[2023-06-05 05:36:33,180] [INFO] DFAST_QC pipeline started.
[2023-06-05 05:36:33,182] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 05:36:33,182] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c517727-829e-42ea-9211-44b13eb090c0/dqc_reference
[2023-06-05 05:36:35,605] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 05:36:35,606] [INFO] Task started: Prodigal
[2023-06-05 05:36:35,607] [INFO] Running command: gunzip -c /var/lib/cwl/stg0721a0ac-ab35-4cf9-9d30-5222994d291b/GCA_934230655.1_ERR7738594_bin.29_genomic.fna.gz | prodigal -d GCA_934230655.1_ERR7738594_bin.29_genomic.fna/cds.fna -a GCA_934230655.1_ERR7738594_bin.29_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 05:36:43,565] [INFO] Task succeeded: Prodigal
[2023-06-05 05:36:43,566] [INFO] Task started: HMMsearch
[2023-06-05 05:36:43,566] [INFO] Running command: hmmsearch --tblout GCA_934230655.1_ERR7738594_bin.29_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c517727-829e-42ea-9211-44b13eb090c0/dqc_reference/reference_markers.hmm GCA_934230655.1_ERR7738594_bin.29_genomic.fna/protein.faa > /dev/null
[2023-06-05 05:36:43,812] [INFO] Task succeeded: HMMsearch
[2023-06-05 05:36:43,814] [INFO] Found 6/6 markers.
[2023-06-05 05:36:43,842] [INFO] Query marker FASTA was written to GCA_934230655.1_ERR7738594_bin.29_genomic.fna/markers.fasta
[2023-06-05 05:36:43,843] [INFO] Task started: Blastn
[2023-06-05 05:36:43,843] [INFO] Running command: blastn -query GCA_934230655.1_ERR7738594_bin.29_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c517727-829e-42ea-9211-44b13eb090c0/dqc_reference/reference_markers.fasta -out GCA_934230655.1_ERR7738594_bin.29_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 05:36:44,421] [INFO] Task succeeded: Blastn
[2023-06-05 05:36:44,426] [INFO] Selected 15 target genomes.
[2023-06-05 05:36:44,426] [INFO] Target genome list was writen to GCA_934230655.1_ERR7738594_bin.29_genomic.fna/target_genomes.txt
[2023-06-05 05:36:44,429] [INFO] Task started: fastANI
[2023-06-05 05:36:44,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg0721a0ac-ab35-4cf9-9d30-5222994d291b/GCA_934230655.1_ERR7738594_bin.29_genomic.fna.gz --refList GCA_934230655.1_ERR7738594_bin.29_genomic.fna/target_genomes.txt --output GCA_934230655.1_ERR7738594_bin.29_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 05:36:52,758] [INFO] Task succeeded: fastANI
[2023-06-05 05:36:52,759] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c517727-829e-42ea-9211-44b13eb090c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 05:36:52,759] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c517727-829e-42ea-9211-44b13eb090c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 05:36:52,761] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 05:36:52,761] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 05:36:52,761] [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 05:36:52,763] [INFO] DFAST Taxonomy check result was written to GCA_934230655.1_ERR7738594_bin.29_genomic.fna/tc_result.tsv
[2023-06-05 05:36:52,763] [INFO] ===== Taxonomy check completed =====
[2023-06-05 05:36:52,764] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 05:36:52,764] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c517727-829e-42ea-9211-44b13eb090c0/dqc_reference/checkm_data
[2023-06-05 05:36:52,767] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 05:36:52,799] [INFO] Task started: CheckM
[2023-06-05 05:36:52,799] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934230655.1_ERR7738594_bin.29_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934230655.1_ERR7738594_bin.29_genomic.fna/checkm_input GCA_934230655.1_ERR7738594_bin.29_genomic.fna/checkm_result
[2023-06-05 05:37:20,441] [INFO] Task succeeded: CheckM
[2023-06-05 05:37:20,443] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 05:37:20,463] [INFO] ===== Completeness check finished =====
[2023-06-05 05:37:20,463] [INFO] ===== Start GTDB Search =====
[2023-06-05 05:37:20,464] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934230655.1_ERR7738594_bin.29_genomic.fna/markers.fasta)
[2023-06-05 05:37:20,464] [INFO] Task started: Blastn
[2023-06-05 05:37:20,464] [INFO] Running command: blastn -query GCA_934230655.1_ERR7738594_bin.29_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c517727-829e-42ea-9211-44b13eb090c0/dqc_reference/reference_markers_gtdb.fasta -out GCA_934230655.1_ERR7738594_bin.29_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 05:37:21,216] [INFO] Task succeeded: Blastn
[2023-06-05 05:37:21,221] [INFO] Selected 14 target genomes.
[2023-06-05 05:37:21,221] [INFO] Target genome list was writen to GCA_934230655.1_ERR7738594_bin.29_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 05:37:21,271] [INFO] Task started: fastANI
[2023-06-05 05:37:21,271] [INFO] Running command: fastANI --query /var/lib/cwl/stg0721a0ac-ab35-4cf9-9d30-5222994d291b/GCA_934230655.1_ERR7738594_bin.29_genomic.fna.gz --refList GCA_934230655.1_ERR7738594_bin.29_genomic.fna/target_genomes_gtdb.txt --output GCA_934230655.1_ERR7738594_bin.29_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 05:37:26,169] [INFO] Task succeeded: fastANI
[2023-06-05 05:37:26,181] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 05:37:26,181] [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_900769665.1	s__Fimimonas sp900769665	95.4917	625	799	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-314;g__Fimimonas	95.0	96.81	96.81	0.74	0.74	2	conclusive
GCA_003537755.1	s__Fimimonas sp003537755	80.7988	320	799	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-314;g__Fimimonas	95.0	97.28	97.18	0.87	0.84	4	-
GCA_000433775.1	s__Fimimonas gallinarum	77.6827	98	799	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-314;g__Fimimonas	95.0	98.11	97.98	0.92	0.91	5	-
GCA_017457305.1	s__Fimimonas sp017457305	77.5255	59	799	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-314;g__Fimimonas	95.0	97.10	96.96	0.90	0.87	5	-
GCA_910587795.1	s__Fimimonas sp910587795	77.3116	50	799	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-314;g__Fimimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586625.1	s__Fimimonas sp910586625	77.1137	66	799	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-314;g__Fimimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017500855.1	s__Fimimonas sp017500855	76.8387	75	799	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-314;g__Fimimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018713905.1	s__Fimimonas merdipullorum	76.7296	61	799	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-314;g__Fimimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 05:37:26,205] [INFO] GTDB search result was written to GCA_934230655.1_ERR7738594_bin.29_genomic.fna/result_gtdb.tsv
[2023-06-05 05:37:26,206] [INFO] ===== GTDB Search completed =====
[2023-06-05 05:37:26,210] [INFO] DFAST_QC result json was written to GCA_934230655.1_ERR7738594_bin.29_genomic.fna/dqc_result.json
[2023-06-05 05:37:26,210] [INFO] DFAST_QC completed!
[2023-06-05 05:37:26,210] [INFO] Total running time: 0h0m53s