[2023-03-17 05:39:41,255] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:39:41,255] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:39:41,255] [INFO] DQC Reference Directory: /var/lib/cwl/stg469689bf-9f9d-4283-a8ff-f2368f25cfb6/dqc_reference
[2023-03-17 05:39:42,365] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:39:42,366] [INFO] Task started: Prodigal
[2023-03-17 05:39:42,366] [INFO] Running command: cat /var/lib/cwl/stg88fa2ff3-926c-4829-b92a-e20bfe51d6f2/OceanDNA-a2419.fa | prodigal -d OceanDNA-a2419/cds.fna -a OceanDNA-a2419/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:39:54,485] [INFO] Task succeeded: Prodigal
[2023-03-17 05:39:54,485] [INFO] Task started: HMMsearch
[2023-03-17 05:39:54,485] [INFO] Running command: hmmsearch --tblout OceanDNA-a2419/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg469689bf-9f9d-4283-a8ff-f2368f25cfb6/dqc_reference/reference_markers.hmm OceanDNA-a2419/protein.faa > /dev/null
[2023-03-17 05:39:54,656] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:39:54,656] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg88fa2ff3-926c-4829-b92a-e20bfe51d6f2/OceanDNA-a2419.fa]
[2023-03-17 05:39:54,670] [INFO] Query marker FASTA was written to OceanDNA-a2419/markers.fasta
[2023-03-17 05:39:54,671] [INFO] Task started: Blastn
[2023-03-17 05:39:54,671] [INFO] Running command: blastn -query OceanDNA-a2419/markers.fasta -db /var/lib/cwl/stg469689bf-9f9d-4283-a8ff-f2368f25cfb6/dqc_reference/reference_markers.fasta -out OceanDNA-a2419/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:39:55,096] [INFO] Task succeeded: Blastn
[2023-03-17 05:39:55,097] [INFO] Selected 5 target genomes.
[2023-03-17 05:39:55,097] [INFO] Target genome list was writen to OceanDNA-a2419/target_genomes.txt
[2023-03-17 05:39:55,100] [INFO] Task started: fastANI
[2023-03-17 05:39:55,100] [INFO] Running command: fastANI --query /var/lib/cwl/stg88fa2ff3-926c-4829-b92a-e20bfe51d6f2/OceanDNA-a2419.fa --refList OceanDNA-a2419/target_genomes.txt --output OceanDNA-a2419/fastani_result.tsv --threads 1
[2023-03-17 05:39:57,715] [INFO] Task succeeded: fastANI
[2023-03-17 05:39:57,716] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg469689bf-9f9d-4283-a8ff-f2368f25cfb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:39:57,716] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg469689bf-9f9d-4283-a8ff-f2368f25cfb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:39:57,716] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:39:57,716] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 05:39:57,716] [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 05:39:57,716] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2419/tc_result.tsv
[2023-03-17 05:39:57,716] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:39:57,716] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:39:57,717] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg469689bf-9f9d-4283-a8ff-f2368f25cfb6/dqc_reference/checkm_data
[2023-03-17 05:39:57,720] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:39:57,723] [INFO] Task started: CheckM
[2023-03-17 05:39:57,723] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2419/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2419/checkm_input OceanDNA-a2419/checkm_result
[2023-03-17 05:40:32,216] [INFO] Task succeeded: CheckM
[2023-03-17 05:40:32,216] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:40:32,218] [INFO] ===== Completeness check finished =====
[2023-03-17 05:40:32,218] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:40:32,219] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2419/markers.fasta)
[2023-03-17 05:40:32,220] [INFO] Task started: Blastn
[2023-03-17 05:40:32,220] [INFO] Running command: blastn -query OceanDNA-a2419/markers.fasta -db /var/lib/cwl/stg469689bf-9f9d-4283-a8ff-f2368f25cfb6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2419/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:40:32,618] [INFO] Task succeeded: Blastn
[2023-03-17 05:40:32,619] [INFO] Selected 8 target genomes.
[2023-03-17 05:40:32,619] [INFO] Target genome list was writen to OceanDNA-a2419/target_genomes_gtdb.txt
[2023-03-17 05:40:32,678] [INFO] Task started: fastANI
[2023-03-17 05:40:32,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg88fa2ff3-926c-4829-b92a-e20bfe51d6f2/OceanDNA-a2419.fa --refList OceanDNA-a2419/target_genomes_gtdb.txt --output OceanDNA-a2419/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:40:35,402] [INFO] Task succeeded: fastANI
[2023-03-17 05:40:35,406] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 05:40:35,406] [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_002687075.1	s__MGIIa-L1 sp002687075	79.6618	395	659	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	96.38	95.66	0.88	0.80	4	-
GCA_018701175.1	s__MGIIa-L1 sp018701175	78.0654	191	659	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.50	99.46	0.87	0.84	5	-
GCA_003602605.1	s__MGIIa-L1 sp003602605	77.9842	199	659	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_018691345.1	s__MGIIa-L1 sp018691345	77.7042	163	659	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_018662825.1	s__MGIIa-L1 sp018662825	77.6623	159	659	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.67	99.65	0.92	0.89	8	-
--------------------------------------------------------------------------------
[2023-03-17 05:40:35,407] [INFO] GTDB search result was written to OceanDNA-a2419/result_gtdb.tsv
[2023-03-17 05:40:35,407] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:40:35,408] [INFO] DFAST_QC result json was written to OceanDNA-a2419/dqc_result.json
[2023-03-17 05:40:35,408] [INFO] DFAST_QC completed!
[2023-03-17 05:40:35,408] [INFO] Total running time: 0h0m54s