[2023-03-18 09:26:42,702] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:26:42,702] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:26:42,702] [INFO] DQC Reference Directory: /var/lib/cwl/stg26618cbb-cc26-4668-b475-ca8576bada84/dqc_reference
[2023-03-18 09:26:43,816] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:26:43,816] [INFO] Task started: Prodigal
[2023-03-18 09:26:43,816] [INFO] Running command: cat /var/lib/cwl/stg2ea231d8-d01e-4d5d-9129-514019f2f9ab/OceanDNA-b20501.fa | prodigal -d OceanDNA-b20501/cds.fna -a OceanDNA-b20501/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:26:47,990] [INFO] Task succeeded: Prodigal
[2023-03-18 09:26:47,990] [INFO] Task started: HMMsearch
[2023-03-18 09:26:47,990] [INFO] Running command: hmmsearch --tblout OceanDNA-b20501/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg26618cbb-cc26-4668-b475-ca8576bada84/dqc_reference/reference_markers.hmm OceanDNA-b20501/protein.faa > /dev/null
[2023-03-18 09:26:48,118] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:26:48,118] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2ea231d8-d01e-4d5d-9129-514019f2f9ab/OceanDNA-b20501.fa]
[2023-03-18 09:26:48,125] [INFO] Query marker FASTA was written to OceanDNA-b20501/markers.fasta
[2023-03-18 09:26:48,127] [INFO] Task started: Blastn
[2023-03-18 09:26:48,127] [INFO] Running command: blastn -query OceanDNA-b20501/markers.fasta -db /var/lib/cwl/stg26618cbb-cc26-4668-b475-ca8576bada84/dqc_reference/reference_markers.fasta -out OceanDNA-b20501/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:26:48,645] [INFO] Task succeeded: Blastn
[2023-03-18 09:26:48,645] [INFO] Selected 7 target genomes.
[2023-03-18 09:26:48,645] [INFO] Target genome list was writen to OceanDNA-b20501/target_genomes.txt
[2023-03-18 09:26:48,649] [INFO] Task started: fastANI
[2023-03-18 09:26:48,649] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ea231d8-d01e-4d5d-9129-514019f2f9ab/OceanDNA-b20501.fa --refList OceanDNA-b20501/target_genomes.txt --output OceanDNA-b20501/fastani_result.tsv --threads 1
[2023-03-18 09:26:51,101] [INFO] Task succeeded: fastANI
[2023-03-18 09:26:51,101] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg26618cbb-cc26-4668-b475-ca8576bada84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:26:51,101] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg26618cbb-cc26-4668-b475-ca8576bada84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:26:51,101] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:26:51,101] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:26:51,101] [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 09:26:51,102] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20501/tc_result.tsv
[2023-03-18 09:26:51,102] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:26:51,102] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:26:51,102] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg26618cbb-cc26-4668-b475-ca8576bada84/dqc_reference/checkm_data
[2023-03-18 09:26:51,157] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:26:51,160] [INFO] Task started: CheckM
[2023-03-18 09:26:51,160] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20501/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20501/checkm_input OceanDNA-b20501/checkm_result
[2023-03-18 09:27:08,850] [INFO] Task succeeded: CheckM
[2023-03-18 09:27:08,851] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:27:08,852] [INFO] ===== Completeness check finished =====
[2023-03-18 09:27:08,852] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:27:08,852] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20501/markers.fasta)
[2023-03-18 09:27:08,854] [INFO] Task started: Blastn
[2023-03-18 09:27:08,854] [INFO] Running command: blastn -query OceanDNA-b20501/markers.fasta -db /var/lib/cwl/stg26618cbb-cc26-4668-b475-ca8576bada84/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20501/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:27:09,620] [INFO] Task succeeded: Blastn
[2023-03-18 09:27:09,621] [INFO] Selected 20 target genomes.
[2023-03-18 09:27:09,621] [INFO] Target genome list was writen to OceanDNA-b20501/target_genomes_gtdb.txt
[2023-03-18 09:27:09,696] [INFO] Task started: fastANI
[2023-03-18 09:27:09,697] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ea231d8-d01e-4d5d-9129-514019f2f9ab/OceanDNA-b20501.fa --refList OceanDNA-b20501/target_genomes_gtdb.txt --output OceanDNA-b20501/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:27:15,306] [INFO] Task succeeded: fastANI
[2023-03-18 09:27:15,310] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:27:15,310] [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_002705605.1	s__GCA-002707645 sp002705605	76.504	62	284	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_002717625.1	s__GCA-2717625 sp002717625	76.3855	55	284	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_002707645.1	s__GCA-002707645 sp002707645	76.176	59	284	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_002704685.1	s__GCA-002707645 sp002704685	76.0185	59	284	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_002693365.1	s__GCA-002707645 sp002693365	75.7863	53	284	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	-
--------------------------------------------------------------------------------
[2023-03-18 09:27:15,310] [INFO] GTDB search result was written to OceanDNA-b20501/result_gtdb.tsv
[2023-03-18 09:27:15,310] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:27:15,311] [INFO] DFAST_QC result json was written to OceanDNA-b20501/dqc_result.json
[2023-03-18 09:27:15,311] [INFO] DFAST_QC completed!
[2023-03-18 09:27:15,311] [INFO] Total running time: 0h0m33s