[2023-03-18 04:16:54,164] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:16:54,164] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:16:54,164] [INFO] DQC Reference Directory: /var/lib/cwl/stg59f9275e-29cf-43ef-a4e5-bac02820a8fc/dqc_reference
[2023-03-18 04:16:55,828] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:16:55,828] [INFO] Task started: Prodigal
[2023-03-18 04:16:55,828] [INFO] Running command: cat /var/lib/cwl/stga69e6c6b-483e-4b85-8b26-9355e9c3bc62/OceanDNA-a5011.fa | prodigal -d OceanDNA-a5011/cds.fna -a OceanDNA-a5011/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:17:02,975] [INFO] Task succeeded: Prodigal
[2023-03-18 04:17:02,975] [INFO] Task started: HMMsearch
[2023-03-18 04:17:02,976] [INFO] Running command: hmmsearch --tblout OceanDNA-a5011/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59f9275e-29cf-43ef-a4e5-bac02820a8fc/dqc_reference/reference_markers.hmm OceanDNA-a5011/protein.faa > /dev/null
[2023-03-18 04:17:03,133] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:17:03,134] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga69e6c6b-483e-4b85-8b26-9355e9c3bc62/OceanDNA-a5011.fa]
[2023-03-18 04:17:03,144] [INFO] Query marker FASTA was written to OceanDNA-a5011/markers.fasta
[2023-03-18 04:17:03,144] [INFO] Task started: Blastn
[2023-03-18 04:17:03,144] [INFO] Running command: blastn -query OceanDNA-a5011/markers.fasta -db /var/lib/cwl/stg59f9275e-29cf-43ef-a4e5-bac02820a8fc/dqc_reference/reference_markers.fasta -out OceanDNA-a5011/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:17:03,572] [INFO] Task succeeded: Blastn
[2023-03-18 04:17:03,573] [INFO] Selected 6 target genomes.
[2023-03-18 04:17:03,573] [INFO] Target genome list was writen to OceanDNA-a5011/target_genomes.txt
[2023-03-18 04:17:03,577] [INFO] Task started: fastANI
[2023-03-18 04:17:03,577] [INFO] Running command: fastANI --query /var/lib/cwl/stga69e6c6b-483e-4b85-8b26-9355e9c3bc62/OceanDNA-a5011.fa --refList OceanDNA-a5011/target_genomes.txt --output OceanDNA-a5011/fastani_result.tsv --threads 1
[2023-03-18 04:17:06,669] [INFO] Task succeeded: fastANI
[2023-03-18 04:17:06,669] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59f9275e-29cf-43ef-a4e5-bac02820a8fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:17:06,669] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59f9275e-29cf-43ef-a4e5-bac02820a8fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:17:06,670] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:17:06,670] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 04:17:06,670] [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
--------------------------------------------------------------------------------
[2023-03-18 04:17:06,670] [INFO] DFAST Taxonomy check result was written to OceanDNA-a5011/tc_result.tsv
[2023-03-18 04:17:06,670] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:17:06,670] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:17:06,670] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59f9275e-29cf-43ef-a4e5-bac02820a8fc/dqc_reference/checkm_data
[2023-03-18 04:17:06,673] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:17:06,676] [INFO] Task started: CheckM
[2023-03-18 04:17:06,676] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a5011/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a5011/checkm_input OceanDNA-a5011/checkm_result
[2023-03-18 04:17:29,946] [INFO] Task succeeded: CheckM
[2023-03-18 04:17:29,946] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.07%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 04:17:29,949] [INFO] ===== Completeness check finished =====
[2023-03-18 04:17:29,949] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:17:29,949] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a5011/markers.fasta)
[2023-03-18 04:17:29,949] [INFO] Task started: Blastn
[2023-03-18 04:17:29,949] [INFO] Running command: blastn -query OceanDNA-a5011/markers.fasta -db /var/lib/cwl/stg59f9275e-29cf-43ef-a4e5-bac02820a8fc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a5011/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:17:30,364] [INFO] Task succeeded: Blastn
[2023-03-18 04:17:30,367] [INFO] Selected 7 target genomes.
[2023-03-18 04:17:30,367] [INFO] Target genome list was writen to OceanDNA-a5011/target_genomes_gtdb.txt
[2023-03-18 04:17:30,385] [INFO] Task started: fastANI
[2023-03-18 04:17:30,385] [INFO] Running command: fastANI --query /var/lib/cwl/stga69e6c6b-483e-4b85-8b26-9355e9c3bc62/OceanDNA-a5011.fa --refList OceanDNA-a5011/target_genomes_gtdb.txt --output OceanDNA-a5011/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:17:32,386] [INFO] Task succeeded: fastANI
[2023-03-18 04:17:32,390] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 04:17:32,390] [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	99.1868	282	386	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004195715.1	s__Thalassarchaeum sp004195715	93.7509	357	386	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	89.0446	271	386	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	88.5812	266	386	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	85.6058	298	386	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	80.4645	157	386	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	98.54	98.42	0.77	0.74	3	-
--------------------------------------------------------------------------------
[2023-03-18 04:17:32,403] [INFO] GTDB search result was written to OceanDNA-a5011/result_gtdb.tsv
[2023-03-18 04:17:32,403] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:17:32,404] [INFO] DFAST_QC result json was written to OceanDNA-a5011/dqc_result.json
[2023-03-18 04:17:32,404] [INFO] DFAST_QC completed!
[2023-03-18 04:17:32,404] [INFO] Total running time: 0h0m38s