[2023-06-06 00:01:23,278] [INFO] DFAST_QC pipeline started.
[2023-06-06 00:01:23,280] [INFO] DFAST_QC version: 0.5.7
[2023-06-06 00:01:23,280] [INFO] DQC Reference Directory: /var/lib/cwl/stgd9671afa-87de-43bd-8fde-3547eebc6b4b/dqc_reference
[2023-06-06 00:01:24,430] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-06 00:01:24,431] [INFO] Task started: Prodigal
[2023-06-06 00:01:24,431] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b3eb96f-617f-4b19-86d8-b26296d1919b/GCA_934680005.1_ERR7738558_bin.54_genomic.fna.gz | prodigal -d GCA_934680005.1_ERR7738558_bin.54_genomic.fna/cds.fna -a GCA_934680005.1_ERR7738558_bin.54_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-06 00:01:33,079] [INFO] Task succeeded: Prodigal
[2023-06-06 00:01:33,079] [INFO] Task started: HMMsearch
[2023-06-06 00:01:33,079] [INFO] Running command: hmmsearch --tblout GCA_934680005.1_ERR7738558_bin.54_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd9671afa-87de-43bd-8fde-3547eebc6b4b/dqc_reference/reference_markers.hmm GCA_934680005.1_ERR7738558_bin.54_genomic.fna/protein.faa > /dev/null
[2023-06-06 00:01:33,281] [INFO] Task succeeded: HMMsearch
[2023-06-06 00:01:33,282] [INFO] Found 6/6 markers.
[2023-06-06 00:01:33,300] [INFO] Query marker FASTA was written to GCA_934680005.1_ERR7738558_bin.54_genomic.fna/markers.fasta
[2023-06-06 00:01:33,301] [INFO] Task started: Blastn
[2023-06-06 00:01:33,301] [INFO] Running command: blastn -query GCA_934680005.1_ERR7738558_bin.54_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9671afa-87de-43bd-8fde-3547eebc6b4b/dqc_reference/reference_markers.fasta -out GCA_934680005.1_ERR7738558_bin.54_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-06 00:01:33,845] [INFO] Task succeeded: Blastn
[2023-06-06 00:01:33,849] [INFO] Selected 25 target genomes.
[2023-06-06 00:01:33,849] [INFO] Target genome list was writen to GCA_934680005.1_ERR7738558_bin.54_genomic.fna/target_genomes.txt
[2023-06-06 00:01:33,852] [INFO] Task started: fastANI
[2023-06-06 00:01:33,852] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b3eb96f-617f-4b19-86d8-b26296d1919b/GCA_934680005.1_ERR7738558_bin.54_genomic.fna.gz --refList GCA_934680005.1_ERR7738558_bin.54_genomic.fna/target_genomes.txt --output GCA_934680005.1_ERR7738558_bin.54_genomic.fna/fastani_result.tsv --threads 1
[2023-06-06 00:01:46,448] [INFO] Task succeeded: fastANI
[2023-06-06 00:01:46,448] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd9671afa-87de-43bd-8fde-3547eebc6b4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-06 00:01:46,449] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd9671afa-87de-43bd-8fde-3547eebc6b4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-06 00:01:46,450] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-06 00:01:46,450] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-06 00:01:46,450] [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
--------------------------------------------------------------------------------
[2023-06-06 00:01:46,454] [INFO] DFAST Taxonomy check result was written to GCA_934680005.1_ERR7738558_bin.54_genomic.fna/tc_result.tsv
[2023-06-06 00:01:46,454] [INFO] ===== Taxonomy check completed =====
[2023-06-06 00:01:46,454] [INFO] ===== Start completeness check using CheckM =====
[2023-06-06 00:01:46,454] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd9671afa-87de-43bd-8fde-3547eebc6b4b/dqc_reference/checkm_data
[2023-06-06 00:01:46,456] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-06 00:01:46,476] [INFO] Task started: CheckM
[2023-06-06 00:01:46,476] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934680005.1_ERR7738558_bin.54_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934680005.1_ERR7738558_bin.54_genomic.fna/checkm_input GCA_934680005.1_ERR7738558_bin.54_genomic.fna/checkm_result
[2023-06-06 00:02:16,075] [INFO] Task succeeded: CheckM
[2023-06-06 00:02:16,076] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-06 00:02:16,099] [INFO] ===== Completeness check finished =====
[2023-06-06 00:02:16,099] [INFO] ===== Start GTDB Search =====
[2023-06-06 00:02:16,100] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934680005.1_ERR7738558_bin.54_genomic.fna/markers.fasta)
[2023-06-06 00:02:16,100] [INFO] Task started: Blastn
[2023-06-06 00:02:16,100] [INFO] Running command: blastn -query GCA_934680005.1_ERR7738558_bin.54_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9671afa-87de-43bd-8fde-3547eebc6b4b/dqc_reference/reference_markers_gtdb.fasta -out GCA_934680005.1_ERR7738558_bin.54_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-06 00:02:16,879] [INFO] Task succeeded: Blastn
[2023-06-06 00:02:16,888] [INFO] Selected 25 target genomes.
[2023-06-06 00:02:16,889] [INFO] Target genome list was writen to GCA_934680005.1_ERR7738558_bin.54_genomic.fna/target_genomes_gtdb.txt
[2023-06-06 00:02:16,915] [INFO] Task started: fastANI
[2023-06-06 00:02:16,916] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b3eb96f-617f-4b19-86d8-b26296d1919b/GCA_934680005.1_ERR7738558_bin.54_genomic.fna.gz --refList GCA_934680005.1_ERR7738558_bin.54_genomic.fna/target_genomes_gtdb.txt --output GCA_934680005.1_ERR7738558_bin.54_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-06 00:02:26,667] [INFO] Task succeeded: fastANI
[2023-06-06 00:02:26,674] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-06 00:02:26,674] [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_900546445.1	s__Cryptobacteroides sp900546445	96.3608	458	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.53	96.27	0.86	0.83	5	conclusive
GCA_002438635.1	s__Cryptobacteroides sp002438635	78.2867	150	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	99.38	99.25	0.92	0.82	10	-
GCA_900319375.1	s__Cryptobacteroides sp900319375	77.2029	64	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.13	97.22	0.89	0.84	4	-
GCA_900769905.1	s__Cryptobacteroides sp900769905	76.9502	53	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.32	98.32	0.78	0.78	2	-
GCA_905234775.1	s__Cryptobacteroides sp905234775	76.8874	55	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016286145.1	s__Cryptobacteroides sp016286145	76.8805	58	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.77	98.72	0.82	0.81	3	-
GCA_905234485.1	s__Cryptobacteroides sp905234485	76.5741	65	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	99.26	99.26	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-06-06 00:02:26,676] [INFO] GTDB search result was written to GCA_934680005.1_ERR7738558_bin.54_genomic.fna/result_gtdb.tsv
[2023-06-06 00:02:26,677] [INFO] ===== GTDB Search completed =====
[2023-06-06 00:02:26,679] [INFO] DFAST_QC result json was written to GCA_934680005.1_ERR7738558_bin.54_genomic.fna/dqc_result.json
[2023-06-06 00:02:26,679] [INFO] DFAST_QC completed!
[2023-06-06 00:02:26,680] [INFO] Total running time: 0h1m3s