[2023-03-15 17:46:31,610] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:46:31,614] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:46:31,614] [INFO] DQC Reference Directory: /var/lib/cwl/stgbdaada03-56e4-41aa-8be8-c70ef5ee7be7/dqc_reference
[2023-03-15 17:46:32,791] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:46:32,792] [INFO] Task started: Prodigal
[2023-03-15 17:46:32,792] [INFO] Running command: cat /var/lib/cwl/stgc63c53c5-175a-4d0e-a5db-59e0df6857fa/OceanDNA-a2182.fa | prodigal -d OceanDNA-a2182/cds.fna -a OceanDNA-a2182/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:46:36,697] [INFO] Task succeeded: Prodigal
[2023-03-15 17:46:36,697] [INFO] Task started: HMMsearch
[2023-03-15 17:46:36,697] [INFO] Running command: hmmsearch --tblout OceanDNA-a2182/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbdaada03-56e4-41aa-8be8-c70ef5ee7be7/dqc_reference/reference_markers.hmm OceanDNA-a2182/protein.faa > /dev/null
[2023-03-15 17:46:36,849] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:46:36,849] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc63c53c5-175a-4d0e-a5db-59e0df6857fa/OceanDNA-a2182.fa]
[2023-03-15 17:46:36,868] [INFO] Query marker FASTA was written to OceanDNA-a2182/markers.fasta
[2023-03-15 17:46:36,869] [INFO] Task started: Blastn
[2023-03-15 17:46:36,869] [INFO] Running command: blastn -query OceanDNA-a2182/markers.fasta -db /var/lib/cwl/stgbdaada03-56e4-41aa-8be8-c70ef5ee7be7/dqc_reference/reference_markers.fasta -out OceanDNA-a2182/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:46:37,300] [INFO] Task succeeded: Blastn
[2023-03-15 17:46:37,305] [INFO] Selected 5 target genomes.
[2023-03-15 17:46:37,305] [INFO] Target genome list was writen to OceanDNA-a2182/target_genomes.txt
[2023-03-15 17:46:37,309] [INFO] Task started: fastANI
[2023-03-15 17:46:37,309] [INFO] Running command: fastANI --query /var/lib/cwl/stgc63c53c5-175a-4d0e-a5db-59e0df6857fa/OceanDNA-a2182.fa --refList OceanDNA-a2182/target_genomes.txt --output OceanDNA-a2182/fastani_result.tsv --threads 1
[2023-03-15 17:46:40,765] [INFO] Task succeeded: fastANI
[2023-03-15 17:46:40,765] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbdaada03-56e4-41aa-8be8-c70ef5ee7be7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:46:40,765] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbdaada03-56e4-41aa-8be8-c70ef5ee7be7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:46:40,766] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:46:40,766] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 17:46:40,766] [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 17:46:40,767] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2182/tc_result.tsv
[2023-03-15 17:46:40,767] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:46:40,767] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:46:40,767] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbdaada03-56e4-41aa-8be8-c70ef5ee7be7/dqc_reference/checkm_data
[2023-03-15 17:46:40,770] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:46:40,775] [INFO] Task started: CheckM
[2023-03-15 17:46:40,775] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2182/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2182/checkm_input OceanDNA-a2182/checkm_result
[2023-03-15 17:46:58,013] [INFO] Task succeeded: CheckM
[2023-03-15 17:46:58,014] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.40%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 17:46:58,038] [INFO] ===== Completeness check finished =====
[2023-03-15 17:46:58,038] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:46:58,039] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2182/markers.fasta)
[2023-03-15 17:46:58,040] [INFO] Task started: Blastn
[2023-03-15 17:46:58,040] [INFO] Running command: blastn -query OceanDNA-a2182/markers.fasta -db /var/lib/cwl/stgbdaada03-56e4-41aa-8be8-c70ef5ee7be7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2182/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:46:58,577] [INFO] Task succeeded: Blastn
[2023-03-15 17:46:58,580] [INFO] Selected 10 target genomes.
[2023-03-15 17:46:58,580] [INFO] Target genome list was writen to OceanDNA-a2182/target_genomes_gtdb.txt
[2023-03-15 17:46:58,594] [INFO] Task started: fastANI
[2023-03-15 17:46:58,595] [INFO] Running command: fastANI --query /var/lib/cwl/stgc63c53c5-175a-4d0e-a5db-59e0df6857fa/OceanDNA-a2182.fa --refList OceanDNA-a2182/target_genomes_gtdb.txt --output OceanDNA-a2182/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:47:01,443] [INFO] Task succeeded: fastANI
[2023-03-15 17:47:01,446] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:47:01,446] [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_011526375.1	s__MGIIa-L1 sp011526375	81.1781	147	189	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013329295.1	s__MGIIa-L1 sp9596u	78.3985	65	189	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.51	99.26	0.88	0.84	4	-
--------------------------------------------------------------------------------
[2023-03-15 17:47:01,448] [INFO] GTDB search result was written to OceanDNA-a2182/result_gtdb.tsv
[2023-03-15 17:47:01,448] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:47:01,449] [INFO] DFAST_QC result json was written to OceanDNA-a2182/dqc_result.json
[2023-03-15 17:47:01,449] [INFO] DFAST_QC completed!
[2023-03-15 17:47:01,449] [INFO] Total running time: 0h0m30s