[2023-03-16 12:37:44,840] [INFO] DFAST_QC pipeline started.
[2023-03-16 12:37:44,840] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 12:37:44,840] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e4cf911-67ad-42b1-8e80-3b4c1ce90539/dqc_reference
[2023-03-16 12:37:45,956] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 12:37:45,956] [INFO] Task started: Prodigal
[2023-03-16 12:37:45,956] [INFO] Running command: cat /var/lib/cwl/stg4f4261dd-84bb-4783-b992-9aa79abc40ed/OceanDNA-b20509.fa | prodigal -d OceanDNA-b20509/cds.fna -a OceanDNA-b20509/protein.faa -g 11 -q > /dev/null
[2023-03-16 12:37:51,245] [INFO] Task succeeded: Prodigal
[2023-03-16 12:37:51,245] [INFO] Task started: HMMsearch
[2023-03-16 12:37:51,245] [INFO] Running command: hmmsearch --tblout OceanDNA-b20509/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e4cf911-67ad-42b1-8e80-3b4c1ce90539/dqc_reference/reference_markers.hmm OceanDNA-b20509/protein.faa > /dev/null
[2023-03-16 12:37:51,455] [INFO] Task succeeded: HMMsearch
[2023-03-16 12:37:51,455] [INFO] Found 6/6 markers.
[2023-03-16 12:37:51,466] [INFO] Query marker FASTA was written to OceanDNA-b20509/markers.fasta
[2023-03-16 12:37:51,466] [INFO] Task started: Blastn
[2023-03-16 12:37:51,466] [INFO] Running command: blastn -query OceanDNA-b20509/markers.fasta -db /var/lib/cwl/stg8e4cf911-67ad-42b1-8e80-3b4c1ce90539/dqc_reference/reference_markers.fasta -out OceanDNA-b20509/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 12:37:52,530] [INFO] Task succeeded: Blastn
[2023-03-16 12:37:52,531] [INFO] Selected 21 target genomes.
[2023-03-16 12:37:52,531] [INFO] Target genome list was writen to OceanDNA-b20509/target_genomes.txt
[2023-03-16 12:37:52,542] [INFO] Task started: fastANI
[2023-03-16 12:37:52,542] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f4261dd-84bb-4783-b992-9aa79abc40ed/OceanDNA-b20509.fa --refList OceanDNA-b20509/target_genomes.txt --output OceanDNA-b20509/fastani_result.tsv --threads 1
[2023-03-16 12:38:01,241] [INFO] Task succeeded: fastANI
[2023-03-16 12:38:01,241] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e4cf911-67ad-42b1-8e80-3b4c1ce90539/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 12:38:01,242] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e4cf911-67ad-42b1-8e80-3b4c1ce90539/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 12:38:01,242] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 12:38:01,242] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 12:38:01,242] [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 12:38:01,242] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20509/tc_result.tsv
[2023-03-16 12:38:01,242] [INFO] ===== Taxonomy check completed =====
[2023-03-16 12:38:01,242] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 12:38:01,242] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e4cf911-67ad-42b1-8e80-3b4c1ce90539/dqc_reference/checkm_data
[2023-03-16 12:38:01,441] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 12:38:01,497] [INFO] Task started: CheckM
[2023-03-16 12:38:01,497] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20509/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20509/checkm_input OceanDNA-b20509/checkm_result
[2023-03-16 12:38:29,531] [INFO] Task succeeded: CheckM
[2023-03-16 12:38:29,532] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.81%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 12:38:29,533] [INFO] ===== Completeness check finished =====
[2023-03-16 12:38:29,533] [INFO] ===== Start GTDB Search =====
[2023-03-16 12:38:29,533] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20509/markers.fasta)
[2023-03-16 12:38:29,534] [INFO] Task started: Blastn
[2023-03-16 12:38:29,534] [INFO] Running command: blastn -query OceanDNA-b20509/markers.fasta -db /var/lib/cwl/stg8e4cf911-67ad-42b1-8e80-3b4c1ce90539/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20509/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 12:38:31,646] [INFO] Task succeeded: Blastn
[2023-03-16 12:38:31,647] [INFO] Selected 30 target genomes.
[2023-03-16 12:38:31,647] [INFO] Target genome list was writen to OceanDNA-b20509/target_genomes_gtdb.txt
[2023-03-16 12:38:32,225] [INFO] Task started: fastANI
[2023-03-16 12:38:32,225] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f4261dd-84bb-4783-b992-9aa79abc40ed/OceanDNA-b20509.fa --refList OceanDNA-b20509/target_genomes_gtdb.txt --output OceanDNA-b20509/fastani_result_gtdb.tsv --threads 1
[2023-03-16 12:38:44,817] [INFO] Task succeeded: fastANI
[2023-03-16 12:38:44,821] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 12:38:44,821] [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_002717625.1	s__GCA-2717625 sp002717625	76.6723	84	339	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-2717625	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002705605.1	s__GCA-002707645 sp002705605	76.6454	54	339	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002707645	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002718585.1	s__GCA-002718585 sp002718585	76.346	64	339	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002718585	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002693365.1	s__GCA-002707645 sp002693365	76.2823	52	339	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002707645	95.0	98.01	98.01	0.73	0.73	2	-
GCA_002704685.1	s__GCA-002707645 sp002704685	75.9953	63	339	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002707645	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 12:38:44,821] [INFO] GTDB search result was written to OceanDNA-b20509/result_gtdb.tsv
[2023-03-16 12:38:44,821] [INFO] ===== GTDB Search completed =====
[2023-03-16 12:38:44,822] [INFO] DFAST_QC result json was written to OceanDNA-b20509/dqc_result.json
[2023-03-16 12:38:44,822] [INFO] DFAST_QC completed!
[2023-03-16 12:38:44,822] [INFO] Total running time: 0h0m60s