[2023-03-15 08:55:06,630] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:55:06,630] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:55:06,630] [INFO] DQC Reference Directory: /var/lib/cwl/stg492b3ace-c5a5-4002-b495-5ae706aa2814/dqc_reference
[2023-03-15 08:55:08,347] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:55:08,347] [INFO] Task started: Prodigal
[2023-03-15 08:55:08,347] [INFO] Running command: cat /var/lib/cwl/stg77c690b5-2bee-4ca4-9bd6-b74b72ee8603/OceanDNA-b8757.fa | prodigal -d OceanDNA-b8757/cds.fna -a OceanDNA-b8757/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:55:15,907] [INFO] Task succeeded: Prodigal
[2023-03-15 08:55:15,907] [INFO] Task started: HMMsearch
[2023-03-15 08:55:15,907] [INFO] Running command: hmmsearch --tblout OceanDNA-b8757/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg492b3ace-c5a5-4002-b495-5ae706aa2814/dqc_reference/reference_markers.hmm OceanDNA-b8757/protein.faa > /dev/null
[2023-03-15 08:55:16,113] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:55:16,114] [INFO] Found 6/6 markers.
[2023-03-15 08:55:16,124] [INFO] Query marker FASTA was written to OceanDNA-b8757/markers.fasta
[2023-03-15 08:55:16,124] [INFO] Task started: Blastn
[2023-03-15 08:55:16,124] [INFO] Running command: blastn -query OceanDNA-b8757/markers.fasta -db /var/lib/cwl/stg492b3ace-c5a5-4002-b495-5ae706aa2814/dqc_reference/reference_markers.fasta -out OceanDNA-b8757/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:55:16,756] [INFO] Task succeeded: Blastn
[2023-03-15 08:55:16,757] [INFO] Selected 33 target genomes.
[2023-03-15 08:55:16,757] [INFO] Target genome list was writen to OceanDNA-b8757/target_genomes.txt
[2023-03-15 08:55:16,781] [INFO] Task started: fastANI
[2023-03-15 08:55:16,782] [INFO] Running command: fastANI --query /var/lib/cwl/stg77c690b5-2bee-4ca4-9bd6-b74b72ee8603/OceanDNA-b8757.fa --refList OceanDNA-b8757/target_genomes.txt --output OceanDNA-b8757/fastani_result.tsv --threads 1
[2023-03-15 08:55:35,539] [INFO] Task succeeded: fastANI
[2023-03-15 08:55:35,540] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg492b3ace-c5a5-4002-b495-5ae706aa2814/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:55:35,540] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg492b3ace-c5a5-4002-b495-5ae706aa2814/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:55:35,540] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:55:35,540] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 08:55:35,540] [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
--------------------------------------------------------------------------------
[2023-03-15 08:55:35,540] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8757/tc_result.tsv
[2023-03-15 08:55:35,541] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:55:35,541] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:55:35,541] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg492b3ace-c5a5-4002-b495-5ae706aa2814/dqc_reference/checkm_data
[2023-03-15 08:55:35,544] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:55:35,547] [INFO] Task started: CheckM
[2023-03-15 08:55:35,547] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8757/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8757/checkm_input OceanDNA-b8757/checkm_result
[2023-03-15 08:55:59,733] [INFO] Task succeeded: CheckM
[2023-03-15 08:55:59,734] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.65%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 08:55:59,736] [INFO] ===== Completeness check finished =====
[2023-03-15 08:55:59,736] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:55:59,736] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8757/markers.fasta)
[2023-03-15 08:55:59,736] [INFO] Task started: Blastn
[2023-03-15 08:55:59,736] [INFO] Running command: blastn -query OceanDNA-b8757/markers.fasta -db /var/lib/cwl/stg492b3ace-c5a5-4002-b495-5ae706aa2814/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8757/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:56:00,695] [INFO] Task succeeded: Blastn
[2023-03-15 08:56:00,696] [INFO] Selected 10 target genomes.
[2023-03-15 08:56:00,696] [INFO] Target genome list was writen to OceanDNA-b8757/target_genomes_gtdb.txt
[2023-03-15 08:56:00,767] [INFO] Task started: fastANI
[2023-03-15 08:56:00,767] [INFO] Running command: fastANI --query /var/lib/cwl/stg77c690b5-2bee-4ca4-9bd6-b74b72ee8603/OceanDNA-b8757.fa --refList OceanDNA-b8757/target_genomes_gtdb.txt --output OceanDNA-b8757/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:56:03,396] [INFO] Task succeeded: fastANI
[2023-03-15 08:56:03,402] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 08:56:03,403] [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_002702745.1	s__MED-G13 sp002702745	99.4293	323	402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002691265.1	s__MED-G13 sp002691265	89.6441	305	402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	97.61	95.49	0.82	0.79	4	-
GCA_902518355.1	s__MED-G13 sp902518355	89.542	314	402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	96.57	96.00	0.86	0.83	4	-
GCA_902581145.1	s__MED-G13 sp902581145	88.954	273	402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008081325.1	s__MED-G13 sp008081325	82.4721	208	402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902626365.1	s__MED-G13 sp902626365	82.1782	225	402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	96.07	96.07	0.74	0.74	2	-
GCA_902519075.1	s__MED-G13 sp902519075	81.7005	227	402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902526075.1	s__MED-G13 sp902526075	81.1738	207	402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902517895.1	s__MED-G13 sp902517895	81.1559	220	402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902510415.1	s__MED-G13 sp902510415	79.2262	187	402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	98.10	98.10	0.69	0.69	2	-
--------------------------------------------------------------------------------
[2023-03-15 08:56:03,403] [INFO] GTDB search result was written to OceanDNA-b8757/result_gtdb.tsv
[2023-03-15 08:56:03,403] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:56:03,404] [INFO] DFAST_QC result json was written to OceanDNA-b8757/dqc_result.json
[2023-03-15 08:56:03,404] [INFO] DFAST_QC completed!
[2023-03-15 08:56:03,404] [INFO] Total running time: 0h0m57s