[2023-03-16 08:25:40,165] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:25:40,168] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:25:40,168] [INFO] DQC Reference Directory: /var/lib/cwl/stg42a67180-7672-4389-9993-b9967194151c/dqc_reference
[2023-03-16 08:25:41,284] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:25:41,284] [INFO] Task started: Prodigal
[2023-03-16 08:25:41,285] [INFO] Running command: cat /var/lib/cwl/stgebb56949-599b-46a3-b4af-e58931469b98/OceanDNA-a4171.fa | prodigal -d OceanDNA-a4171/cds.fna -a OceanDNA-a4171/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:25:47,921] [INFO] Task succeeded: Prodigal
[2023-03-16 08:25:47,922] [INFO] Task started: HMMsearch
[2023-03-16 08:25:47,922] [INFO] Running command: hmmsearch --tblout OceanDNA-a4171/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg42a67180-7672-4389-9993-b9967194151c/dqc_reference/reference_markers.hmm OceanDNA-a4171/protein.faa > /dev/null
[2023-03-16 08:25:48,057] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:25:48,058] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgebb56949-599b-46a3-b4af-e58931469b98/OceanDNA-a4171.fa]
[2023-03-16 08:25:48,095] [INFO] Query marker FASTA was written to OceanDNA-a4171/markers.fasta
[2023-03-16 08:25:48,096] [INFO] Task started: Blastn
[2023-03-16 08:25:48,096] [INFO] Running command: blastn -query OceanDNA-a4171/markers.fasta -db /var/lib/cwl/stg42a67180-7672-4389-9993-b9967194151c/dqc_reference/reference_markers.fasta -out OceanDNA-a4171/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:25:48,566] [INFO] Task succeeded: Blastn
[2023-03-16 08:25:48,576] [INFO] Selected 3 target genomes.
[2023-03-16 08:25:48,576] [INFO] Target genome list was writen to OceanDNA-a4171/target_genomes.txt
[2023-03-16 08:25:48,578] [INFO] Task started: fastANI
[2023-03-16 08:25:48,578] [INFO] Running command: fastANI --query /var/lib/cwl/stgebb56949-599b-46a3-b4af-e58931469b98/OceanDNA-a4171.fa --refList OceanDNA-a4171/target_genomes.txt --output OceanDNA-a4171/fastani_result.tsv --threads 1
[2023-03-16 08:25:50,126] [INFO] Task succeeded: fastANI
[2023-03-16 08:25:50,127] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg42a67180-7672-4389-9993-b9967194151c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:25:50,127] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg42a67180-7672-4389-9993-b9967194151c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:25:50,127] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:25:50,127] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 08:25:50,127] [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 08:25:50,130] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4171/tc_result.tsv
[2023-03-16 08:25:50,135] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:25:50,135] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:25:50,136] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg42a67180-7672-4389-9993-b9967194151c/dqc_reference/checkm_data
[2023-03-16 08:25:50,138] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:25:50,144] [INFO] Task started: CheckM
[2023-03-16 08:25:50,144] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4171/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4171/checkm_input OceanDNA-a4171/checkm_result
[2023-03-16 08:26:13,246] [INFO] Task succeeded: CheckM
[2023-03-16 08:26:13,246] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.19%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:26:13,259] [INFO] ===== Completeness check finished =====
[2023-03-16 08:26:13,260] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:26:13,260] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4171/markers.fasta)
[2023-03-16 08:26:13,262] [INFO] Task started: Blastn
[2023-03-16 08:26:13,262] [INFO] Running command: blastn -query OceanDNA-a4171/markers.fasta -db /var/lib/cwl/stg42a67180-7672-4389-9993-b9967194151c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4171/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:26:14,115] [INFO] Task succeeded: Blastn
[2023-03-16 08:26:14,123] [INFO] Selected 12 target genomes.
[2023-03-16 08:26:14,123] [INFO] Target genome list was writen to OceanDNA-a4171/target_genomes_gtdb.txt
[2023-03-16 08:26:14,234] [INFO] Task started: fastANI
[2023-03-16 08:26:14,234] [INFO] Running command: fastANI --query /var/lib/cwl/stgebb56949-599b-46a3-b4af-e58931469b98/OceanDNA-a4171.fa --refList OceanDNA-a4171/target_genomes_gtdb.txt --output OceanDNA-a4171/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:26:17,097] [INFO] Task succeeded: fastANI
[2023-03-16 08:26:17,103] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 08:26:17,103] [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_003602515.1	s__MGIIb-O3 sp003602515	93.799	316	370	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	99.42	99.42	0.80	0.80	2	-
GCA_002723045.1	s__MGIIb-O3 sp002723045	88.3098	205	370	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002457155.1	s__MGIIb-O3 sp002457155	83.4983	280	370	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002683155.1	s__MGIIb-O3 sp002683155	81.466	152	370	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239955.1	s__MGIIb-O3 sp014239955	79.2954	198	370	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902601345.1	s__MGIIb-O3 sp902601345	77.8192	73	370	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001629255.1	s__MGIIb-O3 sp001629255	77.5202	88	370	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	98.42	97.36	0.80	0.70	6	-
GCA_902573015.1	s__MGIIb-O3 sp902573015	77.2863	83	370	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002506755.1	s__MGIIb-O3 sp002506755	76.7389	54	370	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	99.90	99.90	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-16 08:26:17,108] [INFO] GTDB search result was written to OceanDNA-a4171/result_gtdb.tsv
[2023-03-16 08:26:17,117] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:26:17,121] [INFO] DFAST_QC result json was written to OceanDNA-a4171/dqc_result.json
[2023-03-16 08:26:17,121] [INFO] DFAST_QC completed!
[2023-03-16 08:26:17,121] [INFO] Total running time: 0h0m37s