[2023-06-13 15:27:03,726] [INFO] DFAST_QC pipeline started.
[2023-06-13 15:27:03,728] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 15:27:03,728] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9ec6ce3-587f-4dd7-85e0-b1e0c3d03034/dqc_reference
[2023-06-13 15:27:05,156] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 15:27:05,156] [INFO] Task started: Prodigal
[2023-06-13 15:27:05,157] [INFO] Running command: gunzip -c /var/lib/cwl/stgc917596d-6536-4a66-8c55-8b055762aaca/GCA_947464205.1_RE-27jun17-42_genomic.fna.gz | prodigal -d GCA_947464205.1_RE-27jun17-42_genomic.fna/cds.fna -a GCA_947464205.1_RE-27jun17-42_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 15:27:15,875] [INFO] Task succeeded: Prodigal
[2023-06-13 15:27:15,875] [INFO] Task started: HMMsearch
[2023-06-13 15:27:15,875] [INFO] Running command: hmmsearch --tblout GCA_947464205.1_RE-27jun17-42_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9ec6ce3-587f-4dd7-85e0-b1e0c3d03034/dqc_reference/reference_markers.hmm GCA_947464205.1_RE-27jun17-42_genomic.fna/protein.faa > /dev/null
[2023-06-13 15:27:16,002] [INFO] Task succeeded: HMMsearch
[2023-06-13 15:27:16,003] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc917596d-6536-4a66-8c55-8b055762aaca/GCA_947464205.1_RE-27jun17-42_genomic.fna.gz]
[2023-06-13 15:27:16,021] [INFO] Query marker FASTA was written to GCA_947464205.1_RE-27jun17-42_genomic.fna/markers.fasta
[2023-06-13 15:27:16,021] [INFO] Task started: Blastn
[2023-06-13 15:27:16,021] [INFO] Running command: blastn -query GCA_947464205.1_RE-27jun17-42_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9ec6ce3-587f-4dd7-85e0-b1e0c3d03034/dqc_reference/reference_markers.fasta -out GCA_947464205.1_RE-27jun17-42_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:27:16,532] [INFO] Task succeeded: Blastn
[2023-06-13 15:27:16,535] [INFO] Selected 10 target genomes.
[2023-06-13 15:27:16,536] [INFO] Target genome list was writen to GCA_947464205.1_RE-27jun17-42_genomic.fna/target_genomes.txt
[2023-06-13 15:27:16,538] [INFO] Task started: fastANI
[2023-06-13 15:27:16,538] [INFO] Running command: fastANI --query /var/lib/cwl/stgc917596d-6536-4a66-8c55-8b055762aaca/GCA_947464205.1_RE-27jun17-42_genomic.fna.gz --refList GCA_947464205.1_RE-27jun17-42_genomic.fna/target_genomes.txt --output GCA_947464205.1_RE-27jun17-42_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 15:27:22,805] [INFO] Task succeeded: fastANI
[2023-06-13 15:27:22,806] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9ec6ce3-587f-4dd7-85e0-b1e0c3d03034/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 15:27:22,806] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9ec6ce3-587f-4dd7-85e0-b1e0c3d03034/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 15:27:22,807] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 15:27:22,807] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 15:27:22,807] [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 15:27:22,809] [INFO] DFAST Taxonomy check result was written to GCA_947464205.1_RE-27jun17-42_genomic.fna/tc_result.tsv
[2023-06-13 15:27:22,810] [INFO] ===== Taxonomy check completed =====
[2023-06-13 15:27:22,810] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 15:27:22,810] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9ec6ce3-587f-4dd7-85e0-b1e0c3d03034/dqc_reference/checkm_data
[2023-06-13 15:27:22,812] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 15:27:22,831] [INFO] Task started: CheckM
[2023-06-13 15:27:22,831] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947464205.1_RE-27jun17-42_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947464205.1_RE-27jun17-42_genomic.fna/checkm_input GCA_947464205.1_RE-27jun17-42_genomic.fna/checkm_result
[2023-06-13 15:27:56,481] [INFO] Task succeeded: CheckM
[2023-06-13 15:27:56,482] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.90%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 15:27:56,503] [INFO] ===== Completeness check finished =====
[2023-06-13 15:27:56,504] [INFO] ===== Start GTDB Search =====
[2023-06-13 15:27:56,504] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947464205.1_RE-27jun17-42_genomic.fna/markers.fasta)
[2023-06-13 15:27:56,504] [INFO] Task started: Blastn
[2023-06-13 15:27:56,504] [INFO] Running command: blastn -query GCA_947464205.1_RE-27jun17-42_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9ec6ce3-587f-4dd7-85e0-b1e0c3d03034/dqc_reference/reference_markers_gtdb.fasta -out GCA_947464205.1_RE-27jun17-42_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:27:57,176] [INFO] Task succeeded: Blastn
[2023-06-13 15:27:57,180] [INFO] Selected 11 target genomes.
[2023-06-13 15:27:57,181] [INFO] Target genome list was writen to GCA_947464205.1_RE-27jun17-42_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 15:27:57,185] [INFO] Task started: fastANI
[2023-06-13 15:27:57,185] [INFO] Running command: fastANI --query /var/lib/cwl/stgc917596d-6536-4a66-8c55-8b055762aaca/GCA_947464205.1_RE-27jun17-42_genomic.fna.gz --refList GCA_947464205.1_RE-27jun17-42_genomic.fna/target_genomes_gtdb.txt --output GCA_947464205.1_RE-27jun17-42_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 15:28:04,084] [INFO] Task succeeded: fastANI
[2023-06-13 15:28:04,092] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 15:28:04,092] [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_903939515.1	s__SXXZ01 sp903939515	82.5118	341	444	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__SXXZ01	95.0	99.92	99.88	0.96	0.95	11	-
GCA_903854475.1	s__SXXZ01 sp903854475	82.1226	329	444	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__SXXZ01	95.0	98.91	98.91	0.88	0.88	2	-
GCA_005805505.1	s__SXXZ01 sp005805505	81.9569	296	444	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__SXXZ01	95.0	98.37	96.99	0.84	0.81	3	-
GCA_005789375.1	s__SXXZ01 sp005789375	81.8969	218	444	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__SXXZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871615.1	s__SXXZ01 sp016871615	79.9629	252	444	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__SXXZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903858835.1	s__SXXZ01 sp903858835	79.9394	209	444	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__SXXZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903916195.1	s__CAIVQB01 sp903916195	76.9497	67	444	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__CAIVQB01	95.0	99.38	98.88	0.92	0.89	6	-
--------------------------------------------------------------------------------
[2023-06-13 15:28:04,094] [INFO] GTDB search result was written to GCA_947464205.1_RE-27jun17-42_genomic.fna/result_gtdb.tsv
[2023-06-13 15:28:04,095] [INFO] ===== GTDB Search completed =====
[2023-06-13 15:28:04,098] [INFO] DFAST_QC result json was written to GCA_947464205.1_RE-27jun17-42_genomic.fna/dqc_result.json
[2023-06-13 15:28:04,098] [INFO] DFAST_QC completed!
[2023-06-13 15:28:04,098] [INFO] Total running time: 0h1m0s