[2023-03-14 10:55:58,916] [INFO] DFAST_QC pipeline started.
[2023-03-14 10:55:58,946] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 10:55:58,946] [INFO] DQC Reference Directory: /var/lib/cwl/stg35320859-4ccf-425f-ab54-39a9842d67f7/dqc_reference
[2023-03-14 10:56:00,753] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 10:56:00,753] [INFO] Task started: Prodigal
[2023-03-14 10:56:00,753] [INFO] Running command: cat /var/lib/cwl/stg9a499c3e-d9a1-49b9-827e-3b2de466dff1/OceanDNA-b358.fa | prodigal -d OceanDNA-b358/cds.fna -a OceanDNA-b358/protein.faa -g 11 -q > /dev/null
[2023-03-14 10:56:11,117] [INFO] Task succeeded: Prodigal
[2023-03-14 10:56:11,117] [INFO] Task started: HMMsearch
[2023-03-14 10:56:11,117] [INFO] Running command: hmmsearch --tblout OceanDNA-b358/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35320859-4ccf-425f-ab54-39a9842d67f7/dqc_reference/reference_markers.hmm OceanDNA-b358/protein.faa > /dev/null
[2023-03-14 10:56:11,297] [INFO] Task succeeded: HMMsearch
[2023-03-14 10:56:11,297] [INFO] Found 6/6 markers.
[2023-03-14 10:56:11,313] [INFO] Query marker FASTA was written to OceanDNA-b358/markers.fasta
[2023-03-14 10:56:11,313] [INFO] Task started: Blastn
[2023-03-14 10:56:11,313] [INFO] Running command: blastn -query OceanDNA-b358/markers.fasta -db /var/lib/cwl/stg35320859-4ccf-425f-ab54-39a9842d67f7/dqc_reference/reference_markers.fasta -out OceanDNA-b358/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:11,834] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:11,835] [INFO] Selected 13 target genomes.
[2023-03-14 10:56:11,835] [INFO] Target genome list was writen to OceanDNA-b358/target_genomes.txt
[2023-03-14 10:56:11,844] [INFO] Task started: fastANI
[2023-03-14 10:56:11,844] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a499c3e-d9a1-49b9-827e-3b2de466dff1/OceanDNA-b358.fa --refList OceanDNA-b358/target_genomes.txt --output OceanDNA-b358/fastani_result.tsv --threads 1
[2023-03-14 10:56:17,755] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:17,755] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35320859-4ccf-425f-ab54-39a9842d67f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 10:56:17,755] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35320859-4ccf-425f-ab54-39a9842d67f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 10:56:17,755] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 10:56:17,755] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 10:56:17,755] [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 10:56:17,756] [INFO] DFAST Taxonomy check result was written to OceanDNA-b358/tc_result.tsv
[2023-03-14 10:56:17,756] [INFO] ===== Taxonomy check completed =====
[2023-03-14 10:56:17,756] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 10:56:17,756] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35320859-4ccf-425f-ab54-39a9842d67f7/dqc_reference/checkm_data
[2023-03-14 10:56:17,759] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 10:56:17,762] [INFO] Task started: CheckM
[2023-03-14 10:56:17,762] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b358/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b358/checkm_input OceanDNA-b358/checkm_result
[2023-03-14 10:56:47,733] [INFO] Task succeeded: CheckM
[2023-03-14 10:56:47,733] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 10:56:47,735] [INFO] ===== Completeness check finished =====
[2023-03-14 10:56:47,735] [INFO] ===== Start GTDB Search =====
[2023-03-14 10:56:47,736] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b358/markers.fasta)
[2023-03-14 10:56:47,736] [INFO] Task started: Blastn
[2023-03-14 10:56:47,736] [INFO] Running command: blastn -query OceanDNA-b358/markers.fasta -db /var/lib/cwl/stg35320859-4ccf-425f-ab54-39a9842d67f7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b358/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:48,413] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:48,414] [INFO] Selected 14 target genomes.
[2023-03-14 10:56:48,414] [INFO] Target genome list was writen to OceanDNA-b358/target_genomes_gtdb.txt
[2023-03-14 10:56:48,428] [INFO] Task started: fastANI
[2023-03-14 10:56:48,428] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a499c3e-d9a1-49b9-827e-3b2de466dff1/OceanDNA-b358.fa --refList OceanDNA-b358/target_genomes_gtdb.txt --output OceanDNA-b358/fastani_result_gtdb.tsv --threads 1
[2023-03-14 10:56:52,712] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:52,716] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 10:56:52,716] [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_009703975.1	s__BACL27 sp009703975	88.7585	310	511	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	97.18	96.93	0.73	0.69	4	-
GCA_003569125.1	s__BACL27 sp003569125	82.5759	368	511	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014190295.1	s__BACL27 sp014190295	79.8677	246	511	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463105.1	s__BACL27 sp016463105	79.5154	213	511	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016462185.1	s__BACL27 sp016462185	77.8398	138	511	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	98.92	98.92	0.88	0.88	2	-
GCA_009927565.1	s__BACL27 sp009927565	77.2107	74	511	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 10:56:52,717] [INFO] GTDB search result was written to OceanDNA-b358/result_gtdb.tsv
[2023-03-14 10:56:52,717] [INFO] ===== GTDB Search completed =====
[2023-03-14 10:56:52,717] [INFO] DFAST_QC result json was written to OceanDNA-b358/dqc_result.json
[2023-03-14 10:56:52,718] [INFO] DFAST_QC completed!
[2023-03-14 10:56:52,718] [INFO] Total running time: 0h0m54s