[2023-03-14 13:38:12,540] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:38:12,540] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:38:12,540] [INFO] DQC Reference Directory: /var/lib/cwl/stg06640ab4-d3ee-4d83-8d68-4b50c373ef46/dqc_reference
[2023-03-14 13:38:13,701] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:38:13,702] [INFO] Task started: Prodigal
[2023-03-14 13:38:13,702] [INFO] Running command: cat /var/lib/cwl/stgf522a020-4509-4602-80aa-57f4282f1c76/OceanDNA-b22262.fa | prodigal -d OceanDNA-b22262/cds.fna -a OceanDNA-b22262/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:38:24,227] [INFO] Task succeeded: Prodigal
[2023-03-14 13:38:24,227] [INFO] Task started: HMMsearch
[2023-03-14 13:38:24,227] [INFO] Running command: hmmsearch --tblout OceanDNA-b22262/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06640ab4-d3ee-4d83-8d68-4b50c373ef46/dqc_reference/reference_markers.hmm OceanDNA-b22262/protein.faa > /dev/null
[2023-03-14 13:38:24,399] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:38:24,399] [INFO] Found 6/6 markers.
[2023-03-14 13:38:24,414] [INFO] Query marker FASTA was written to OceanDNA-b22262/markers.fasta
[2023-03-14 13:38:24,415] [INFO] Task started: Blastn
[2023-03-14 13:38:24,415] [INFO] Running command: blastn -query OceanDNA-b22262/markers.fasta -db /var/lib/cwl/stg06640ab4-d3ee-4d83-8d68-4b50c373ef46/dqc_reference/reference_markers.fasta -out OceanDNA-b22262/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:38:24,937] [INFO] Task succeeded: Blastn
[2023-03-14 13:38:24,938] [INFO] Selected 29 target genomes.
[2023-03-14 13:38:24,938] [INFO] Target genome list was writen to OceanDNA-b22262/target_genomes.txt
[2023-03-14 13:38:24,952] [INFO] Task started: fastANI
[2023-03-14 13:38:24,952] [INFO] Running command: fastANI --query /var/lib/cwl/stgf522a020-4509-4602-80aa-57f4282f1c76/OceanDNA-b22262.fa --refList OceanDNA-b22262/target_genomes.txt --output OceanDNA-b22262/fastani_result.tsv --threads 1
[2023-03-14 13:38:44,362] [INFO] Task succeeded: fastANI
[2023-03-14 13:38:44,362] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06640ab4-d3ee-4d83-8d68-4b50c373ef46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:38:44,363] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06640ab4-d3ee-4d83-8d68-4b50c373ef46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:38:44,363] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:38:44,363] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:38:44,363] [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
--------------------------------------------------------------------------------
[2023-03-14 13:38:44,363] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22262/tc_result.tsv
[2023-03-14 13:38:44,363] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:38:44,363] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:38:44,363] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06640ab4-d3ee-4d83-8d68-4b50c373ef46/dqc_reference/checkm_data
[2023-03-14 13:38:44,366] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:38:44,369] [INFO] Task started: CheckM
[2023-03-14 13:38:44,369] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22262/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22262/checkm_input OceanDNA-b22262/checkm_result
[2023-03-14 13:39:30,619] [INFO] Task succeeded: CheckM
[2023-03-14 13:39:30,619] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.69%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:39:30,622] [INFO] ===== Completeness check finished =====
[2023-03-14 13:39:30,622] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:39:30,623] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22262/markers.fasta)
[2023-03-14 13:39:30,624] [INFO] Task started: Blastn
[2023-03-14 13:39:30,624] [INFO] Running command: blastn -query OceanDNA-b22262/markers.fasta -db /var/lib/cwl/stg06640ab4-d3ee-4d83-8d68-4b50c373ef46/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22262/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:39:32,905] [INFO] Task succeeded: Blastn
[2023-03-14 13:39:32,906] [INFO] Selected 19 target genomes.
[2023-03-14 13:39:32,906] [INFO] Target genome list was writen to OceanDNA-b22262/target_genomes_gtdb.txt
[2023-03-14 13:39:32,924] [INFO] Task started: fastANI
[2023-03-14 13:39:32,924] [INFO] Running command: fastANI --query /var/lib/cwl/stgf522a020-4509-4602-80aa-57f4282f1c76/OceanDNA-b22262.fa --refList OceanDNA-b22262/target_genomes_gtdb.txt --output OceanDNA-b22262/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:39:45,091] [INFO] Task succeeded: fastANI
[2023-03-14 13:39:45,097] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 13:39:45,097] [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_002591705.1	s__UBA854 sp002591705	99.2027	456	524	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA854	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002295885.1	s__UBA854 sp002295885	86.4835	478	524	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA854	95.0	99.78	99.78	0.94	0.94	2	-
GCA_002364485.1	s__UBA854 sp002364485	79.4536	320	524	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA854	95.0	99.87	99.87	0.97	0.97	2	-
GCA_002722935.1	s__SP202 sp002722935	77.2456	85	524	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__SP202	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014238205.1	s__SP202 sp014238205	76.8639	90	524	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__SP202	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017859745.1	s__VGXO01 sp017859745	76.5344	60	524	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__VGXO01	95.0	99.59	99.54	0.95	0.94	4	-
GCA_002709295.1	s__GCA-002862325 sp002709295	76.5003	62	524	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002862325	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364555.1	s__UBA1668 sp002364555	76.4609	52	524	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA1668	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862305.1	s__UBA8087 sp002862305	76.3302	71	524	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA8087	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 13:39:45,098] [INFO] GTDB search result was written to OceanDNA-b22262/result_gtdb.tsv
[2023-03-14 13:39:45,098] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:39:45,099] [INFO] DFAST_QC result json was written to OceanDNA-b22262/dqc_result.json
[2023-03-14 13:39:45,099] [INFO] DFAST_QC completed!
[2023-03-14 13:39:45,099] [INFO] Total running time: 0h1m33s