[2023-06-05 01:05:12,481] [INFO] DFAST_QC pipeline started.
[2023-06-05 01:05:12,483] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 01:05:12,483] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f75add0-81e1-4033-b3f7-09321842f83e/dqc_reference
[2023-06-05 01:05:16,332] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 01:05:16,333] [INFO] Task started: Prodigal
[2023-06-05 01:05:16,333] [INFO] Running command: gunzip -c /var/lib/cwl/stg0404f38e-3434-4c76-ba72-df03c7c4a621/GCA_934169925.1_ERR7746773_bin.119_genomic.fna.gz | prodigal -d GCA_934169925.1_ERR7746773_bin.119_genomic.fna/cds.fna -a GCA_934169925.1_ERR7746773_bin.119_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 01:05:18,213] [INFO] Task succeeded: Prodigal
[2023-06-05 01:05:18,214] [INFO] Task started: HMMsearch
[2023-06-05 01:05:18,214] [INFO] Running command: hmmsearch --tblout GCA_934169925.1_ERR7746773_bin.119_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f75add0-81e1-4033-b3f7-09321842f83e/dqc_reference/reference_markers.hmm GCA_934169925.1_ERR7746773_bin.119_genomic.fna/protein.faa > /dev/null
[2023-06-05 01:05:18,450] [INFO] Task succeeded: HMMsearch
[2023-06-05 01:05:18,451] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0404f38e-3434-4c76-ba72-df03c7c4a621/GCA_934169925.1_ERR7746773_bin.119_genomic.fna.gz]
[2023-06-05 01:05:18,473] [INFO] Query marker FASTA was written to GCA_934169925.1_ERR7746773_bin.119_genomic.fna/markers.fasta
[2023-06-05 01:05:18,474] [INFO] Task started: Blastn
[2023-06-05 01:05:18,474] [INFO] Running command: blastn -query GCA_934169925.1_ERR7746773_bin.119_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f75add0-81e1-4033-b3f7-09321842f83e/dqc_reference/reference_markers.fasta -out GCA_934169925.1_ERR7746773_bin.119_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:05:22,789] [INFO] Task succeeded: Blastn
[2023-06-05 01:05:22,793] [INFO] Selected 18 target genomes.
[2023-06-05 01:05:22,793] [INFO] Target genome list was writen to GCA_934169925.1_ERR7746773_bin.119_genomic.fna/target_genomes.txt
[2023-06-05 01:05:22,798] [INFO] Task started: fastANI
[2023-06-05 01:05:22,798] [INFO] Running command: fastANI --query /var/lib/cwl/stg0404f38e-3434-4c76-ba72-df03c7c4a621/GCA_934169925.1_ERR7746773_bin.119_genomic.fna.gz --refList GCA_934169925.1_ERR7746773_bin.119_genomic.fna/target_genomes.txt --output GCA_934169925.1_ERR7746773_bin.119_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 01:05:32,326] [INFO] Task succeeded: fastANI
[2023-06-05 01:05:32,327] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f75add0-81e1-4033-b3f7-09321842f83e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 01:05:32,327] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f75add0-81e1-4033-b3f7-09321842f83e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 01:05:32,337] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 01:05:32,337] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 01:05:32,337] [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 01:05:32,339] [INFO] DFAST Taxonomy check result was written to GCA_934169925.1_ERR7746773_bin.119_genomic.fna/tc_result.tsv
[2023-06-05 01:05:32,340] [INFO] ===== Taxonomy check completed =====
[2023-06-05 01:05:32,340] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 01:05:32,341] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f75add0-81e1-4033-b3f7-09321842f83e/dqc_reference/checkm_data
[2023-06-05 01:05:32,344] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 01:05:32,363] [INFO] Task started: CheckM
[2023-06-05 01:05:32,363] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934169925.1_ERR7746773_bin.119_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934169925.1_ERR7746773_bin.119_genomic.fna/checkm_input GCA_934169925.1_ERR7746773_bin.119_genomic.fna/checkm_result
[2023-06-05 01:05:49,146] [INFO] Task succeeded: CheckM
[2023-06-05 01:05:49,147] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 01:05:49,162] [INFO] ===== Completeness check finished =====
[2023-06-05 01:05:49,162] [INFO] ===== Start GTDB Search =====
[2023-06-05 01:05:49,163] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934169925.1_ERR7746773_bin.119_genomic.fna/markers.fasta)
[2023-06-05 01:05:49,163] [INFO] Task started: Blastn
[2023-06-05 01:05:49,163] [INFO] Running command: blastn -query GCA_934169925.1_ERR7746773_bin.119_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f75add0-81e1-4033-b3f7-09321842f83e/dqc_reference/reference_markers_gtdb.fasta -out GCA_934169925.1_ERR7746773_bin.119_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:05:49,917] [INFO] Task succeeded: Blastn
[2023-06-05 01:05:49,921] [INFO] Selected 15 target genomes.
[2023-06-05 01:05:49,921] [INFO] Target genome list was writen to GCA_934169925.1_ERR7746773_bin.119_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 01:05:49,927] [INFO] Task started: fastANI
[2023-06-05 01:05:49,928] [INFO] Running command: fastANI --query /var/lib/cwl/stg0404f38e-3434-4c76-ba72-df03c7c4a621/GCA_934169925.1_ERR7746773_bin.119_genomic.fna.gz --refList GCA_934169925.1_ERR7746773_bin.119_genomic.fna/target_genomes_gtdb.txt --output GCA_934169925.1_ERR7746773_bin.119_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 01:05:54,187] [INFO] Task succeeded: fastANI
[2023-06-05 01:05:54,196] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 01:05:54,197] [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_000433755.1	s__CAG-465 sp000433755	78.2629	106	406	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-465;g__CAG-465	95.0	97.80	97.49	0.91	0.90	4	-
GCA_000433135.1	s__CAG-465 sp000433135	78.1414	107	406	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-465;g__CAG-465	95.0	98.44	98.40	0.85	0.84	3	-
GCA_900772475.1	s__CAG-465 sp900772475	78.09	121	406	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-465;g__CAG-465	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905204915.1	s__CAG-465 sp905204915	77.9522	89	406	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-465;g__CAG-465	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554875.1	s__CAG-465 sp900554875	77.7549	80	406	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-465;g__CAG-465	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000433335.1	s__CAG-465 sp000433335	77.6041	74	406	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-465;g__CAG-465	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017626395.1	s__RGIG5622 sp017626395	77.5983	114	406	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-465;g__RGIG5622	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017534305.1	s__RGIG5622 sp017534305	77.1629	90	406	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-465;g__RGIG5622	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017478805.1	s__RGIG5057 sp017478805	76.1763	55	406	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-465;g__RGIG5057	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015056545.1	s__SIG350 sp015056545	75.9946	54	406	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__SIG350;g__SIG350	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 01:05:54,199] [INFO] GTDB search result was written to GCA_934169925.1_ERR7746773_bin.119_genomic.fna/result_gtdb.tsv
[2023-06-05 01:05:54,199] [INFO] ===== GTDB Search completed =====
[2023-06-05 01:05:54,202] [INFO] DFAST_QC result json was written to GCA_934169925.1_ERR7746773_bin.119_genomic.fna/dqc_result.json
[2023-06-05 01:05:54,202] [INFO] DFAST_QC completed!
[2023-06-05 01:05:54,202] [INFO] Total running time: 0h0m42s