[2023-03-16 08:47:19,706] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:47:19,707] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:47:19,707] [INFO] DQC Reference Directory: /var/lib/cwl/stg8041061e-f82b-4356-8fbf-7b5e0f250b05/dqc_reference
[2023-03-16 08:47:20,858] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:47:20,858] [INFO] Task started: Prodigal
[2023-03-16 08:47:20,858] [INFO] Running command: cat /var/lib/cwl/stg3ad2607e-8006-44ec-bf5b-444e4cf09130/OceanDNA-a2891.fa | prodigal -d OceanDNA-a2891/cds.fna -a OceanDNA-a2891/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:47:27,152] [INFO] Task succeeded: Prodigal
[2023-03-16 08:47:27,152] [INFO] Task started: HMMsearch
[2023-03-16 08:47:27,152] [INFO] Running command: hmmsearch --tblout OceanDNA-a2891/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8041061e-f82b-4356-8fbf-7b5e0f250b05/dqc_reference/reference_markers.hmm OceanDNA-a2891/protein.faa > /dev/null
[2023-03-16 08:47:27,339] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:47:27,339] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg3ad2607e-8006-44ec-bf5b-444e4cf09130/OceanDNA-a2891.fa]
[2023-03-16 08:47:27,350] [INFO] Query marker FASTA was written to OceanDNA-a2891/markers.fasta
[2023-03-16 08:47:27,351] [INFO] Task started: Blastn
[2023-03-16 08:47:27,351] [INFO] Running command: blastn -query OceanDNA-a2891/markers.fasta -db /var/lib/cwl/stg8041061e-f82b-4356-8fbf-7b5e0f250b05/dqc_reference/reference_markers.fasta -out OceanDNA-a2891/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:47:28,035] [INFO] Task succeeded: Blastn
[2023-03-16 08:47:28,035] [INFO] Selected 5 target genomes.
[2023-03-16 08:47:28,036] [INFO] Target genome list was writen to OceanDNA-a2891/target_genomes.txt
[2023-03-16 08:47:28,038] [INFO] Task started: fastANI
[2023-03-16 08:47:28,038] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ad2607e-8006-44ec-bf5b-444e4cf09130/OceanDNA-a2891.fa --refList OceanDNA-a2891/target_genomes.txt --output OceanDNA-a2891/fastani_result.tsv --threads 1
[2023-03-16 08:47:31,297] [INFO] Task succeeded: fastANI
[2023-03-16 08:47:31,298] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8041061e-f82b-4356-8fbf-7b5e0f250b05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:47:31,298] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8041061e-f82b-4356-8fbf-7b5e0f250b05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:47:31,298] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:47:31,298] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 08:47:31,298] [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 08:47:31,298] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2891/tc_result.tsv
[2023-03-16 08:47:31,298] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:47:31,298] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:47:31,298] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8041061e-f82b-4356-8fbf-7b5e0f250b05/dqc_reference/checkm_data
[2023-03-16 08:47:31,347] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:47:31,351] [INFO] Task started: CheckM
[2023-03-16 08:47:31,351] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2891/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2891/checkm_input OceanDNA-a2891/checkm_result
[2023-03-16 08:48:04,719] [INFO] Task succeeded: CheckM
[2023-03-16 08:48:04,719] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.80%
Contamintation: 1.42%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-16 08:48:04,721] [INFO] ===== Completeness check finished =====
[2023-03-16 08:48:04,722] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:48:04,722] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2891/markers.fasta)
[2023-03-16 08:48:04,723] [INFO] Task started: Blastn
[2023-03-16 08:48:04,723] [INFO] Running command: blastn -query OceanDNA-a2891/markers.fasta -db /var/lib/cwl/stg8041061e-f82b-4356-8fbf-7b5e0f250b05/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2891/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:48:05,548] [INFO] Task succeeded: Blastn
[2023-03-16 08:48:05,549] [INFO] Selected 5 target genomes.
[2023-03-16 08:48:05,549] [INFO] Target genome list was writen to OceanDNA-a2891/target_genomes_gtdb.txt
[2023-03-16 08:48:05,556] [INFO] Task started: fastANI
[2023-03-16 08:48:05,556] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ad2607e-8006-44ec-bf5b-444e4cf09130/OceanDNA-a2891.fa --refList OceanDNA-a2891/target_genomes_gtdb.txt --output OceanDNA-a2891/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:48:07,075] [INFO] Task succeeded: fastANI
[2023-03-16 08:48:07,079] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 08:48:07,079] [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_002722135.1	s__MGIIa-L3 sp002722135	85.5025	196	212	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L3	95.0	99.74	99.72	0.92	0.89	4	-
GCA_002694585.1	s__MGIIa-L3 sp002694585	85.2816	180	212	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002731395.1	s__MGIIa-L3 sp002731395	83.0251	154	212	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L3	95.0	99.15	99.02	0.81	0.76	3	-
GCA_002496845.1	s__MGIIa-L3 sp002496845	81.5734	169	212	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L3	95.0	99.68	99.68	0.95	0.95	2	-
GCA_003602635.1	s__MGIIa-L3 sp003602635	81.5019	163	212	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L3	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 08:48:07,080] [INFO] GTDB search result was written to OceanDNA-a2891/result_gtdb.tsv
[2023-03-16 08:48:07,080] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:48:07,080] [INFO] DFAST_QC result json was written to OceanDNA-a2891/dqc_result.json
[2023-03-16 08:48:07,080] [INFO] DFAST_QC completed!
[2023-03-16 08:48:07,080] [INFO] Total running time: 0h0m47s