[2023-06-05 02:34:48,735] [INFO] DFAST_QC pipeline started.
[2023-06-05 02:34:48,737] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 02:34:48,738] [INFO] DQC Reference Directory: /var/lib/cwl/stg70bfe690-1381-4cd7-9cae-62747a2119b7/dqc_reference
[2023-06-05 02:34:49,936] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 02:34:49,937] [INFO] Task started: Prodigal
[2023-06-05 02:34:49,937] [INFO] Running command: gunzip -c /var/lib/cwl/stg1173074e-a5df-4d06-9b66-699a4dd339f9/GCA_934754375.1_ERR7745787_bin.180_genomic.fna.gz | prodigal -d GCA_934754375.1_ERR7745787_bin.180_genomic.fna/cds.fna -a GCA_934754375.1_ERR7745787_bin.180_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 02:34:52,744] [INFO] Task succeeded: Prodigal
[2023-06-05 02:34:52,744] [INFO] Task started: HMMsearch
[2023-06-05 02:34:52,745] [INFO] Running command: hmmsearch --tblout GCA_934754375.1_ERR7745787_bin.180_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70bfe690-1381-4cd7-9cae-62747a2119b7/dqc_reference/reference_markers.hmm GCA_934754375.1_ERR7745787_bin.180_genomic.fna/protein.faa > /dev/null
[2023-06-05 02:34:52,959] [INFO] Task succeeded: HMMsearch
[2023-06-05 02:34:52,961] [INFO] Found 6/6 markers.
[2023-06-05 02:34:52,976] [INFO] Query marker FASTA was written to GCA_934754375.1_ERR7745787_bin.180_genomic.fna/markers.fasta
[2023-06-05 02:34:52,977] [INFO] Task started: Blastn
[2023-06-05 02:34:52,977] [INFO] Running command: blastn -query GCA_934754375.1_ERR7745787_bin.180_genomic.fna/markers.fasta -db /var/lib/cwl/stg70bfe690-1381-4cd7-9cae-62747a2119b7/dqc_reference/reference_markers.fasta -out GCA_934754375.1_ERR7745787_bin.180_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:34:53,599] [INFO] Task succeeded: Blastn
[2023-06-05 02:34:53,603] [INFO] Selected 20 target genomes.
[2023-06-05 02:34:53,604] [INFO] Target genome list was writen to GCA_934754375.1_ERR7745787_bin.180_genomic.fna/target_genomes.txt
[2023-06-05 02:34:53,609] [INFO] Task started: fastANI
[2023-06-05 02:34:53,609] [INFO] Running command: fastANI --query /var/lib/cwl/stg1173074e-a5df-4d06-9b66-699a4dd339f9/GCA_934754375.1_ERR7745787_bin.180_genomic.fna.gz --refList GCA_934754375.1_ERR7745787_bin.180_genomic.fna/target_genomes.txt --output GCA_934754375.1_ERR7745787_bin.180_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 02:35:00,360] [INFO] Task succeeded: fastANI
[2023-06-05 02:35:00,361] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70bfe690-1381-4cd7-9cae-62747a2119b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 02:35:00,361] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70bfe690-1381-4cd7-9cae-62747a2119b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 02:35:00,364] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 02:35:00,364] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 02:35:00,364] [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
--------------------------------------------------------------------------------
[2023-06-05 02:35:00,366] [INFO] DFAST Taxonomy check result was written to GCA_934754375.1_ERR7745787_bin.180_genomic.fna/tc_result.tsv
[2023-06-05 02:35:00,367] [INFO] ===== Taxonomy check completed =====
[2023-06-05 02:35:00,367] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 02:35:00,367] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70bfe690-1381-4cd7-9cae-62747a2119b7/dqc_reference/checkm_data
[2023-06-05 02:35:00,371] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 02:35:00,390] [INFO] Task started: CheckM
[2023-06-05 02:35:00,390] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934754375.1_ERR7745787_bin.180_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934754375.1_ERR7745787_bin.180_genomic.fna/checkm_input GCA_934754375.1_ERR7745787_bin.180_genomic.fna/checkm_result
[2023-06-05 02:35:16,853] [INFO] Task succeeded: CheckM
[2023-06-05 02:35:16,855] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 02:35:16,873] [INFO] ===== Completeness check finished =====
[2023-06-05 02:35:16,873] [INFO] ===== Start GTDB Search =====
[2023-06-05 02:35:16,874] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934754375.1_ERR7745787_bin.180_genomic.fna/markers.fasta)
[2023-06-05 02:35:16,874] [INFO] Task started: Blastn
[2023-06-05 02:35:16,874] [INFO] Running command: blastn -query GCA_934754375.1_ERR7745787_bin.180_genomic.fna/markers.fasta -db /var/lib/cwl/stg70bfe690-1381-4cd7-9cae-62747a2119b7/dqc_reference/reference_markers_gtdb.fasta -out GCA_934754375.1_ERR7745787_bin.180_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:35:17,883] [INFO] Task succeeded: Blastn
[2023-06-05 02:35:17,888] [INFO] Selected 22 target genomes.
[2023-06-05 02:35:17,888] [INFO] Target genome list was writen to GCA_934754375.1_ERR7745787_bin.180_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 02:35:17,954] [INFO] Task started: fastANI
[2023-06-05 02:35:17,954] [INFO] Running command: fastANI --query /var/lib/cwl/stg1173074e-a5df-4d06-9b66-699a4dd339f9/GCA_934754375.1_ERR7745787_bin.180_genomic.fna.gz --refList GCA_934754375.1_ERR7745787_bin.180_genomic.fna/target_genomes_gtdb.txt --output GCA_934754375.1_ERR7745787_bin.180_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 02:35:22,850] [INFO] Task succeeded: fastANI
[2023-06-05 02:35:22,857] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 02:35:22,857] [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_002406115.1	s__Onthoplasma sp002406115	80.5521	185	330	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA1242;g__Onthoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019120295.1	s__Onthoplasma faecipullorum	78.1887	55	330	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA1242;g__Onthoplasma	95.0	99.99	99.99	1.00	1.00	2	-
GCA_017531805.1	s__Onthoplasma sp017531805	77.6015	69	330	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA1242;g__Onthoplasma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 02:35:22,859] [INFO] GTDB search result was written to GCA_934754375.1_ERR7745787_bin.180_genomic.fna/result_gtdb.tsv
[2023-06-05 02:35:22,860] [INFO] ===== GTDB Search completed =====
[2023-06-05 02:35:22,862] [INFO] DFAST_QC result json was written to GCA_934754375.1_ERR7745787_bin.180_genomic.fna/dqc_result.json
[2023-06-05 02:35:22,862] [INFO] DFAST_QC completed!
[2023-06-05 02:35:22,862] [INFO] Total running time: 0h0m34s