[2023-03-18 23:40:00,417] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:40:00,417] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:40:00,417] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0180bbb-9c7b-432a-88ae-ae4d9acf2556/dqc_reference
[2023-03-18 23:40:01,520] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:40:01,521] [INFO] Task started: Prodigal
[2023-03-18 23:40:01,521] [INFO] Running command: cat /var/lib/cwl/stg120bf179-3501-4caa-850c-338d5bf9e835/OceanDNA-b22204.fa | prodigal -d OceanDNA-b22204/cds.fna -a OceanDNA-b22204/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:40:13,190] [INFO] Task succeeded: Prodigal
[2023-03-18 23:40:13,191] [INFO] Task started: HMMsearch
[2023-03-18 23:40:13,191] [INFO] Running command: hmmsearch --tblout OceanDNA-b22204/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0180bbb-9c7b-432a-88ae-ae4d9acf2556/dqc_reference/reference_markers.hmm OceanDNA-b22204/protein.faa > /dev/null
[2023-03-18 23:40:13,364] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:40:13,365] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg120bf179-3501-4caa-850c-338d5bf9e835/OceanDNA-b22204.fa]
[2023-03-18 23:40:13,384] [INFO] Query marker FASTA was written to OceanDNA-b22204/markers.fasta
[2023-03-18 23:40:13,384] [INFO] Task started: Blastn
[2023-03-18 23:40:13,384] [INFO] Running command: blastn -query OceanDNA-b22204/markers.fasta -db /var/lib/cwl/stgc0180bbb-9c7b-432a-88ae-ae4d9acf2556/dqc_reference/reference_markers.fasta -out OceanDNA-b22204/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:40:13,900] [INFO] Task succeeded: Blastn
[2023-03-18 23:40:13,901] [INFO] Selected 15 target genomes.
[2023-03-18 23:40:13,901] [INFO] Target genome list was writen to OceanDNA-b22204/target_genomes.txt
[2023-03-18 23:40:13,910] [INFO] Task started: fastANI
[2023-03-18 23:40:13,910] [INFO] Running command: fastANI --query /var/lib/cwl/stg120bf179-3501-4caa-850c-338d5bf9e835/OceanDNA-b22204.fa --refList OceanDNA-b22204/target_genomes.txt --output OceanDNA-b22204/fastani_result.tsv --threads 1
[2023-03-18 23:40:26,321] [INFO] Task succeeded: fastANI
[2023-03-18 23:40:26,322] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0180bbb-9c7b-432a-88ae-ae4d9acf2556/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:40:26,322] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0180bbb-9c7b-432a-88ae-ae4d9acf2556/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:40:26,322] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:40:26,322] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:40:26,322] [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 23:40:26,322] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22204/tc_result.tsv
[2023-03-18 23:40:26,322] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:40:26,322] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:40:26,322] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0180bbb-9c7b-432a-88ae-ae4d9acf2556/dqc_reference/checkm_data
[2023-03-18 23:40:26,325] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:40:26,330] [INFO] Task started: CheckM
[2023-03-18 23:40:26,330] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22204/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22204/checkm_input OceanDNA-b22204/checkm_result
[2023-03-18 23:40:58,258] [INFO] Task succeeded: CheckM
[2023-03-18 23:40:58,258] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 2.43%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:40:58,260] [INFO] ===== Completeness check finished =====
[2023-03-18 23:40:58,261] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:40:58,261] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22204/markers.fasta)
[2023-03-18 23:40:58,262] [INFO] Task started: Blastn
[2023-03-18 23:40:58,262] [INFO] Running command: blastn -query OceanDNA-b22204/markers.fasta -db /var/lib/cwl/stgc0180bbb-9c7b-432a-88ae-ae4d9acf2556/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22204/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:40:58,955] [INFO] Task succeeded: Blastn
[2023-03-18 23:40:58,956] [INFO] Selected 7 target genomes.
[2023-03-18 23:40:58,956] [INFO] Target genome list was writen to OceanDNA-b22204/target_genomes_gtdb.txt
[2023-03-18 23:40:58,960] [INFO] Task started: fastANI
[2023-03-18 23:40:58,960] [INFO] Running command: fastANI --query /var/lib/cwl/stg120bf179-3501-4caa-850c-338d5bf9e835/OceanDNA-b22204.fa --refList OceanDNA-b22204/target_genomes_gtdb.txt --output OceanDNA-b22204/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:41:02,827] [INFO] Task succeeded: fastANI
[2023-03-18 23:41:02,832] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:41:02,832] [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_002684755.1	s__UBA12014 sp002684755	98.0386	437	541	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002690755.1	s__UBA12014 sp002690755	87.692	476	541	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	99.96	99.96	0.92	0.92	2	-
GCA_002683215.1	s__UBA12014 sp002683215	87.4579	395	541	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009936695.1	s__UBA12014 sp009936695	86.8504	384	541	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002684855.1	s__UBA12014 sp002684855	83.5734	355	541	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167845.2	s__UBA12014 sp002167845	79.7533	270	541	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	99.48	99.48	0.92	0.92	2	-
GCA_002709295.1	s__GCA-002862325 sp002709295	78.3478	222	541	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002862325	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:41:02,832] [INFO] GTDB search result was written to OceanDNA-b22204/result_gtdb.tsv
[2023-03-18 23:41:02,833] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:41:02,833] [INFO] DFAST_QC result json was written to OceanDNA-b22204/dqc_result.json
[2023-03-18 23:41:02,833] [INFO] DFAST_QC completed!
[2023-03-18 23:41:02,833] [INFO] Total running time: 0h1m2s