[2023-03-16 01:21:12,689] [INFO] DFAST_QC pipeline started.
[2023-03-16 01:21:12,700] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 01:21:12,700] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b55a66f-82c4-41f6-bc79-2e9470f49969/dqc_reference
[2023-03-16 01:21:13,791] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 01:21:13,791] [INFO] Task started: Prodigal
[2023-03-16 01:21:13,792] [INFO] Running command: cat /var/lib/cwl/stg1b74ab86-0231-4d72-839d-8ecacf8f07bb/OceanDNA-b18433.fa | prodigal -d OceanDNA-b18433/cds.fna -a OceanDNA-b18433/protein.faa -g 11 -q > /dev/null
[2023-03-16 01:21:24,136] [INFO] Task succeeded: Prodigal
[2023-03-16 01:21:24,137] [INFO] Task started: HMMsearch
[2023-03-16 01:21:24,137] [INFO] Running command: hmmsearch --tblout OceanDNA-b18433/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b55a66f-82c4-41f6-bc79-2e9470f49969/dqc_reference/reference_markers.hmm OceanDNA-b18433/protein.faa > /dev/null
[2023-03-16 01:21:24,283] [INFO] Task succeeded: HMMsearch
[2023-03-16 01:21:24,284] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1b74ab86-0231-4d72-839d-8ecacf8f07bb/OceanDNA-b18433.fa]
[2023-03-16 01:21:24,360] [INFO] Query marker FASTA was written to OceanDNA-b18433/markers.fasta
[2023-03-16 01:21:24,360] [INFO] Task started: Blastn
[2023-03-16 01:21:24,360] [INFO] Running command: blastn -query OceanDNA-b18433/markers.fasta -db /var/lib/cwl/stg5b55a66f-82c4-41f6-bc79-2e9470f49969/dqc_reference/reference_markers.fasta -out OceanDNA-b18433/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:21:24,851] [INFO] Task succeeded: Blastn
[2023-03-16 01:21:24,875] [INFO] Selected 9 target genomes.
[2023-03-16 01:21:24,875] [INFO] Target genome list was writen to OceanDNA-b18433/target_genomes.txt
[2023-03-16 01:21:24,913] [INFO] Task started: fastANI
[2023-03-16 01:21:24,913] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b74ab86-0231-4d72-839d-8ecacf8f07bb/OceanDNA-b18433.fa --refList OceanDNA-b18433/target_genomes.txt --output OceanDNA-b18433/fastani_result.tsv --threads 1
[2023-03-16 01:21:29,720] [INFO] Task succeeded: fastANI
[2023-03-16 01:21:29,721] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b55a66f-82c4-41f6-bc79-2e9470f49969/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 01:21:29,721] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b55a66f-82c4-41f6-bc79-2e9470f49969/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 01:21:29,721] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 01:21:29,721] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 01:21:29,721] [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 01:21:29,735] [INFO] DFAST Taxonomy check result was written to OceanDNA-b18433/tc_result.tsv
[2023-03-16 01:21:29,760] [INFO] ===== Taxonomy check completed =====
[2023-03-16 01:21:29,760] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 01:21:29,760] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b55a66f-82c4-41f6-bc79-2e9470f49969/dqc_reference/checkm_data
[2023-03-16 01:21:29,763] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 01:21:29,773] [INFO] Task started: CheckM
[2023-03-16 01:21:29,773] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b18433/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b18433/checkm_input OceanDNA-b18433/checkm_result
[2023-03-16 01:22:00,219] [INFO] Task succeeded: CheckM
[2023-03-16 01:22:00,220] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 01:22:00,324] [INFO] ===== Completeness check finished =====
[2023-03-16 01:22:00,324] [INFO] ===== Start GTDB Search =====
[2023-03-16 01:22:00,324] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b18433/markers.fasta)
[2023-03-16 01:22:00,325] [INFO] Task started: Blastn
[2023-03-16 01:22:00,325] [INFO] Running command: blastn -query OceanDNA-b18433/markers.fasta -db /var/lib/cwl/stg5b55a66f-82c4-41f6-bc79-2e9470f49969/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b18433/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:22:00,984] [INFO] Task succeeded: Blastn
[2023-03-16 01:22:01,024] [INFO] Selected 11 target genomes.
[2023-03-16 01:22:01,025] [INFO] Target genome list was writen to OceanDNA-b18433/target_genomes_gtdb.txt
[2023-03-16 01:22:01,253] [INFO] Task started: fastANI
[2023-03-16 01:22:01,253] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b74ab86-0231-4d72-839d-8ecacf8f07bb/OceanDNA-b18433.fa --refList OceanDNA-b18433/target_genomes_gtdb.txt --output OceanDNA-b18433/fastani_result_gtdb.tsv --threads 1
[2023-03-16 01:22:06,558] [INFO] Task succeeded: fastANI
[2023-03-16 01:22:06,562] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 01:22:06,562] [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_012964825.1	s__UBA2125 sp002311275	99.6167	563	588	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__S15-B10;g__UBA2125	95.0	99.57	99.39	0.92	0.84	10	conclusive
GCA_004124465.1	s__UBA2125 sp004124465	86.9155	307	588	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__S15-B10;g__UBA2125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002329125.1	s__UBA2125 sp002329125	85.1695	386	588	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__S15-B10;g__UBA2125	95.0	97.65	95.42	0.79	0.68	5	-
GCA_002448795.1	s__S15-B10 sp002448795	76.2872	62	588	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__S15-B10;g__S15-B10	95.0	99.97	99.96	0.93	0.86	3	-
GCA_001626655.1	s__S15-B10 sp001626655	75.7089	50	588	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__S15-B10;g__S15-B10	95.0	98.13	97.75	0.76	0.70	4	-
--------------------------------------------------------------------------------
[2023-03-16 01:22:06,566] [INFO] GTDB search result was written to OceanDNA-b18433/result_gtdb.tsv
[2023-03-16 01:22:06,575] [INFO] ===== GTDB Search completed =====
[2023-03-16 01:22:06,583] [INFO] DFAST_QC result json was written to OceanDNA-b18433/dqc_result.json
[2023-03-16 01:22:06,583] [INFO] DFAST_QC completed!
[2023-03-16 01:22:06,583] [INFO] Total running time: 0h0m54s