[2023-03-15 07:29:11,757] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:29:11,757] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:29:11,757] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9604fc2-c21f-4cee-9ffa-38e92c6dccc3/dqc_reference
[2023-03-15 07:29:13,590] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:29:13,590] [INFO] Task started: Prodigal
[2023-03-15 07:29:13,590] [INFO] Running command: cat /var/lib/cwl/stga6a5752f-3967-4e31-b5c9-ac88c7f5f881/OceanDNA-a4141.fa | prodigal -d OceanDNA-a4141/cds.fna -a OceanDNA-a4141/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:29:19,767] [INFO] Task succeeded: Prodigal
[2023-03-15 07:29:19,767] [INFO] Task started: HMMsearch
[2023-03-15 07:29:19,767] [INFO] Running command: hmmsearch --tblout OceanDNA-a4141/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9604fc2-c21f-4cee-9ffa-38e92c6dccc3/dqc_reference/reference_markers.hmm OceanDNA-a4141/protein.faa > /dev/null
[2023-03-15 07:29:19,902] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:29:19,903] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga6a5752f-3967-4e31-b5c9-ac88c7f5f881/OceanDNA-a4141.fa]
[2023-03-15 07:29:19,913] [INFO] Query marker FASTA was written to OceanDNA-a4141/markers.fasta
[2023-03-15 07:29:19,913] [INFO] Task started: Blastn
[2023-03-15 07:29:19,913] [INFO] Running command: blastn -query OceanDNA-a4141/markers.fasta -db /var/lib/cwl/stgf9604fc2-c21f-4cee-9ffa-38e92c6dccc3/dqc_reference/reference_markers.fasta -out OceanDNA-a4141/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:29:20,335] [INFO] Task succeeded: Blastn
[2023-03-15 07:29:20,336] [INFO] Selected 1 target genomes.
[2023-03-15 07:29:20,336] [INFO] Target genome list was writen to OceanDNA-a4141/target_genomes.txt
[2023-03-15 07:29:20,337] [INFO] Task started: fastANI
[2023-03-15 07:29:20,337] [INFO] Running command: fastANI --query /var/lib/cwl/stga6a5752f-3967-4e31-b5c9-ac88c7f5f881/OceanDNA-a4141.fa --refList OceanDNA-a4141/target_genomes.txt --output OceanDNA-a4141/fastani_result.tsv --threads 1
[2023-03-15 07:29:21,038] [INFO] Task succeeded: fastANI
[2023-03-15 07:29:21,038] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9604fc2-c21f-4cee-9ffa-38e92c6dccc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:29:21,039] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9604fc2-c21f-4cee-9ffa-38e92c6dccc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:29:21,039] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:29:21,039] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 07:29:21,039] [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 07:29:21,039] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4141/tc_result.tsv
[2023-03-15 07:29:21,039] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:29:21,039] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:29:21,039] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9604fc2-c21f-4cee-9ffa-38e92c6dccc3/dqc_reference/checkm_data
[2023-03-15 07:29:21,042] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:29:21,044] [INFO] Task started: CheckM
[2023-03-15 07:29:21,044] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4141/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4141/checkm_input OceanDNA-a4141/checkm_result
[2023-03-15 07:29:43,306] [INFO] Task succeeded: CheckM
[2023-03-15 07:29:43,307] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.78%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 07:29:43,309] [INFO] ===== Completeness check finished =====
[2023-03-15 07:29:43,309] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:29:43,309] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4141/markers.fasta)
[2023-03-15 07:29:43,310] [INFO] Task started: Blastn
[2023-03-15 07:29:43,310] [INFO] Running command: blastn -query OceanDNA-a4141/markers.fasta -db /var/lib/cwl/stgf9604fc2-c21f-4cee-9ffa-38e92c6dccc3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4141/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:29:43,707] [INFO] Task succeeded: Blastn
[2023-03-15 07:29:43,708] [INFO] Selected 7 target genomes.
[2023-03-15 07:29:43,708] [INFO] Target genome list was writen to OceanDNA-a4141/target_genomes_gtdb.txt
[2023-03-15 07:29:43,713] [INFO] Task started: fastANI
[2023-03-15 07:29:43,713] [INFO] Running command: fastANI --query /var/lib/cwl/stga6a5752f-3967-4e31-b5c9-ac88c7f5f881/OceanDNA-a4141.fa --refList OceanDNA-a4141/target_genomes_gtdb.txt --output OceanDNA-a4141/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:29:45,326] [INFO] Task succeeded: fastANI
[2023-03-15 07:29:45,332] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:29:45,332] [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_002457155.1	s__MGIIb-O3 sp002457155	82.519	239	327	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_003602515.1	s__MGIIb-O3 sp003602515	81.4656	252	327	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_001629235.1	s__MGIIb-O3 sp001629235	78.3989	93	327	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	97.45	95.03	0.80	0.68	7	-
GCA_902573015.1	s__MGIIb-O3 sp902573015	78.1788	84	327	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_001628485.1	s__MGIIb-O3 sp001628485	78.1596	111	327	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	98.15	97.12	0.88	0.79	10	-
GCA_902625325.1	s__MGIIb-O3 sp902625325	77.7063	93	327	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_902573085.1	s__MGIIb-O3 sp902573085	77.5635	63	327	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:29:45,332] [INFO] GTDB search result was written to OceanDNA-a4141/result_gtdb.tsv
[2023-03-15 07:29:45,332] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:29:45,333] [INFO] DFAST_QC result json was written to OceanDNA-a4141/dqc_result.json
[2023-03-15 07:29:45,333] [INFO] DFAST_QC completed!
[2023-03-15 07:29:45,333] [INFO] Total running time: 0h0m34s