[2023-03-14 14:20:16,053] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:20:16,053] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:20:16,053] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b5ba98d-a001-4667-a0dd-c469257b2cff/dqc_reference
[2023-03-14 14:20:18,694] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:20:18,694] [INFO] Task started: Prodigal
[2023-03-14 14:20:18,694] [INFO] Running command: cat /var/lib/cwl/stg6fed7cf6-bd37-4b27-8b62-7fbf5ff03f85/OceanDNA-b20689.fa | prodigal -d OceanDNA-b20689/cds.fna -a OceanDNA-b20689/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:20:27,367] [INFO] Task succeeded: Prodigal
[2023-03-14 14:20:27,367] [INFO] Task started: HMMsearch
[2023-03-14 14:20:27,367] [INFO] Running command: hmmsearch --tblout OceanDNA-b20689/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b5ba98d-a001-4667-a0dd-c469257b2cff/dqc_reference/reference_markers.hmm OceanDNA-b20689/protein.faa > /dev/null
[2023-03-14 14:20:27,608] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:20:27,609] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6fed7cf6-bd37-4b27-8b62-7fbf5ff03f85/OceanDNA-b20689.fa]
[2023-03-14 14:20:27,622] [INFO] Query marker FASTA was written to OceanDNA-b20689/markers.fasta
[2023-03-14 14:20:27,623] [INFO] Task started: Blastn
[2023-03-14 14:20:27,623] [INFO] Running command: blastn -query OceanDNA-b20689/markers.fasta -db /var/lib/cwl/stg8b5ba98d-a001-4667-a0dd-c469257b2cff/dqc_reference/reference_markers.fasta -out OceanDNA-b20689/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:20:28,153] [INFO] Task succeeded: Blastn
[2023-03-14 14:20:28,154] [INFO] Selected 16 target genomes.
[2023-03-14 14:20:28,155] [INFO] Target genome list was writen to OceanDNA-b20689/target_genomes.txt
[2023-03-14 14:20:28,194] [INFO] Task started: fastANI
[2023-03-14 14:20:28,194] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fed7cf6-bd37-4b27-8b62-7fbf5ff03f85/OceanDNA-b20689.fa --refList OceanDNA-b20689/target_genomes.txt --output OceanDNA-b20689/fastani_result.tsv --threads 1
[2023-03-14 14:20:35,211] [INFO] Task succeeded: fastANI
[2023-03-14 14:20:35,212] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b5ba98d-a001-4667-a0dd-c469257b2cff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:20:35,212] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b5ba98d-a001-4667-a0dd-c469257b2cff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:20:35,212] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:20:35,212] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 14:20:35,212] [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 14:20:35,213] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20689/tc_result.tsv
[2023-03-14 14:20:35,213] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:20:35,213] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:20:35,213] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b5ba98d-a001-4667-a0dd-c469257b2cff/dqc_reference/checkm_data
[2023-03-14 14:20:35,217] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:20:35,228] [INFO] Task started: CheckM
[2023-03-14 14:20:35,228] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20689/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20689/checkm_input OceanDNA-b20689/checkm_result
[2023-03-14 14:21:09,087] [INFO] Task succeeded: CheckM
[2023-03-14 14:21:09,087] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 14:21:09,090] [INFO] ===== Completeness check finished =====
[2023-03-14 14:21:09,090] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:21:09,090] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20689/markers.fasta)
[2023-03-14 14:21:09,091] [INFO] Task started: Blastn
[2023-03-14 14:21:09,091] [INFO] Running command: blastn -query OceanDNA-b20689/markers.fasta -db /var/lib/cwl/stg8b5ba98d-a001-4667-a0dd-c469257b2cff/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20689/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:21:09,926] [INFO] Task succeeded: Blastn
[2023-03-14 14:21:09,928] [INFO] Selected 19 target genomes.
[2023-03-14 14:21:09,928] [INFO] Target genome list was writen to OceanDNA-b20689/target_genomes_gtdb.txt
[2023-03-14 14:21:09,953] [INFO] Task started: fastANI
[2023-03-14 14:21:09,953] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fed7cf6-bd37-4b27-8b62-7fbf5ff03f85/OceanDNA-b20689.fa --refList OceanDNA-b20689/target_genomes_gtdb.txt --output OceanDNA-b20689/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:21:15,290] [INFO] Task succeeded: fastANI
[2023-03-14 14:21:15,293] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 14:21:15,293] [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_002171125.1	s__TMED161 sp002171125	99.1441	326	472	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED161;g__TMED161	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002731795.1	s__TMED161 sp002731795	91.3184	325	472	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED161;g__TMED161	95.0	98.59	98.59	0.77	0.77	2	-
GCA_002591605.1	s__TMED161 sp002591605	90.9814	142	472	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED161;g__TMED161	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002703645.1	s__TMED161 sp002703645	77.0221	125	472	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED161;g__TMED161	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 14:21:15,294] [INFO] GTDB search result was written to OceanDNA-b20689/result_gtdb.tsv
[2023-03-14 14:21:15,294] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:21:15,295] [INFO] DFAST_QC result json was written to OceanDNA-b20689/dqc_result.json
[2023-03-14 14:21:15,295] [INFO] DFAST_QC completed!
[2023-03-14 14:21:15,295] [INFO] Total running time: 0h0m59s