[2023-03-18 01:08:39,234] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:08:39,234] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:08:39,234] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d283dec-f877-4f5f-a73a-833927aa88bb/dqc_reference
[2023-03-18 01:08:40,369] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:08:40,370] [INFO] Task started: Prodigal
[2023-03-18 01:08:40,370] [INFO] Running command: cat /var/lib/cwl/stg80ec6f18-6200-4de8-902f-0e0d70b109d4/OceanDNA-b13579.fa | prodigal -d OceanDNA-b13579/cds.fna -a OceanDNA-b13579/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:08:59,978] [INFO] Task succeeded: Prodigal
[2023-03-18 01:08:59,978] [INFO] Task started: HMMsearch
[2023-03-18 01:08:59,978] [INFO] Running command: hmmsearch --tblout OceanDNA-b13579/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d283dec-f877-4f5f-a73a-833927aa88bb/dqc_reference/reference_markers.hmm OceanDNA-b13579/protein.faa > /dev/null
[2023-03-18 01:09:00,214] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:09:00,215] [INFO] Found 6/6 markers.
[2023-03-18 01:09:00,250] [INFO] Query marker FASTA was written to OceanDNA-b13579/markers.fasta
[2023-03-18 01:09:00,251] [INFO] Task started: Blastn
[2023-03-18 01:09:00,251] [INFO] Running command: blastn -query OceanDNA-b13579/markers.fasta -db /var/lib/cwl/stg2d283dec-f877-4f5f-a73a-833927aa88bb/dqc_reference/reference_markers.fasta -out OceanDNA-b13579/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:09:00,783] [INFO] Task succeeded: Blastn
[2023-03-18 01:09:00,784] [INFO] Selected 21 target genomes.
[2023-03-18 01:09:00,784] [INFO] Target genome list was writen to OceanDNA-b13579/target_genomes.txt
[2023-03-18 01:09:00,797] [INFO] Task started: fastANI
[2023-03-18 01:09:00,797] [INFO] Running command: fastANI --query /var/lib/cwl/stg80ec6f18-6200-4de8-902f-0e0d70b109d4/OceanDNA-b13579.fa --refList OceanDNA-b13579/target_genomes.txt --output OceanDNA-b13579/fastani_result.tsv --threads 1
[2023-03-18 01:09:14,144] [INFO] Task succeeded: fastANI
[2023-03-18 01:09:14,145] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d283dec-f877-4f5f-a73a-833927aa88bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:09:14,145] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d283dec-f877-4f5f-a73a-833927aa88bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:09:14,148] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:09:14,148] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:09:14,148] [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
Litorilinea aerophila	strain=ATCC BAA-2444	GCA_006569185.2	1204385	1204385	type	True	76.0011	121	805	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:09:14,148] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13579/tc_result.tsv
[2023-03-18 01:09:14,148] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:09:14,148] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:09:14,148] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d283dec-f877-4f5f-a73a-833927aa88bb/dqc_reference/checkm_data
[2023-03-18 01:09:14,149] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:09:14,155] [INFO] Task started: CheckM
[2023-03-18 01:09:14,155] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13579/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13579/checkm_input OceanDNA-b13579/checkm_result
[2023-03-18 01:10:04,745] [INFO] Task succeeded: CheckM
[2023-03-18 01:10:04,746] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.04%
Contamintation: 4.55%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 01:10:04,750] [INFO] ===== Completeness check finished =====
[2023-03-18 01:10:04,750] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:10:04,750] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13579/markers.fasta)
[2023-03-18 01:10:04,751] [INFO] Task started: Blastn
[2023-03-18 01:10:04,751] [INFO] Running command: blastn -query OceanDNA-b13579/markers.fasta -db /var/lib/cwl/stg2d283dec-f877-4f5f-a73a-833927aa88bb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13579/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:10:05,510] [INFO] Task succeeded: Blastn
[2023-03-18 01:10:05,511] [INFO] Selected 24 target genomes.
[2023-03-18 01:10:05,511] [INFO] Target genome list was writen to OceanDNA-b13579/target_genomes_gtdb.txt
[2023-03-18 01:10:05,527] [INFO] Task started: fastANI
[2023-03-18 01:10:05,527] [INFO] Running command: fastANI --query /var/lib/cwl/stg80ec6f18-6200-4de8-902f-0e0d70b109d4/OceanDNA-b13579.fa --refList OceanDNA-b13579/target_genomes_gtdb.txt --output OceanDNA-b13579/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:10:24,167] [INFO] Task succeeded: fastANI
[2023-03-18 01:10:24,174] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:10:24,174] [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_016199425.1	s__JACQGT01 sp016199425	81.1026	399	805	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__JACQGT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018003515.1	s__JAGNDO01 sp018003515	76.3875	156	805	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__JAGNDO01	95.0	99.87	99.85	0.92	0.92	4	-
GCA_015494005.1	s__S144-5 sp015494005	76.3012	90	805	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__S144-5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124945.1	s__RI-153 sp016124945	76.0479	108	805	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__RI-153	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006569185.1	s__Litorilinea aerophila	76.0015	121	805	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Litorilinea	95.0	99.85	99.85	0.99	0.99	2	-
GCA_016710365.1	s__Caldilinea sp016710365	75.7874	65	805	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Caldilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523365.1	s__Bin5 sp011523365	75.6868	65	805	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Bin5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002238445.1	s__Bin5 sp002238445	75.6606	58	805	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Bin5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840225.1	s__Bin5 sp009840225	75.4211	64	805	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Bin5	95.0	97.63	95.35	0.89	0.84	3	-
GCA_003577005.1	s__CFX5 sp003577005	75.3433	72	805	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__CFX5	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:10:24,174] [INFO] GTDB search result was written to OceanDNA-b13579/result_gtdb.tsv
[2023-03-18 01:10:24,174] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:10:24,175] [INFO] DFAST_QC result json was written to OceanDNA-b13579/dqc_result.json
[2023-03-18 01:10:24,175] [INFO] DFAST_QC completed!
[2023-03-18 01:10:24,175] [INFO] Total running time: 0h1m45s