.txt --output GCA_910587465.1_MGBC157433_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 18:15:08,453] [INFO] Task succeeded: fastANI
[2023-06-29 18:15:08,462] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 18:15:08,463] [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_910587465.1	s__CAG-115 sp910587465	100.0	953	964	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014799395.1	s__CAG-115 sp014799395	84.8971	607	964	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579125.1	s__CAG-115 sp910579125	82.0891	542	964	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577365.1	s__CAG-115 sp910577365	78.3624	170	964	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002425305.1	s__CAG-115 sp002425305	78.3288	239	964	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014799385.1	s__CAG-115 sp014799385	78.1182	226	964	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002492075.1	s__CAG-115 sp002492075	78.067	236	964	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	97.62	97.62	0.68	0.67	3	-
GCA_002304735.1	s__CAG-115 sp002304735	77.8856	180	964	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017847835.1	s__CAG-115 sp017847835	77.6484	180	964	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004554555.1	s__CAG-115 sp004554555	77.4429	182	964	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017848155.1	s__CAG-115 sp017848155	76.627	67	964	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 18:15:08,465] [INFO] GTDB search result was written to GCA_910587465.1_MGBC157433_genomic.fna/result_gtdb.tsv
[2023-06-29 18:15:08,465] [INFO] ===== GTDB Search completed =====
[2023-06-29 18:15:08,468] [INFO] DFAST_QC result json was written to GCA_910587465.1_MGBC157433_genomic.fna/dqc_result.json
[2023-06-29 18:15:08,468] [INFO] DFAST_QC completed!
[2023-06-29 18:15:08,468] [INFO] Total running time: 0h0m50s