[2023-06-05 09:25:11,403] [INFO] DFAST_QC pipeline started.
[2023-06-05 09:25:11,408] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 09:25:11,408] [INFO] DQC Reference Directory: /var/lib/cwl/stg1574cc4e-c23e-4a34-8cad-7e6bf84dacbf/dqc_reference
[2023-06-05 09:25:13,030] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 09:25:13,030] [INFO] Task started: Prodigal
[2023-06-05 09:25:13,031] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e43f95a-9623-4ffd-ad0c-9c8e0ecb4f7e/GCA_934481365.1_ERR7738162_bin.48_genomic.fna.gz | prodigal -d GCA_934481365.1_ERR7738162_bin.48_genomic.fna/cds.fna -a GCA_934481365.1_ERR7738162_bin.48_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 09:25:17,548] [INFO] Task succeeded: Prodigal
[2023-06-05 09:25:17,548] [INFO] Task started: HMMsearch
[2023-06-05 09:25:17,548] [INFO] Running command: hmmsearch --tblout GCA_934481365.1_ERR7738162_bin.48_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1574cc4e-c23e-4a34-8cad-7e6bf84dacbf/dqc_reference/reference_markers.hmm GCA_934481365.1_ERR7738162_bin.48_genomic.fna/protein.faa > /dev/null
[2023-06-05 09:25:17,784] [INFO] Task succeeded: HMMsearch
[2023-06-05 09:25:17,785] [INFO] Found 6/6 markers.
[2023-06-05 09:25:17,831] [INFO] Query marker FASTA was written to GCA_934481365.1_ERR7738162_bin.48_genomic.fna/markers.fasta
[2023-06-05 09:25:17,832] [INFO] Task started: Blastn
[2023-06-05 09:25:17,832] [INFO] Running command: blastn -query GCA_934481365.1_ERR7738162_bin.48_genomic.fna/markers.fasta -db /var/lib/cwl/stg1574cc4e-c23e-4a34-8cad-7e6bf84dacbf/dqc_reference/reference_markers.fasta -out GCA_934481365.1_ERR7738162_bin.48_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:25:18,545] [INFO] Task succeeded: Blastn
[2023-06-05 09:25:18,548] [INFO] Selected 16 target genomes.
[2023-06-05 09:25:18,549] [INFO] Target genome list was writen to GCA_934481365.1_ERR7738162_bin.48_genomic.fna/target_genomes.txt
[2023-06-05 09:25:18,551] [INFO] Task started: fastANI
[2023-06-05 09:25:18,551] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e43f95a-9623-4ffd-ad0c-9c8e0ecb4f7e/GCA_934481365.1_ERR7738162_bin.48_genomic.fna.gz --refList GCA_934481365.1_ERR7738162_bin.48_genomic.fna/target_genomes.txt --output GCA_934481365.1_ERR7738162_bin.48_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 09:25:28,171] [INFO] Task succeeded: fastANI
[2023-06-05 09:25:28,171] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1574cc4e-c23e-4a34-8cad-7e6bf84dacbf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 09:25:28,172] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1574cc4e-c23e-4a34-8cad-7e6bf84dacbf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 09:25:28,174] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 09:25:28,174] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 09:25:28,174] [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 09:25:28,176] [INFO] DFAST Taxonomy check result was written to GCA_934481365.1_ERR7738162_bin.48_genomic.fna/tc_result.tsv
[2023-06-05 09:25:28,177] [INFO] ===== Taxonomy check completed =====
[2023-06-05 09:25:28,177] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 09:25:28,177] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1574cc4e-c23e-4a34-8cad-7e6bf84dacbf/dqc_reference/checkm_data
[2023-06-05 09:25:28,180] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 09:25:28,207] [INFO] Task started: CheckM
[2023-06-05 09:25:28,208] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934481365.1_ERR7738162_bin.48_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934481365.1_ERR7738162_bin.48_genomic.fna/checkm_input GCA_934481365.1_ERR7738162_bin.48_genomic.fna/checkm_result
[2023-06-05 09:25:48,483] [INFO] Task succeeded: CheckM
[2023-06-05 09:25:48,484] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 09:25:48,501] [INFO] ===== Completeness check finished =====
[2023-06-05 09:25:48,501] [INFO] ===== Start GTDB Search =====
[2023-06-05 09:25:48,501] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934481365.1_ERR7738162_bin.48_genomic.fna/markers.fasta)
[2023-06-05 09:25:48,502] [INFO] Task started: Blastn
[2023-06-05 09:25:48,502] [INFO] Running command: blastn -query GCA_934481365.1_ERR7738162_bin.48_genomic.fna/markers.fasta -db /var/lib/cwl/stg1574cc4e-c23e-4a34-8cad-7e6bf84dacbf/dqc_reference/reference_markers_gtdb.fasta -out GCA_934481365.1_ERR7738162_bin.48_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:25:49,554] [INFO] Task succeeded: Blastn
[2023-06-05 09:25:49,558] [INFO] Selected 13 target genomes.
[2023-06-05 09:25:49,558] [INFO] Target genome list was writen to GCA_934481365.1_ERR7738162_bin.48_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 09:25:49,566] [INFO] Task started: fastANI
[2023-06-05 09:25:49,567] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e43f95a-9623-4ffd-ad0c-9c8e0ecb4f7e/GCA_934481365.1_ERR7738162_bin.48_genomic.fna.gz --refList GCA_934481365.1_ERR7738162_bin.48_genomic.fna/target_genomes_gtdb.txt --output GCA_934481365.1_ERR7738162_bin.48_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 09:25:53,785] [INFO] Task succeeded: fastANI
[2023-06-05 09:25:53,794] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 09:25:53,794] [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_900768105.1	s__UMGS1668 sp900768105	98.5357	453	539	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UMGS1668	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004556975.1	s__UMGS1668 sp004556975	83.4962	371	539	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UMGS1668	95.0	97.44	96.73	0.87	0.85	6	-
GCA_900553955.1	s__UMGS1668 sp900553955	83.0352	339	539	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UMGS1668	95.0	98.96	97.93	0.95	0.91	3	-
GCA_017468365.1	s__UMGS1668 sp017468365	78.033	150	539	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UMGS1668	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017521825.1	s__UMGS1668 sp017521825	78.02	150	539	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UMGS1668	95.0	96.46	96.46	0.85	0.85	2	-
GCA_016296485.1	s__UMGS1668 sp016296485	78.0094	126	539	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UMGS1668	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017436125.1	s__UMGS1668 sp017436125	77.6402	147	539	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UMGS1668	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015067125.1	s__UMGS1668 sp015067125	77.4258	125	539	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UMGS1668	95.0	97.47	97.35	0.81	0.76	4	-
--------------------------------------------------------------------------------
[2023-06-05 09:25:53,796] [INFO] GTDB search result was written to GCA_934481365.1_ERR7738162_bin.48_genomic.fna/result_gtdb.tsv
[2023-06-05 09:25:53,797] [INFO] ===== GTDB Search completed =====
[2023-06-05 09:25:53,800] [INFO] DFAST_QC result json was written to GCA_934481365.1_ERR7738162_bin.48_genomic.fna/dqc_result.json
[2023-06-05 09:25:53,800] [INFO] DFAST_QC completed!
[2023-06-05 09:25:53,800] [INFO] Total running time: 0h0m42s