[2023-03-16 18:40:20,530] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:40:20,530] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:40:20,530] [INFO] DQC Reference Directory: /var/lib/cwl/stg1fe69819-b009-483f-94e7-ab576d2df2ae/dqc_reference
[2023-03-16 18:40:22,807] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:40:22,807] [INFO] Task started: Prodigal
[2023-03-16 18:40:22,807] [INFO] Running command: cat /var/lib/cwl/stg729fc572-d939-48ab-b66f-cb132b1e96ce/OceanDNA-b45210.fa | prodigal -d OceanDNA-b45210/cds.fna -a OceanDNA-b45210/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:41:00,356] [INFO] Task succeeded: Prodigal
[2023-03-16 18:41:00,356] [INFO] Task started: HMMsearch
[2023-03-16 18:41:00,356] [INFO] Running command: hmmsearch --tblout OceanDNA-b45210/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1fe69819-b009-483f-94e7-ab576d2df2ae/dqc_reference/reference_markers.hmm OceanDNA-b45210/protein.faa > /dev/null
[2023-03-16 18:41:00,602] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:41:00,603] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg729fc572-d939-48ab-b66f-cb132b1e96ce/OceanDNA-b45210.fa]
[2023-03-16 18:41:00,636] [INFO] Query marker FASTA was written to OceanDNA-b45210/markers.fasta
[2023-03-16 18:41:00,637] [INFO] Task started: Blastn
[2023-03-16 18:41:00,637] [INFO] Running command: blastn -query OceanDNA-b45210/markers.fasta -db /var/lib/cwl/stg1fe69819-b009-483f-94e7-ab576d2df2ae/dqc_reference/reference_markers.fasta -out OceanDNA-b45210/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:41:01,508] [INFO] Task succeeded: Blastn
[2023-03-16 18:41:01,509] [INFO] Selected 16 target genomes.
[2023-03-16 18:41:01,509] [INFO] Target genome list was writen to OceanDNA-b45210/target_genomes.txt
[2023-03-16 18:41:01,528] [INFO] Task started: fastANI
[2023-03-16 18:41:01,528] [INFO] Running command: fastANI --query /var/lib/cwl/stg729fc572-d939-48ab-b66f-cb132b1e96ce/OceanDNA-b45210.fa --refList OceanDNA-b45210/target_genomes.txt --output OceanDNA-b45210/fastani_result.tsv --threads 1
[2023-03-16 18:41:10,615] [INFO] Task succeeded: fastANI
[2023-03-16 18:41:10,616] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1fe69819-b009-483f-94e7-ab576d2df2ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:41:10,616] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1fe69819-b009-483f-94e7-ab576d2df2ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:41:10,616] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:41:10,616] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 18:41:10,616] [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
--------------------------------------------------------------------------------
[2023-03-16 18:41:10,616] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45210/tc_result.tsv
[2023-03-16 18:41:10,616] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:41:10,616] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:41:10,617] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1fe69819-b009-483f-94e7-ab576d2df2ae/dqc_reference/checkm_data
[2023-03-16 18:41:10,620] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:41:10,714] [INFO] Task started: CheckM
[2023-03-16 18:41:10,714] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45210/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45210/checkm_input OceanDNA-b45210/checkm_result
[2023-03-16 18:42:26,449] [INFO] Task succeeded: CheckM
[2023-03-16 18:42:26,449] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:42:26,453] [INFO] ===== Completeness check finished =====
[2023-03-16 18:42:26,453] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:42:26,453] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45210/markers.fasta)
[2023-03-16 18:42:26,455] [INFO] Task started: Blastn
[2023-03-16 18:42:26,455] [INFO] Running command: blastn -query OceanDNA-b45210/markers.fasta -db /var/lib/cwl/stg1fe69819-b009-483f-94e7-ab576d2df2ae/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45210/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:42:28,161] [INFO] Task succeeded: Blastn
[2023-03-16 18:42:28,162] [INFO] Selected 21 target genomes.
[2023-03-16 18:42:28,162] [INFO] Target genome list was writen to OceanDNA-b45210/target_genomes_gtdb.txt
[2023-03-16 18:42:28,438] [INFO] Task started: fastANI
[2023-03-16 18:42:28,438] [INFO] Running command: fastANI --query /var/lib/cwl/stg729fc572-d939-48ab-b66f-cb132b1e96ce/OceanDNA-b45210.fa --refList OceanDNA-b45210/target_genomes_gtdb.txt --output OceanDNA-b45210/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:42:46,652] [INFO] Task succeeded: fastANI
[2023-03-16 18:42:46,654] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 18:42:46,654] [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_018645005.1	s__JAHJRI01 sp018645005	98.4671	768	1629	d__Bacteria;p__SAR324;c__SAR324;o__XYD2-FULL-50-16;f__XYD2-FULL-50-16;g__JAHJRI01	95.0	99.66	99.41	0.88	0.82	6	conclusive
GCA_018830885.1	s__JAHJRI01 sp018830885	77.3357	353	1629	d__Bacteria;p__SAR324;c__SAR324;o__XYD2-FULL-50-16;f__XYD2-FULL-50-16;g__JAHJRI01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 18:42:46,654] [INFO] GTDB search result was written to OceanDNA-b45210/result_gtdb.tsv
[2023-03-16 18:42:46,654] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:42:46,655] [INFO] DFAST_QC result json was written to OceanDNA-b45210/dqc_result.json
[2023-03-16 18:42:46,655] [INFO] DFAST_QC completed!
[2023-03-16 18:42:46,655] [INFO] Total running time: 0h2m26s