[2023-03-17 05:59:13,005] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:59:13,005] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:59:13,005] [INFO] DQC Reference Directory: /var/lib/cwl/stg023f1c89-ca2d-46d6-ace6-1d258533d47f/dqc_reference
[2023-03-17 05:59:14,086] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:59:14,086] [INFO] Task started: Prodigal
[2023-03-17 05:59:14,086] [INFO] Running command: cat /var/lib/cwl/stg3e553c28-a4d1-4074-9cf9-765abf1e22ea/OceanDNA-a1599.fa | prodigal -d OceanDNA-a1599/cds.fna -a OceanDNA-a1599/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:59:17,597] [INFO] Task succeeded: Prodigal
[2023-03-17 05:59:17,598] [INFO] Task started: HMMsearch
[2023-03-17 05:59:17,598] [INFO] Running command: hmmsearch --tblout OceanDNA-a1599/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg023f1c89-ca2d-46d6-ace6-1d258533d47f/dqc_reference/reference_markers.hmm OceanDNA-a1599/protein.faa > /dev/null
[2023-03-17 05:59:17,734] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:59:17,734] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg3e553c28-a4d1-4074-9cf9-765abf1e22ea/OceanDNA-a1599.fa]
[2023-03-17 05:59:17,742] [INFO] Query marker FASTA was written to OceanDNA-a1599/markers.fasta
[2023-03-17 05:59:17,742] [INFO] Task started: Blastn
[2023-03-17 05:59:17,742] [INFO] Running command: blastn -query OceanDNA-a1599/markers.fasta -db /var/lib/cwl/stg023f1c89-ca2d-46d6-ace6-1d258533d47f/dqc_reference/reference_markers.fasta -out OceanDNA-a1599/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:59:18,166] [INFO] Task succeeded: Blastn
[2023-03-17 05:59:18,167] [INFO] Selected 5 target genomes.
[2023-03-17 05:59:18,167] [INFO] Target genome list was writen to OceanDNA-a1599/target_genomes.txt
[2023-03-17 05:59:18,170] [INFO] Task started: fastANI
[2023-03-17 05:59:18,170] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e553c28-a4d1-4074-9cf9-765abf1e22ea/OceanDNA-a1599.fa --refList OceanDNA-a1599/target_genomes.txt --output OceanDNA-a1599/fastani_result.tsv --threads 1
[2023-03-17 05:59:20,511] [INFO] Task succeeded: fastANI
[2023-03-17 05:59:20,512] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg023f1c89-ca2d-46d6-ace6-1d258533d47f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:59:20,512] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg023f1c89-ca2d-46d6-ace6-1d258533d47f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:59:20,512] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:59:20,512] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 05:59:20,512] [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
--------------------------------------------------------------------------------
[2023-03-17 05:59:20,512] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1599/tc_result.tsv
[2023-03-17 05:59:20,512] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:59:20,513] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:59:20,513] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg023f1c89-ca2d-46d6-ace6-1d258533d47f/dqc_reference/checkm_data
[2023-03-17 05:59:20,569] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:59:20,909] [INFO] Task started: CheckM
[2023-03-17 05:59:20,909] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1599/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1599/checkm_input OceanDNA-a1599/checkm_result
[2023-03-17 05:59:39,196] [INFO] Task succeeded: CheckM
[2023-03-17 05:59:39,196] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.04%
Contamintation: 4.63%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 05:59:39,198] [INFO] ===== Completeness check finished =====
[2023-03-17 05:59:39,198] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:59:39,198] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1599/markers.fasta)
[2023-03-17 05:59:39,200] [INFO] Task started: Blastn
[2023-03-17 05:59:39,200] [INFO] Running command: blastn -query OceanDNA-a1599/markers.fasta -db /var/lib/cwl/stg023f1c89-ca2d-46d6-ace6-1d258533d47f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1599/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:59:39,822] [INFO] Task succeeded: Blastn
[2023-03-17 05:59:39,823] [INFO] Selected 7 target genomes.
[2023-03-17 05:59:39,823] [INFO] Target genome list was writen to OceanDNA-a1599/target_genomes_gtdb.txt
[2023-03-17 05:59:39,881] [INFO] Task started: fastANI
[2023-03-17 05:59:39,881] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e553c28-a4d1-4074-9cf9-765abf1e22ea/OceanDNA-a1599.fa --refList OceanDNA-a1599/target_genomes_gtdb.txt --output OceanDNA-a1599/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:59:41,279] [INFO] Task succeeded: fastANI
[2023-03-17 05:59:41,283] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 05:59:41,283] [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_002724775.1	s__CG-Epi1 sp002724775	92.8274	163	195	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	96.65	95.92	0.84	0.84	3	-
GCA_016845825.1	s__CG-Epi1 sp016845825	80.9973	126	195	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001875345.1	s__CG-Epi1 sp001875345	80.8705	133	195	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001875365.1	s__CG-Epi1 sp001875365	80.2495	86	195	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002718915.1	s__CG-Epi1 sp002718915	79.9481	97	195	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002497685.1	s__CG-Epi1 sp002497685	78.9706	84	195	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	99.79	99.79	0.70	0.70	2	-
--------------------------------------------------------------------------------
[2023-03-17 05:59:41,284] [INFO] GTDB search result was written to OceanDNA-a1599/result_gtdb.tsv
[2023-03-17 05:59:41,284] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:59:41,284] [INFO] DFAST_QC result json was written to OceanDNA-a1599/dqc_result.json
[2023-03-17 05:59:41,284] [INFO] DFAST_QC completed!
[2023-03-17 05:59:41,284] [INFO] Total running time: 0h0m28s