[2023-03-16 16:53:43,347] [INFO] DFAST_QC pipeline started.
[2023-03-16 16:53:43,347] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 16:53:43,347] [INFO] DQC Reference Directory: /var/lib/cwl/stg934ff590-166e-4be7-bc31-87292abf81f0/dqc_reference
[2023-03-16 16:53:44,469] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 16:53:44,470] [INFO] Task started: Prodigal
[2023-03-16 16:53:44,470] [INFO] Running command: cat /var/lib/cwl/stg5b1d7aef-8c67-4663-8568-ed6231c124c9/OceanDNA-b11076.fa | prodigal -d OceanDNA-b11076/cds.fna -a OceanDNA-b11076/protein.faa -g 11 -q > /dev/null
[2023-03-16 16:53:59,763] [INFO] Task succeeded: Prodigal
[2023-03-16 16:53:59,764] [INFO] Task started: HMMsearch
[2023-03-16 16:53:59,764] [INFO] Running command: hmmsearch --tblout OceanDNA-b11076/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg934ff590-166e-4be7-bc31-87292abf81f0/dqc_reference/reference_markers.hmm OceanDNA-b11076/protein.faa > /dev/null
[2023-03-16 16:53:59,941] [INFO] Task succeeded: HMMsearch
[2023-03-16 16:53:59,942] [INFO] Found 6/6 markers.
[2023-03-16 16:53:59,951] [INFO] Query marker FASTA was written to OceanDNA-b11076/markers.fasta
[2023-03-16 16:53:59,953] [INFO] Task started: Blastn
[2023-03-16 16:53:59,953] [INFO] Running command: blastn -query OceanDNA-b11076/markers.fasta -db /var/lib/cwl/stg934ff590-166e-4be7-bc31-87292abf81f0/dqc_reference/reference_markers.fasta -out OceanDNA-b11076/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:54:00,558] [INFO] Task succeeded: Blastn
[2023-03-16 16:54:00,559] [INFO] Selected 31 target genomes.
[2023-03-16 16:54:00,560] [INFO] Target genome list was writen to OceanDNA-b11076/target_genomes.txt
[2023-03-16 16:54:00,610] [INFO] Task started: fastANI
[2023-03-16 16:54:00,610] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b1d7aef-8c67-4663-8568-ed6231c124c9/OceanDNA-b11076.fa --refList OceanDNA-b11076/target_genomes.txt --output OceanDNA-b11076/fastani_result.tsv --threads 1
[2023-03-16 16:54:26,206] [INFO] Task succeeded: fastANI
[2023-03-16 16:54:26,207] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg934ff590-166e-4be7-bc31-87292abf81f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 16:54:26,207] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg934ff590-166e-4be7-bc31-87292abf81f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 16:54:26,207] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 16:54:26,207] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 16:54:26,207] [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
--------------------------------------------------------------------------------
[2023-03-16 16:54:26,207] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11076/tc_result.tsv
[2023-03-16 16:54:26,207] [INFO] ===== Taxonomy check completed =====
[2023-03-16 16:54:26,207] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 16:54:26,208] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg934ff590-166e-4be7-bc31-87292abf81f0/dqc_reference/checkm_data
[2023-03-16 16:54:26,211] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 16:54:26,214] [INFO] Task started: CheckM
[2023-03-16 16:54:26,214] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11076/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11076/checkm_input OceanDNA-b11076/checkm_result
[2023-03-16 16:54:59,249] [INFO] Task succeeded: CheckM
[2023-03-16 16:54:59,249] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 16:54:59,251] [INFO] ===== Completeness check finished =====
[2023-03-16 16:54:59,251] [INFO] ===== Start GTDB Search =====
[2023-03-16 16:54:59,251] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11076/markers.fasta)
[2023-03-16 16:54:59,252] [INFO] Task started: Blastn
[2023-03-16 16:54:59,252] [INFO] Running command: blastn -query OceanDNA-b11076/markers.fasta -db /var/lib/cwl/stg934ff590-166e-4be7-bc31-87292abf81f0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11076/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:54:59,992] [INFO] Task succeeded: Blastn
[2023-03-16 16:54:59,993] [INFO] Selected 8 target genomes.
[2023-03-16 16:54:59,993] [INFO] Target genome list was writen to OceanDNA-b11076/target_genomes_gtdb.txt
[2023-03-16 16:55:00,001] [INFO] Task started: fastANI
[2023-03-16 16:55:00,001] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b1d7aef-8c67-4663-8568-ed6231c124c9/OceanDNA-b11076.fa --refList OceanDNA-b11076/target_genomes_gtdb.txt --output OceanDNA-b11076/fastani_result_gtdb.tsv --threads 1
[2023-03-16 16:55:02,873] [INFO] Task succeeded: fastANI
[2023-03-16 16:55:02,878] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 16:55:02,878] [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_017856205.1	s__UBA7446 sp017856205	95.0126	368	495	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002478685.1	s__UBA7446 sp002478685	89.8336	366	495	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	99.74	99.74	0.91	0.91	3	-
GCA_009937085.1	s__UBA7446 sp009937085	80.9592	305	495	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003331305.1	s__UBA7446 sp002470745	80.7524	310	495	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	99.36	99.14	0.86	0.83	3	-
GCA_009886265.1	s__UBA7446 sp009886265	78.1311	155	495	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862705.1	s__UBA7446 sp002862705	77.8894	167	495	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	99.06	98.27	0.87	0.83	14	-
GCA_002862645.1	s__UBA7446 sp002862645	77.7183	146	495	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	95.15	95.15	0.79	0.79	2	-
--------------------------------------------------------------------------------
[2023-03-16 16:55:02,878] [INFO] GTDB search result was written to OceanDNA-b11076/result_gtdb.tsv
[2023-03-16 16:55:02,878] [INFO] ===== GTDB Search completed =====
[2023-03-16 16:55:02,879] [INFO] DFAST_QC result json was written to OceanDNA-b11076/dqc_result.json
[2023-03-16 16:55:02,879] [INFO] DFAST_QC completed!
[2023-03-16 16:55:02,879] [INFO] Total running time: 0h1m20s