[2023-03-19 01:08:55,566] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:08:55,566] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:08:55,566] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe2150c6-6343-4b87-bd62-d9068e9cb136/dqc_reference
[2023-03-19 01:08:56,666] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:08:56,666] [INFO] Task started: Prodigal
[2023-03-19 01:08:56,666] [INFO] Running command: cat /var/lib/cwl/stg165438ec-31f6-42c3-8c0d-8538717cf434/OceanDNA-b5832.fa | prodigal -d OceanDNA-b5832/cds.fna -a OceanDNA-b5832/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:09:08,270] [INFO] Task succeeded: Prodigal
[2023-03-19 01:09:08,270] [INFO] Task started: HMMsearch
[2023-03-19 01:09:08,270] [INFO] Running command: hmmsearch --tblout OceanDNA-b5832/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe2150c6-6343-4b87-bd62-d9068e9cb136/dqc_reference/reference_markers.hmm OceanDNA-b5832/protein.faa > /dev/null
[2023-03-19 01:09:08,414] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:09:08,415] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg165438ec-31f6-42c3-8c0d-8538717cf434/OceanDNA-b5832.fa]
[2023-03-19 01:09:08,428] [INFO] Query marker FASTA was written to OceanDNA-b5832/markers.fasta
[2023-03-19 01:09:08,429] [INFO] Task started: Blastn
[2023-03-19 01:09:08,430] [INFO] Running command: blastn -query OceanDNA-b5832/markers.fasta -db /var/lib/cwl/stgbe2150c6-6343-4b87-bd62-d9068e9cb136/dqc_reference/reference_markers.fasta -out OceanDNA-b5832/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:09:08,926] [INFO] Task succeeded: Blastn
[2023-03-19 01:09:08,927] [INFO] Selected 10 target genomes.
[2023-03-19 01:09:08,927] [INFO] Target genome list was writen to OceanDNA-b5832/target_genomes.txt
[2023-03-19 01:09:08,933] [INFO] Task started: fastANI
[2023-03-19 01:09:08,933] [INFO] Running command: fastANI --query /var/lib/cwl/stg165438ec-31f6-42c3-8c0d-8538717cf434/OceanDNA-b5832.fa --refList OceanDNA-b5832/target_genomes.txt --output OceanDNA-b5832/fastani_result.tsv --threads 1
[2023-03-19 01:09:14,348] [INFO] Task succeeded: fastANI
[2023-03-19 01:09:14,348] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe2150c6-6343-4b87-bd62-d9068e9cb136/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:09:14,348] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe2150c6-6343-4b87-bd62-d9068e9cb136/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:09:14,349] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:09:14,349] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:09:14,349] [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
--------------------------------------------------------------------------------
[2023-03-19 01:09:14,349] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5832/tc_result.tsv
[2023-03-19 01:09:14,349] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:09:14,349] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:09:14,349] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe2150c6-6343-4b87-bd62-d9068e9cb136/dqc_reference/checkm_data
[2023-03-19 01:09:14,404] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:09:14,407] [INFO] Task started: CheckM
[2023-03-19 01:09:14,407] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5832/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5832/checkm_input OceanDNA-b5832/checkm_result
[2023-03-19 01:09:49,089] [INFO] Task succeeded: CheckM
[2023-03-19 01:09:49,089] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 01:09:49,091] [INFO] ===== Completeness check finished =====
[2023-03-19 01:09:49,091] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:09:49,092] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5832/markers.fasta)
[2023-03-19 01:09:49,093] [INFO] Task started: Blastn
[2023-03-19 01:09:49,093] [INFO] Running command: blastn -query OceanDNA-b5832/markers.fasta -db /var/lib/cwl/stgbe2150c6-6343-4b87-bd62-d9068e9cb136/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5832/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:09:49,953] [INFO] Task succeeded: Blastn
[2023-03-19 01:09:49,954] [INFO] Selected 11 target genomes.
[2023-03-19 01:09:49,954] [INFO] Target genome list was writen to OceanDNA-b5832/target_genomes_gtdb.txt
[2023-03-19 01:09:49,965] [INFO] Task started: fastANI
[2023-03-19 01:09:49,965] [INFO] Running command: fastANI --query /var/lib/cwl/stg165438ec-31f6-42c3-8c0d-8538717cf434/OceanDNA-b5832.fa --refList OceanDNA-b5832/target_genomes_gtdb.txt --output OceanDNA-b5832/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:09:54,914] [INFO] Task succeeded: fastANI
[2023-03-19 01:09:54,919] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:09:54,919] [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_905182675.1	s__UBA10364 sp905182675	93.9716	364	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003487785.1	s__UBA10364 sp003487785	87.5598	323	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	99.22	99.20	0.81	0.80	3	-
GCA_011525035.1	s__UBA10364 sp011525035	77.5602	85	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003045825.1	s__UBA10364 sp003045825	77.4622	79	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	98.67	96.47	0.88	0.80	20	-
GCA_012269745.1	s__UBA10364 sp012269745	77.1513	80	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402665.1	s__UBA10364 sp018402665	76.9808	79	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	96.42	96.42	0.92	0.92	2	-
GCA_018623275.1	s__UBA10364 sp018623275	76.9069	54	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:09:54,919] [INFO] GTDB search result was written to OceanDNA-b5832/result_gtdb.tsv
[2023-03-19 01:09:54,919] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:09:54,920] [INFO] DFAST_QC result json was written to OceanDNA-b5832/dqc_result.json
[2023-03-19 01:09:54,920] [INFO] DFAST_QC completed!
[2023-03-19 01:09:54,920] [INFO] Total running time: 0h0m59s