[2023-06-08 00:04:41,099] [INFO] DFAST_QC pipeline started.
[2023-06-08 00:04:41,101] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 00:04:41,101] [INFO] DQC Reference Directory: /var/lib/cwl/stg674a2c8d-ca59-429c-abc5-f92ce54ec6c5/dqc_reference
[2023-06-08 00:04:43,299] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 00:04:43,300] [INFO] Task started: Prodigal
[2023-06-08 00:04:43,300] [INFO] Running command: gunzip -c /var/lib/cwl/stg1260abe8-0467-483e-9ddd-9592701baf50/GCA_902528065.1_AG-337-N23_genomic.fna.gz | prodigal -d GCA_902528065.1_AG-337-N23_genomic.fna/cds.fna -a GCA_902528065.1_AG-337-N23_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 00:04:45,188] [INFO] Task succeeded: Prodigal
[2023-06-08 00:04:45,189] [INFO] Task started: HMMsearch
[2023-06-08 00:04:45,189] [INFO] Running command: hmmsearch --tblout GCA_902528065.1_AG-337-N23_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg674a2c8d-ca59-429c-abc5-f92ce54ec6c5/dqc_reference/reference_markers.hmm GCA_902528065.1_AG-337-N23_genomic.fna/protein.faa > /dev/null
[2023-06-08 00:04:45,487] [INFO] Task succeeded: HMMsearch
[2023-06-08 00:04:45,489] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1260abe8-0467-483e-9ddd-9592701baf50/GCA_902528065.1_AG-337-N23_genomic.fna.gz]
[2023-06-08 00:04:45,504] [INFO] Query marker FASTA was written to GCA_902528065.1_AG-337-N23_genomic.fna/markers.fasta
[2023-06-08 00:04:45,505] [INFO] Task started: Blastn
[2023-06-08 00:04:45,505] [INFO] Running command: blastn -query GCA_902528065.1_AG-337-N23_genomic.fna/markers.fasta -db /var/lib/cwl/stg674a2c8d-ca59-429c-abc5-f92ce54ec6c5/dqc_reference/reference_markers.fasta -out GCA_902528065.1_AG-337-N23_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:04:47,614] [INFO] Task succeeded: Blastn
[2023-06-08 00:04:47,636] [INFO] Selected 19 target genomes.
[2023-06-08 00:04:47,637] [INFO] Target genome list was writen to GCA_902528065.1_AG-337-N23_genomic.fna/target_genomes.txt
[2023-06-08 00:04:47,659] [INFO] Task started: fastANI
[2023-06-08 00:04:47,659] [INFO] Running command: fastANI --query /var/lib/cwl/stg1260abe8-0467-483e-9ddd-9592701baf50/GCA_902528065.1_AG-337-N23_genomic.fna.gz --refList GCA_902528065.1_AG-337-N23_genomic.fna/target_genomes.txt --output GCA_902528065.1_AG-337-N23_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 00:04:57,077] [INFO] Task succeeded: fastANI
[2023-06-08 00:04:57,077] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg674a2c8d-ca59-429c-abc5-f92ce54ec6c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 00:04:57,078] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg674a2c8d-ca59-429c-abc5-f92ce54ec6c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 00:04:57,080] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 00:04:57,080] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 00:04:57,080] [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
--------------------------------------------------------------------------------
[2023-06-08 00:04:57,082] [INFO] DFAST Taxonomy check result was written to GCA_902528065.1_AG-337-N23_genomic.fna/tc_result.tsv
[2023-06-08 00:04:57,083] [INFO] ===== Taxonomy check completed =====
[2023-06-08 00:04:57,083] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 00:04:57,084] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg674a2c8d-ca59-429c-abc5-f92ce54ec6c5/dqc_reference/checkm_data
[2023-06-08 00:04:57,088] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 00:04:57,098] [INFO] Task started: CheckM
[2023-06-08 00:04:57,098] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902528065.1_AG-337-N23_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902528065.1_AG-337-N23_genomic.fna/checkm_input GCA_902528065.1_AG-337-N23_genomic.fna/checkm_result
[2023-06-08 00:05:10,892] [INFO] Task succeeded: CheckM
[2023-06-08 00:05:10,893] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-08 00:05:10,914] [INFO] ===== Completeness check finished =====
[2023-06-08 00:05:10,914] [INFO] ===== Start GTDB Search =====
[2023-06-08 00:05:10,915] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902528065.1_AG-337-N23_genomic.fna/markers.fasta)
[2023-06-08 00:05:10,915] [INFO] Task started: Blastn
[2023-06-08 00:05:10,915] [INFO] Running command: blastn -query GCA_902528065.1_AG-337-N23_genomic.fna/markers.fasta -db /var/lib/cwl/stg674a2c8d-ca59-429c-abc5-f92ce54ec6c5/dqc_reference/reference_markers_gtdb.fasta -out GCA_902528065.1_AG-337-N23_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:05:11,697] [INFO] Task succeeded: Blastn
[2023-06-08 00:05:11,701] [INFO] Selected 10 target genomes.
[2023-06-08 00:05:11,701] [INFO] Target genome list was writen to GCA_902528065.1_AG-337-N23_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 00:05:11,704] [INFO] Task started: fastANI
[2023-06-08 00:05:11,705] [INFO] Running command: fastANI --query /var/lib/cwl/stg1260abe8-0467-483e-9ddd-9592701baf50/GCA_902528065.1_AG-337-N23_genomic.fna.gz --refList GCA_902528065.1_AG-337-N23_genomic.fna/target_genomes_gtdb.txt --output GCA_902528065.1_AG-337-N23_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 00:05:13,660] [INFO] Task succeeded: fastANI
[2023-06-08 00:05:13,672] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 00:05:13,672] [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_902606555.1	s__MED-G14 sp902606555	95.5979	114	193	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902610105.1	s__MED-G14 sp902610105	91.6152	83	193	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902535165.1	s__MED-G14 sp902535165	89.4845	148	193	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902546095.1	s__MED-G14 sp902546095	88.5176	110	193	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902597545.1	s__MED-G14 sp902597545	87.9016	149	193	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	96.96	95.61	0.87	0.83	5	-
GCA_902595555.1	s__MED-G14 sp902595555	79.6799	104	193	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	96.27	95.29	0.86	0.83	8	-
GCA_902622575.1	s__MED-G14 sp902622575	79.222	79	193	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003331885.1	s__MED-G14 sp003331885	79.2018	77	193	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	96.85	96.85	0.80	0.80	2	-
GCA_902587325.1	s__MED-G14 sp902587325	77.346	66	193	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	97.53	95.17	0.82	0.78	10	-
--------------------------------------------------------------------------------
[2023-06-08 00:05:13,674] [INFO] GTDB search result was written to GCA_902528065.1_AG-337-N23_genomic.fna/result_gtdb.tsv
[2023-06-08 00:05:13,674] [INFO] ===== GTDB Search completed =====
[2023-06-08 00:05:13,677] [INFO] DFAST_QC result json was written to GCA_902528065.1_AG-337-N23_genomic.fna/dqc_result.json
[2023-06-08 00:05:13,677] [INFO] DFAST_QC completed!
[2023-06-08 00:05:13,677] [INFO] Total running time: 0h0m33s