[2023-03-19 04:43:18,667] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:43:18,667] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:43:18,668] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a573c99-3b7e-4fae-8c0b-96c4eda0f8a8/dqc_reference
[2023-03-19 04:43:19,777] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:43:19,777] [INFO] Task started: Prodigal
[2023-03-19 04:43:19,777] [INFO] Running command: cat /var/lib/cwl/stg071a5d6a-124c-4557-ac5d-751be8ed8068/OceanDNA-a4966.fa | prodigal -d OceanDNA-a4966/cds.fna -a OceanDNA-a4966/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:43:26,791] [INFO] Task succeeded: Prodigal
[2023-03-19 04:43:26,792] [INFO] Task started: HMMsearch
[2023-03-19 04:43:26,792] [INFO] Running command: hmmsearch --tblout OceanDNA-a4966/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a573c99-3b7e-4fae-8c0b-96c4eda0f8a8/dqc_reference/reference_markers.hmm OceanDNA-a4966/protein.faa > /dev/null
[2023-03-19 04:43:26,960] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:43:26,961] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg071a5d6a-124c-4557-ac5d-751be8ed8068/OceanDNA-a4966.fa]
[2023-03-19 04:43:26,971] [INFO] Query marker FASTA was written to OceanDNA-a4966/markers.fasta
[2023-03-19 04:43:26,972] [INFO] Task started: Blastn
[2023-03-19 04:43:26,972] [INFO] Running command: blastn -query OceanDNA-a4966/markers.fasta -db /var/lib/cwl/stg0a573c99-3b7e-4fae-8c0b-96c4eda0f8a8/dqc_reference/reference_markers.fasta -out OceanDNA-a4966/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:43:27,409] [INFO] Task succeeded: Blastn
[2023-03-19 04:43:27,409] [INFO] Selected 4 target genomes.
[2023-03-19 04:43:27,410] [INFO] Target genome list was writen to OceanDNA-a4966/target_genomes.txt
[2023-03-19 04:43:27,414] [INFO] Task started: fastANI
[2023-03-19 04:43:27,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg071a5d6a-124c-4557-ac5d-751be8ed8068/OceanDNA-a4966.fa --refList OceanDNA-a4966/target_genomes.txt --output OceanDNA-a4966/fastani_result.tsv --threads 1
[2023-03-19 04:43:28,834] [INFO] Task succeeded: fastANI
[2023-03-19 04:43:28,835] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a573c99-3b7e-4fae-8c0b-96c4eda0f8a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:43:28,835] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a573c99-3b7e-4fae-8c0b-96c4eda0f8a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:43:28,835] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:43:28,835] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:43:28,835] [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
--------------------------------------------------------------------------------
[2023-03-19 04:43:28,835] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4966/tc_result.tsv
[2023-03-19 04:43:28,835] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:43:28,836] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:43:28,836] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a573c99-3b7e-4fae-8c0b-96c4eda0f8a8/dqc_reference/checkm_data
[2023-03-19 04:43:28,838] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:43:29,080] [INFO] Task started: CheckM
[2023-03-19 04:43:29,080] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4966/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4966/checkm_input OceanDNA-a4966/checkm_result
[2023-03-19 04:43:53,309] [INFO] Task succeeded: CheckM
[2023-03-19 04:43:53,310] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.11%
Contamintation: 2.78%
Strain heterogeneity: 80.00%
--------------------------------------------------------------------------------
[2023-03-19 04:43:53,311] [INFO] ===== Completeness check finished =====
[2023-03-19 04:43:53,312] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:43:53,312] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4966/markers.fasta)
[2023-03-19 04:43:53,313] [INFO] Task started: Blastn
[2023-03-19 04:43:53,313] [INFO] Running command: blastn -query OceanDNA-a4966/markers.fasta -db /var/lib/cwl/stg0a573c99-3b7e-4fae-8c0b-96c4eda0f8a8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4966/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:43:53,768] [INFO] Task succeeded: Blastn
[2023-03-19 04:43:53,769] [INFO] Selected 8 target genomes.
[2023-03-19 04:43:53,769] [INFO] Target genome list was writen to OceanDNA-a4966/target_genomes_gtdb.txt
[2023-03-19 04:43:53,792] [INFO] Task started: fastANI
[2023-03-19 04:43:53,792] [INFO] Running command: fastANI --query /var/lib/cwl/stg071a5d6a-124c-4557-ac5d-751be8ed8068/OceanDNA-a4966.fa --refList OceanDNA-a4966/target_genomes_gtdb.txt --output OceanDNA-a4966/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:43:55,524] [INFO] Task succeeded: fastANI
[2023-03-19 04:43:55,530] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:43:55,530] [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_002495735.1	s__Thalassarchaeum sp002495735	92.6341	132	163	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004195715.1	s__Thalassarchaeum sp004195715	91.9398	155	163	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	99.87	99.86	0.95	0.94	3	-
GCA_002457605.1	s__Thalassarchaeum sp002457605	89.7785	130	163	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002505325.1	s__Thalassarchaeum sp002505325	88.9682	129	163	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014240285.1	s__Thalassarchaeum sp014240285	86.6993	137	163	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002507125.1	s__Thalassarchaeum sp002507125	80.108	78	163	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	98.54	98.42	0.77	0.74	3	-
GCA_003193925.1	s__Thalassarchaeum betae	78.8559	92	163	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	99.52	98.11	0.96	0.90	6	-
--------------------------------------------------------------------------------
[2023-03-19 04:43:55,530] [INFO] GTDB search result was written to OceanDNA-a4966/result_gtdb.tsv
[2023-03-19 04:43:55,530] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:43:55,531] [INFO] DFAST_QC result json was written to OceanDNA-a4966/dqc_result.json
[2023-03-19 04:43:55,531] [INFO] DFAST_QC completed!
[2023-03-19 04:43:55,531] [INFO] Total running time: 0h0m37s