[2023-03-15 16:25:57,000] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:25:57,005] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:25:57,005] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a5be72c-572e-42fd-a2c3-5057eed5238b/dqc_reference
[2023-03-15 16:25:58,595] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:25:58,595] [INFO] Task started: Prodigal
[2023-03-15 16:25:58,595] [INFO] Running command: cat /var/lib/cwl/stg906ea8e2-6841-4f44-9138-7d285b028bbd/OceanDNA-a2152.fa | prodigal -d OceanDNA-a2152/cds.fna -a OceanDNA-a2152/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:26:04,388] [INFO] Task succeeded: Prodigal
[2023-03-15 16:26:04,388] [INFO] Task started: HMMsearch
[2023-03-15 16:26:04,388] [INFO] Running command: hmmsearch --tblout OceanDNA-a2152/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a5be72c-572e-42fd-a2c3-5057eed5238b/dqc_reference/reference_markers.hmm OceanDNA-a2152/protein.faa > /dev/null
[2023-03-15 16:26:04,544] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:26:04,545] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg906ea8e2-6841-4f44-9138-7d285b028bbd/OceanDNA-a2152.fa]
[2023-03-15 16:26:04,591] [INFO] Query marker FASTA was written to OceanDNA-a2152/markers.fasta
[2023-03-15 16:26:04,592] [INFO] Task started: Blastn
[2023-03-15 16:26:04,592] [INFO] Running command: blastn -query OceanDNA-a2152/markers.fasta -db /var/lib/cwl/stg6a5be72c-572e-42fd-a2c3-5057eed5238b/dqc_reference/reference_markers.fasta -out OceanDNA-a2152/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:26:05,675] [INFO] Task succeeded: Blastn
[2023-03-15 16:26:05,679] [INFO] Selected 5 target genomes.
[2023-03-15 16:26:05,679] [INFO] Target genome list was writen to OceanDNA-a2152/target_genomes.txt
[2023-03-15 16:26:05,682] [INFO] Task started: fastANI
[2023-03-15 16:26:05,682] [INFO] Running command: fastANI --query /var/lib/cwl/stg906ea8e2-6841-4f44-9138-7d285b028bbd/OceanDNA-a2152.fa --refList OceanDNA-a2152/target_genomes.txt --output OceanDNA-a2152/fastani_result.tsv --threads 1
[2023-03-15 16:26:07,106] [INFO] Task succeeded: fastANI
[2023-03-15 16:26:07,106] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a5be72c-572e-42fd-a2c3-5057eed5238b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:26:07,107] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a5be72c-572e-42fd-a2c3-5057eed5238b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:26:07,107] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:26:07,107] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 16:26:07,107] [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 16:26:07,110] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2152/tc_result.tsv
[2023-03-15 16:26:07,114] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:26:07,115] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:26:07,115] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a5be72c-572e-42fd-a2c3-5057eed5238b/dqc_reference/checkm_data
[2023-03-15 16:26:07,168] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:26:07,177] [INFO] Task started: CheckM
[2023-03-15 16:26:07,177] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2152/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2152/checkm_input OceanDNA-a2152/checkm_result
[2023-03-15 16:26:29,704] [INFO] Task succeeded: CheckM
[2023-03-15 16:26:29,705] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.01%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 16:26:29,808] [INFO] ===== Completeness check finished =====
[2023-03-15 16:26:29,808] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:26:29,809] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2152/markers.fasta)
[2023-03-15 16:26:29,809] [INFO] Task started: Blastn
[2023-03-15 16:26:29,809] [INFO] Running command: blastn -query OceanDNA-a2152/markers.fasta -db /var/lib/cwl/stg6a5be72c-572e-42fd-a2c3-5057eed5238b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2152/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:26:30,243] [INFO] Task succeeded: Blastn
[2023-03-15 16:26:30,258] [INFO] Selected 11 target genomes.
[2023-03-15 16:26:30,258] [INFO] Target genome list was writen to OceanDNA-a2152/target_genomes_gtdb.txt
[2023-03-15 16:26:30,272] [INFO] Task started: fastANI
[2023-03-15 16:26:30,273] [INFO] Running command: fastANI --query /var/lib/cwl/stg906ea8e2-6841-4f44-9138-7d285b028bbd/OceanDNA-a2152.fa --refList OceanDNA-a2152/target_genomes_gtdb.txt --output OceanDNA-a2152/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:26:33,445] [INFO] Task succeeded: fastANI
[2023-03-15 16:26:33,450] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 16:26:33,450] [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_013329295.1	s__MGIIa-L1 sp9596u	89.3676	225	298	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.51	99.26	0.88	0.84	4	-
GCA_002688825.1	s__MGIIa-L1 sp002688825	77.9764	73	298	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_011526375.1	s__MGIIa-L1 sp011526375	77.8782	143	298	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_009887195.1	s__MGIIa-L1 sp009887195	77.6524	92	298	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	98.91	98.88	0.90	0.86	3	-
GCA_002506025.1	s__MGIIa-L1 sp002506025	77.5527	79	298	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_002726395.1	s__MGIIa-L1 sp002726395	77.5475	85	298	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.39	99.39	0.85	0.85	2	-
GCA_018659375.1	s__MGIIa-L1 sp018659375	77.114	96	298	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.68	99.68	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-03-15 16:26:33,453] [INFO] GTDB search result was written to OceanDNA-a2152/result_gtdb.tsv
[2023-03-15 16:26:33,459] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:26:33,464] [INFO] DFAST_QC result json was written to OceanDNA-a2152/dqc_result.json
[2023-03-15 16:26:33,464] [INFO] DFAST_QC completed!
[2023-03-15 16:26:33,464] [INFO] Total running time: 0h0m36s