[2023-03-15 07:52:40,210] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:52:40,210] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:52:40,210] [INFO] DQC Reference Directory: /var/lib/cwl/stg93c8fb40-6fd2-4485-aba9-ae502a8dd122/dqc_reference
[2023-03-15 07:52:41,440] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:52:41,441] [INFO] Task started: Prodigal
[2023-03-15 07:52:41,441] [INFO] Running command: cat /var/lib/cwl/stga744f70b-674e-4706-93af-48a8c5777faa/OceanDNA-b20512.fa | prodigal -d OceanDNA-b20512/cds.fna -a OceanDNA-b20512/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:52:44,068] [INFO] Task succeeded: Prodigal
[2023-03-15 07:52:44,068] [INFO] Task started: HMMsearch
[2023-03-15 07:52:44,068] [INFO] Running command: hmmsearch --tblout OceanDNA-b20512/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93c8fb40-6fd2-4485-aba9-ae502a8dd122/dqc_reference/reference_markers.hmm OceanDNA-b20512/protein.faa > /dev/null
[2023-03-15 07:52:44,278] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:52:44,278] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga744f70b-674e-4706-93af-48a8c5777faa/OceanDNA-b20512.fa]
[2023-03-15 07:52:44,287] [INFO] Query marker FASTA was written to OceanDNA-b20512/markers.fasta
[2023-03-15 07:52:44,290] [INFO] Task started: Blastn
[2023-03-15 07:52:44,290] [INFO] Running command: blastn -query OceanDNA-b20512/markers.fasta -db /var/lib/cwl/stg93c8fb40-6fd2-4485-aba9-ae502a8dd122/dqc_reference/reference_markers.fasta -out OceanDNA-b20512/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:52:44,947] [INFO] Task succeeded: Blastn
[2023-03-15 07:52:44,948] [INFO] Selected 14 target genomes.
[2023-03-15 07:52:44,948] [INFO] Target genome list was writen to OceanDNA-b20512/target_genomes.txt
[2023-03-15 07:52:44,957] [INFO] Task started: fastANI
[2023-03-15 07:52:44,957] [INFO] Running command: fastANI --query /var/lib/cwl/stga744f70b-674e-4706-93af-48a8c5777faa/OceanDNA-b20512.fa --refList OceanDNA-b20512/target_genomes.txt --output OceanDNA-b20512/fastani_result.tsv --threads 1
[2023-03-15 07:52:52,323] [INFO] Task succeeded: fastANI
[2023-03-15 07:52:52,324] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93c8fb40-6fd2-4485-aba9-ae502a8dd122/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:52:52,324] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93c8fb40-6fd2-4485-aba9-ae502a8dd122/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:52:52,324] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:52:52,324] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 07:52:52,324] [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
--------------------------------------------------------------------------------
[2023-03-15 07:52:52,324] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20512/tc_result.tsv
[2023-03-15 07:52:52,324] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:52:52,325] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:52:52,325] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93c8fb40-6fd2-4485-aba9-ae502a8dd122/dqc_reference/checkm_data
[2023-03-15 07:52:52,327] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:52:52,330] [INFO] Task started: CheckM
[2023-03-15 07:52:52,330] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20512/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20512/checkm_input OceanDNA-b20512/checkm_result
[2023-03-15 07:53:05,931] [INFO] Task succeeded: CheckM
[2023-03-15 07:53:05,932] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.05%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:53:05,933] [INFO] ===== Completeness check finished =====
[2023-03-15 07:53:05,933] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:53:05,933] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20512/markers.fasta)
[2023-03-15 07:53:05,934] [INFO] Task started: Blastn
[2023-03-15 07:53:05,934] [INFO] Running command: blastn -query OceanDNA-b20512/markers.fasta -db /var/lib/cwl/stg93c8fb40-6fd2-4485-aba9-ae502a8dd122/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20512/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:53:06,657] [INFO] Task succeeded: Blastn
[2023-03-15 07:53:06,658] [INFO] Selected 19 target genomes.
[2023-03-15 07:53:06,658] [INFO] Target genome list was writen to OceanDNA-b20512/target_genomes_gtdb.txt
[2023-03-15 07:53:06,713] [INFO] Task started: fastANI
[2023-03-15 07:53:06,714] [INFO] Running command: fastANI --query /var/lib/cwl/stga744f70b-674e-4706-93af-48a8c5777faa/OceanDNA-b20512.fa --refList OceanDNA-b20512/target_genomes_gtdb.txt --output OceanDNA-b20512/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:53:12,409] [INFO] Task succeeded: fastANI
[2023-03-15 07:53:12,412] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:53:12,413] [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	86.0422	99	106	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_002707645.1	s__GCA-002707645 sp002707645	80.771	69	106	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	80.2991	75	106	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	79.9645	76	106	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	-
--------------------------------------------------------------------------------
[2023-03-15 07:53:12,413] [INFO] GTDB search result was written to OceanDNA-b20512/result_gtdb.tsv
[2023-03-15 07:53:12,413] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:53:12,413] [INFO] DFAST_QC result json was written to OceanDNA-b20512/dqc_result.json
[2023-03-15 07:53:12,413] [INFO] DFAST_QC completed!
[2023-03-15 07:53:12,414] [INFO] Total running time: 0h0m32s