[2023-03-15 10:56:32,982] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:56:32,982] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:56:32,982] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c100ad8-1996-45bd-b268-95f21a793802/dqc_reference
[2023-03-15 10:56:34,086] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:56:34,087] [INFO] Task started: Prodigal
[2023-03-15 10:56:34,087] [INFO] Running command: cat /var/lib/cwl/stg79fd92a0-9b29-43c1-b70a-d31fb01aa80a/OceanDNA-a3145.fa | prodigal -d OceanDNA-a3145/cds.fna -a OceanDNA-a3145/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:56:43,168] [INFO] Task succeeded: Prodigal
[2023-03-15 10:56:43,168] [INFO] Task started: HMMsearch
[2023-03-15 10:56:43,168] [INFO] Running command: hmmsearch --tblout OceanDNA-a3145/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c100ad8-1996-45bd-b268-95f21a793802/dqc_reference/reference_markers.hmm OceanDNA-a3145/protein.faa > /dev/null
[2023-03-15 10:56:43,315] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:56:43,315] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg79fd92a0-9b29-43c1-b70a-d31fb01aa80a/OceanDNA-a3145.fa]
[2023-03-15 10:56:43,326] [INFO] Query marker FASTA was written to OceanDNA-a3145/markers.fasta
[2023-03-15 10:56:43,327] [INFO] Task started: Blastn
[2023-03-15 10:56:43,327] [INFO] Running command: blastn -query OceanDNA-a3145/markers.fasta -db /var/lib/cwl/stg6c100ad8-1996-45bd-b268-95f21a793802/dqc_reference/reference_markers.fasta -out OceanDNA-a3145/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:56:43,755] [INFO] Task succeeded: Blastn
[2023-03-15 10:56:43,755] [INFO] Selected 8 target genomes.
[2023-03-15 10:56:43,756] [INFO] Target genome list was writen to OceanDNA-a3145/target_genomes.txt
[2023-03-15 10:56:43,760] [INFO] Task started: fastANI
[2023-03-15 10:56:43,760] [INFO] Running command: fastANI --query /var/lib/cwl/stg79fd92a0-9b29-43c1-b70a-d31fb01aa80a/OceanDNA-a3145.fa --refList OceanDNA-a3145/target_genomes.txt --output OceanDNA-a3145/fastani_result.tsv --threads 1
[2023-03-15 10:56:48,717] [INFO] Task succeeded: fastANI
[2023-03-15 10:56:48,717] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c100ad8-1996-45bd-b268-95f21a793802/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:56:48,718] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c100ad8-1996-45bd-b268-95f21a793802/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:56:48,718] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:56:48,718] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 10:56:48,718] [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 10:56:48,718] [INFO] DFAST Taxonomy check result was written to OceanDNA-a3145/tc_result.tsv
[2023-03-15 10:56:48,718] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:56:48,718] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:56:48,718] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c100ad8-1996-45bd-b268-95f21a793802/dqc_reference/checkm_data
[2023-03-15 10:56:48,721] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:56:48,724] [INFO] Task started: CheckM
[2023-03-15 10:56:48,724] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3145/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3145/checkm_input OceanDNA-a3145/checkm_result
[2023-03-15 10:57:17,632] [INFO] Task succeeded: CheckM
[2023-03-15 10:57:17,632] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.11%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:57:17,634] [INFO] ===== Completeness check finished =====
[2023-03-15 10:57:17,634] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:57:17,634] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3145/markers.fasta)
[2023-03-15 10:57:17,634] [INFO] Task started: Blastn
[2023-03-15 10:57:17,634] [INFO] Running command: blastn -query OceanDNA-a3145/markers.fasta -db /var/lib/cwl/stg6c100ad8-1996-45bd-b268-95f21a793802/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3145/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:57:18,028] [INFO] Task succeeded: Blastn
[2023-03-15 10:57:18,029] [INFO] Selected 16 target genomes.
[2023-03-15 10:57:18,029] [INFO] Target genome list was writen to OceanDNA-a3145/target_genomes_gtdb.txt
[2023-03-15 10:57:18,072] [INFO] Task started: fastANI
[2023-03-15 10:57:18,072] [INFO] Running command: fastANI --query /var/lib/cwl/stg79fd92a0-9b29-43c1-b70a-d31fb01aa80a/OceanDNA-a3145.fa --refList OceanDNA-a3145/target_genomes_gtdb.txt --output OceanDNA-a3145/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:57:22,452] [INFO] Task succeeded: fastANI
[2023-03-15 10:57:22,458] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 10:57:22,458] [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_002728035.1	s__Poseidonia sp002728035	99.4792	376	429	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	96.50	96.50	0.78	0.78	2	conclusive
GCA_002495645.1	s__Poseidonia sp002495645	78.2776	180	429	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.68	99.68	0.84	0.84	2	-
GCA_002714305.1	s__Poseidonia sp002714305	77.5039	126	429	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	98.69	98.28	0.79	0.76	8	-
GCA_002704515.1	s__Poseidonia sp002704515	77.4894	108	429	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779705.1	s__Poseidonia sp016779705	77.4165	121	429	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002502295.1	s__Poseidonia sp002502295	77.2199	122	429	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694525.1	s__Poseidonia sp002694525	76.8029	111	429	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003602485.1	s__Poseidonia sp003602485	76.7851	81	429	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016778305.1	s__Poseidonia sp016778305	76.5588	84	429	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.89	99.85	0.97	0.96	5	-
--------------------------------------------------------------------------------
[2023-03-15 10:57:22,459] [INFO] GTDB search result was written to OceanDNA-a3145/result_gtdb.tsv
[2023-03-15 10:57:22,459] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:57:22,459] [INFO] DFAST_QC result json was written to OceanDNA-a3145/dqc_result.json
[2023-03-15 10:57:22,460] [INFO] DFAST_QC completed!
[2023-03-15 10:57:22,460] [INFO] Total running time: 0h0m49s