[2023-06-30 11:15:23,905] [INFO] DFAST_QC pipeline started.
[2023-06-30 11:15:23,907] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 11:15:23,907] [INFO] DQC Reference Directory: /var/lib/cwl/stgab747e9d-ae3b-4597-a56d-c10a9c2967bf/dqc_reference
[2023-06-30 11:15:25,115] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 11:15:25,116] [INFO] Task started: Prodigal
[2023-06-30 11:15:25,116] [INFO] Running command: gunzip -c /var/lib/cwl/stge5727b76-f3a9-49fb-911f-c6b599c35271/GCA_900754175.1_ERS396440_25_genomic.fna.gz | prodigal -d GCA_900754175.1_ERS396440_25_genomic.fna/cds.fna -a GCA_900754175.1_ERS396440_25_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 11:15:30,105] [INFO] Task succeeded: Prodigal
[2023-06-30 11:15:30,106] [INFO] Task started: HMMsearch
[2023-06-30 11:15:30,106] [INFO] Running command: hmmsearch --tblout GCA_900754175.1_ERS396440_25_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab747e9d-ae3b-4597-a56d-c10a9c2967bf/dqc_reference/reference_markers.hmm GCA_900754175.1_ERS396440_25_genomic.fna/protein.faa > /dev/null
[2023-06-30 11:15:30,342] [INFO] Task succeeded: HMMsearch
[2023-06-30 11:15:30,344] [INFO] Found 6/6 markers.
[2023-06-30 11:15:30,368] [INFO] Query marker FASTA was written to GCA_900754175.1_ERS396440_25_genomic.fna/markers.fasta
[2023-06-30 11:15:30,369] [INFO] Task started: Blastn
[2023-06-30 11:15:30,369] [INFO] Running command: blastn -query GCA_900754175.1_ERS396440_25_genomic.fna/markers.fasta -db /var/lib/cwl/stgab747e9d-ae3b-4597-a56d-c10a9c2967bf/dqc_reference/reference_markers.fasta -out GCA_900754175.1_ERS396440_25_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 11:15:31,015] [INFO] Task succeeded: Blastn
[2023-06-30 11:15:31,018] [INFO] Selected 22 target genomes.
[2023-06-30 11:15:31,019] [INFO] Target genome list was writen to GCA_900754175.1_ERS396440_25_genomic.fna/target_genomes.txt
[2023-06-30 11:15:31,026] [INFO] Task started: fastANI
[2023-06-30 11:15:31,026] [INFO] Running command: fastANI --query /var/lib/cwl/stge5727b76-f3a9-49fb-911f-c6b599c35271/GCA_900754175.1_ERS396440_25_genomic.fna.gz --refList GCA_900754175.1_ERS396440_25_genomic.fna/target_genomes.txt --output GCA_900754175.1_ERS396440_25_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 11:15:44,857] [INFO] Task succeeded: fastANI
[2023-06-30 11:15:44,858] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab747e9d-ae3b-4597-a56d-c10a9c2967bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 11:15:44,858] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab747e9d-ae3b-4597-a56d-c10a9c2967bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 11:15:44,861] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 11:15:44,861] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 11:15:44,861] [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
--------------------------------------------------------------------------------
[2023-06-30 11:15:44,863] [INFO] DFAST Taxonomy check result was written to GCA_900754175.1_ERS396440_25_genomic.fna/tc_result.tsv
[2023-06-30 11:15:44,864] [INFO] ===== Taxonomy check completed =====
[2023-06-30 11:15:44,865] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 11:15:44,865] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab747e9d-ae3b-4597-a56d-c10a9c2967bf/dqc_reference/checkm_data
[2023-06-30 11:15:44,869] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 11:15:44,893] [INFO] Task started: CheckM
[2023-06-30 11:15:44,893] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900754175.1_ERS396440_25_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900754175.1_ERS396440_25_genomic.fna/checkm_input GCA_900754175.1_ERS396440_25_genomic.fna/checkm_result
[2023-06-30 11:16:06,156] [INFO] Task succeeded: CheckM
[2023-06-30 11:16:06,158] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 11:16:06,178] [INFO] ===== Completeness check finished =====
[2023-06-30 11:16:06,179] [INFO] ===== Start GTDB Search =====
[2023-06-30 11:16:06,179] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900754175.1_ERS396440_25_genomic.fna/markers.fasta)
[2023-06-30 11:16:06,180] [INFO] Task started: Blastn
[2023-06-30 11:16:06,180] [INFO] Running command: blastn -query GCA_900754175.1_ERS396440_25_genomic.fna/markers.fasta -db /var/lib/cwl/stgab747e9d-ae3b-4597-a56d-c10a9c2967bf/dqc_reference/reference_markers_gtdb.fasta -out GCA_900754175.1_ERS396440_25_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 11:16:07,296] [INFO] Task succeeded: Blastn
[2023-06-30 11:16:07,301] [INFO] Selected 22 target genomes.
[2023-06-30 11:16:07,301] [INFO] Target genome list was writen to GCA_900754175.1_ERS396440_25_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 11:16:07,313] [INFO] Task started: fastANI
[2023-06-30 11:16:07,313] [INFO] Running command: fastANI --query /var/lib/cwl/stge5727b76-f3a9-49fb-911f-c6b599c35271/GCA_900754175.1_ERS396440_25_genomic.fna.gz --refList GCA_900754175.1_ERS396440_25_genomic.fna/target_genomes_gtdb.txt --output GCA_900754175.1_ERS396440_25_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 11:16:14,503] [INFO] Task succeeded: fastANI
[2023-06-30 11:16:14,518] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 11:16:14,519] [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_900754175.1	s__HGM12713 sp900754175	100.0	591	597	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__HGM12713	95.0	98.77	98.77	0.89	0.89	2	conclusive
GCA_017463065.1	s__HGM12713 sp017463065	77.9441	87	597	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__HGM12713	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017504995.1	s__HGM12713 sp017504995	77.8467	90	597	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__HGM12713	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015063655.1	s__HGM12713 sp015063655	77.556	58	597	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__HGM12713	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015063485.1	s__HGM12713 sp015063485	77.5273	52	597	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__HGM12713	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015063535.1	s__HGM12713 sp015063535	77.2408	96	597	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__HGM12713	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017461745.1	s__HGM12713 sp017461745	77.1826	61	597	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__HGM12713	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017631855.1	s__HGM12713 sp017631855	76.9145	82	597	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__HGM12713	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017504335.1	s__HGM12713 sp017504335	76.8593	61	597	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__HGM12713	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905201895.1	s__UMGS1865 sp905201895	76.6246	61	597	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1865	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905187695.1	s__Firm-07 sp905187695	76.3907	54	597	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__Firm-07	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017507905.1	s__UMGS1865 sp017507905	76.2738	58	597	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1865	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015064005.1	s__Firm-07 sp015064005	76.0195	53	597	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__Firm-07	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 11:16:14,521] [INFO] GTDB search result was written to GCA_900754175.1_ERS396440_25_genomic.fna/result_gtdb.tsv
[2023-06-30 11:16:14,521] [INFO] ===== GTDB Search completed =====
[2023-06-30 11:16:14,525] [INFO] DFAST_QC result json was written to GCA_900754175.1_ERS396440_25_genomic.fna/dqc_result.json
[2023-06-30 11:16:14,525] [INFO] DFAST_QC completed!
[2023-06-30 11:16:14,525] [INFO] Total running time: 0h0m51s