[2023-03-18 21:56:21,185] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:56:21,185] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:56:21,185] [INFO] DQC Reference Directory: /var/lib/cwl/stg239e2abb-27ca-48ce-985b-32597ec121af/dqc_reference
[2023-03-18 21:56:22,276] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:56:22,277] [INFO] Task started: Prodigal
[2023-03-18 21:56:22,277] [INFO] Running command: cat /var/lib/cwl/stgc9f188e0-a552-420e-988a-7cac20f41030/OceanDNA-a4477.fa | prodigal -d OceanDNA-a4477/cds.fna -a OceanDNA-a4477/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:56:29,325] [INFO] Task succeeded: Prodigal
[2023-03-18 21:56:29,325] [INFO] Task started: HMMsearch
[2023-03-18 21:56:29,325] [INFO] Running command: hmmsearch --tblout OceanDNA-a4477/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg239e2abb-27ca-48ce-985b-32597ec121af/dqc_reference/reference_markers.hmm OceanDNA-a4477/protein.faa > /dev/null
[2023-03-18 21:56:29,483] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:56:29,484] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc9f188e0-a552-420e-988a-7cac20f41030/OceanDNA-a4477.fa]
[2023-03-18 21:56:29,497] [INFO] Query marker FASTA was written to OceanDNA-a4477/markers.fasta
[2023-03-18 21:56:30,109] [INFO] Task started: Blastn
[2023-03-18 21:56:30,109] [INFO] Running command: blastn -query OceanDNA-a4477/markers.fasta -db /var/lib/cwl/stg239e2abb-27ca-48ce-985b-32597ec121af/dqc_reference/reference_markers.fasta -out OceanDNA-a4477/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:56:30,594] [INFO] Task succeeded: Blastn
[2023-03-18 21:56:30,599] [INFO] Selected 5 target genomes.
[2023-03-18 21:56:30,599] [INFO] Target genome list was writen to OceanDNA-a4477/target_genomes.txt
[2023-03-18 21:56:30,605] [INFO] Task started: fastANI
[2023-03-18 21:56:30,605] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9f188e0-a552-420e-988a-7cac20f41030/OceanDNA-a4477.fa --refList OceanDNA-a4477/target_genomes.txt --output OceanDNA-a4477/fastani_result.tsv --threads 1
[2023-03-18 21:56:34,028] [INFO] Task succeeded: fastANI
[2023-03-18 21:56:34,028] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg239e2abb-27ca-48ce-985b-32597ec121af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:56:34,028] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg239e2abb-27ca-48ce-985b-32597ec121af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:56:34,029] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:56:34,029] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 21:56:34,029] [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
--------------------------------------------------------------------------------
[2023-03-18 21:56:34,036] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4477/tc_result.tsv
[2023-03-18 21:56:34,038] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:56:34,038] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:56:34,038] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg239e2abb-27ca-48ce-985b-32597ec121af/dqc_reference/checkm_data
[2023-03-18 21:56:34,041] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:56:34,043] [INFO] Task started: CheckM
[2023-03-18 21:56:34,043] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4477/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4477/checkm_input OceanDNA-a4477/checkm_result
[2023-03-18 21:56:58,614] [INFO] Task succeeded: CheckM
[2023-03-18 21:56:58,614] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.07%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:56:58,653] [INFO] ===== Completeness check finished =====
[2023-03-18 21:56:58,653] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:56:58,653] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4477/markers.fasta)
[2023-03-18 21:56:58,654] [INFO] Task started: Blastn
[2023-03-18 21:56:58,655] [INFO] Running command: blastn -query OceanDNA-a4477/markers.fasta -db /var/lib/cwl/stg239e2abb-27ca-48ce-985b-32597ec121af/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4477/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:56:59,234] [INFO] Task succeeded: Blastn
[2023-03-18 21:56:59,246] [INFO] Selected 8 target genomes.
[2023-03-18 21:56:59,246] [INFO] Target genome list was writen to OceanDNA-a4477/target_genomes_gtdb.txt
[2023-03-18 21:56:59,252] [INFO] Task started: fastANI
[2023-03-18 21:56:59,252] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9f188e0-a552-420e-988a-7cac20f41030/OceanDNA-a4477.fa --refList OceanDNA-a4477/target_genomes_gtdb.txt --output OceanDNA-a4477/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:57:01,240] [INFO] Task succeeded: fastANI
[2023-03-18 21:57:01,243] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 21:57:01,243] [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_002496725.1	s__MGIIb-O5 sp002496725	99.8273	360	415	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	99.85	99.85	0.91	0.91	2	conclusive
GCA_002506825.1	s__MGIIb-O5 sp002506825	78.6476	179	415	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	98.02	97.97	0.86	0.84	3	-
GCA_002499865.1	s__MGIIb-O5 sp002499865	78.3264	152	415	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	99.65	99.57	0.89	0.88	3	-
--------------------------------------------------------------------------------
[2023-03-18 21:57:01,246] [INFO] GTDB search result was written to OceanDNA-a4477/result_gtdb.tsv
[2023-03-18 21:57:01,258] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:57:01,259] [INFO] DFAST_QC result json was written to OceanDNA-a4477/dqc_result.json
[2023-03-18 21:57:01,259] [INFO] DFAST_QC completed!
[2023-03-18 21:57:01,259] [INFO] Total running time: 0h0m40s