[2023-03-18 23:27:53,695] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:27:53,696] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:27:53,696] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c0277f4-492d-40ff-872f-9546b06262c3/dqc_reference
[2023-03-18 23:27:55,546] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:27:55,546] [INFO] Task started: Prodigal
[2023-03-18 23:27:55,546] [INFO] Running command: cat /var/lib/cwl/stg260ed14b-36d8-42e4-903f-db0a62d61935/OceanDNA-b22138.fa | prodigal -d OceanDNA-b22138/cds.fna -a OceanDNA-b22138/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:28:04,394] [INFO] Task succeeded: Prodigal
[2023-03-18 23:28:04,394] [INFO] Task started: HMMsearch
[2023-03-18 23:28:04,394] [INFO] Running command: hmmsearch --tblout OceanDNA-b22138/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c0277f4-492d-40ff-872f-9546b06262c3/dqc_reference/reference_markers.hmm OceanDNA-b22138/protein.faa > /dev/null
[2023-03-18 23:28:04,607] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:28:04,608] [INFO] Found 6/6 markers.
[2023-03-18 23:28:04,624] [INFO] Query marker FASTA was written to OceanDNA-b22138/markers.fasta
[2023-03-18 23:28:04,624] [INFO] Task started: Blastn
[2023-03-18 23:28:04,624] [INFO] Running command: blastn -query OceanDNA-b22138/markers.fasta -db /var/lib/cwl/stg0c0277f4-492d-40ff-872f-9546b06262c3/dqc_reference/reference_markers.fasta -out OceanDNA-b22138/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:28:05,230] [INFO] Task succeeded: Blastn
[2023-03-18 23:28:05,231] [INFO] Selected 11 target genomes.
[2023-03-18 23:28:05,231] [INFO] Target genome list was writen to OceanDNA-b22138/target_genomes.txt
[2023-03-18 23:28:05,249] [INFO] Task started: fastANI
[2023-03-18 23:28:05,249] [INFO] Running command: fastANI --query /var/lib/cwl/stg260ed14b-36d8-42e4-903f-db0a62d61935/OceanDNA-b22138.fa --refList OceanDNA-b22138/target_genomes.txt --output OceanDNA-b22138/fastani_result.tsv --threads 1
[2023-03-18 23:28:09,252] [INFO] Task succeeded: fastANI
[2023-03-18 23:28:09,253] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c0277f4-492d-40ff-872f-9546b06262c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:28:09,253] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c0277f4-492d-40ff-872f-9546b06262c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:28:09,253] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:28:09,253] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:28:09,253] [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 23:28:09,253] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22138/tc_result.tsv
[2023-03-18 23:28:09,254] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:28:09,254] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:28:09,254] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c0277f4-492d-40ff-872f-9546b06262c3/dqc_reference/checkm_data
[2023-03-18 23:28:09,257] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:28:09,277] [INFO] Task started: CheckM
[2023-03-18 23:28:09,277] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22138/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22138/checkm_input OceanDNA-b22138/checkm_result
[2023-03-18 23:28:35,795] [INFO] Task succeeded: CheckM
[2023-03-18 23:28:35,795] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:28:35,797] [INFO] ===== Completeness check finished =====
[2023-03-18 23:28:35,798] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:28:35,798] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22138/markers.fasta)
[2023-03-18 23:28:35,798] [INFO] Task started: Blastn
[2023-03-18 23:28:35,798] [INFO] Running command: blastn -query OceanDNA-b22138/markers.fasta -db /var/lib/cwl/stg0c0277f4-492d-40ff-872f-9546b06262c3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22138/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:28:36,699] [INFO] Task succeeded: Blastn
[2023-03-18 23:28:36,700] [INFO] Selected 14 target genomes.
[2023-03-18 23:28:36,700] [INFO] Target genome list was writen to OceanDNA-b22138/target_genomes_gtdb.txt
[2023-03-18 23:28:36,715] [INFO] Task started: fastANI
[2023-03-18 23:28:36,715] [INFO] Running command: fastANI --query /var/lib/cwl/stg260ed14b-36d8-42e4-903f-db0a62d61935/OceanDNA-b22138.fa --refList OceanDNA-b22138/target_genomes_gtdb.txt --output OceanDNA-b22138/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:28:42,173] [INFO] Task succeeded: fastANI
[2023-03-18 23:28:42,177] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:28:42,177] [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_014238125.1	s__GCA-002718515 sp014238125	80.0373	199	445	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018656645.1	s__GCA-002718515 sp018656645	78.9719	169	445	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014238785.1	s__GCA-002718515 sp014238785	78.296	59	445	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014381305.1	s__GCA-002718515 sp014381305	78.178	149	445	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:28:42,177] [INFO] GTDB search result was written to OceanDNA-b22138/result_gtdb.tsv
[2023-03-18 23:28:42,177] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:28:42,178] [INFO] DFAST_QC result json was written to OceanDNA-b22138/dqc_result.json
[2023-03-18 23:28:42,178] [INFO] DFAST_QC completed!
[2023-03-18 23:28:42,178] [INFO] Total running time: 0h0m48s