[2023-03-16 06:31:19,180] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:31:19,181] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:31:19,181] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ff0e185-7b9a-49b1-9749-bda5da95f927/dqc_reference
[2023-03-16 06:31:20,268] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:31:20,269] [INFO] Task started: Prodigal
[2023-03-16 06:31:20,269] [INFO] Running command: cat /var/lib/cwl/stg76e2d4d5-da89-44b5-8f09-7b35617262b8/OceanDNA-a2222.fa | prodigal -d OceanDNA-a2222/cds.fna -a OceanDNA-a2222/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:31:30,060] [INFO] Task succeeded: Prodigal
[2023-03-16 06:31:30,060] [INFO] Task started: HMMsearch
[2023-03-16 06:31:30,060] [INFO] Running command: hmmsearch --tblout OceanDNA-a2222/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ff0e185-7b9a-49b1-9749-bda5da95f927/dqc_reference/reference_markers.hmm OceanDNA-a2222/protein.faa > /dev/null
[2023-03-16 06:31:30,234] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:31:30,234] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg76e2d4d5-da89-44b5-8f09-7b35617262b8/OceanDNA-a2222.fa]
[2023-03-16 06:31:30,333] [INFO] Query marker FASTA was written to OceanDNA-a2222/markers.fasta
[2023-03-16 06:31:30,333] [INFO] Task started: Blastn
[2023-03-16 06:31:30,333] [INFO] Running command: blastn -query OceanDNA-a2222/markers.fasta -db /var/lib/cwl/stg7ff0e185-7b9a-49b1-9749-bda5da95f927/dqc_reference/reference_markers.fasta -out OceanDNA-a2222/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:31:30,773] [INFO] Task succeeded: Blastn
[2023-03-16 06:31:30,806] [INFO] Selected 3 target genomes.
[2023-03-16 06:31:30,806] [INFO] Target genome list was writen to OceanDNA-a2222/target_genomes.txt
[2023-03-16 06:31:30,808] [INFO] Task started: fastANI
[2023-03-16 06:31:30,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg76e2d4d5-da89-44b5-8f09-7b35617262b8/OceanDNA-a2222.fa --refList OceanDNA-a2222/target_genomes.txt --output OceanDNA-a2222/fastani_result.tsv --threads 1
[2023-03-16 06:31:32,689] [INFO] Task succeeded: fastANI
[2023-03-16 06:31:32,689] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ff0e185-7b9a-49b1-9749-bda5da95f927/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:31:32,690] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ff0e185-7b9a-49b1-9749-bda5da95f927/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:31:32,690] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:31:32,690] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 06:31:32,690] [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
--------------------------------------------------------------------------------
[2023-03-16 06:31:32,691] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2222/tc_result.tsv
[2023-03-16 06:31:32,691] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:31:32,691] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:31:32,691] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ff0e185-7b9a-49b1-9749-bda5da95f927/dqc_reference/checkm_data
[2023-03-16 06:31:32,694] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:31:32,698] [INFO] Task started: CheckM
[2023-03-16 06:31:32,699] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2222/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2222/checkm_input OceanDNA-a2222/checkm_result
[2023-03-16 06:32:03,723] [INFO] Task succeeded: CheckM
[2023-03-16 06:32:03,724] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.68%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:32:03,922] [INFO] ===== Completeness check finished =====
[2023-03-16 06:32:03,922] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:32:03,922] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2222/markers.fasta)
[2023-03-16 06:32:03,923] [INFO] Task started: Blastn
[2023-03-16 06:32:03,923] [INFO] Running command: blastn -query OceanDNA-a2222/markers.fasta -db /var/lib/cwl/stg7ff0e185-7b9a-49b1-9749-bda5da95f927/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2222/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:32:04,361] [INFO] Task succeeded: Blastn
[2023-03-16 06:32:04,365] [INFO] Selected 9 target genomes.
[2023-03-16 06:32:04,365] [INFO] Target genome list was writen to OceanDNA-a2222/target_genomes_gtdb.txt
[2023-03-16 06:32:04,375] [INFO] Task started: fastANI
[2023-03-16 06:32:04,375] [INFO] Running command: fastANI --query /var/lib/cwl/stg76e2d4d5-da89-44b5-8f09-7b35617262b8/OceanDNA-a2222.fa --refList OceanDNA-a2222/target_genomes_gtdb.txt --output OceanDNA-a2222/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:32:07,182] [INFO] Task succeeded: fastANI
[2023-03-16 06:32:07,187] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 06:32:07,187] [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_905182125.1	s__MGIIa-L1 sp905182125	99.6082	418	490	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905181785.1	s__MGIIa-L1 sp905181785	79.262	231	490	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_000246735.1	s__MGIIa-L1 sp000246735	78.6093	218	490	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.40	99.32	0.97	0.89	6	-
GCA_013330285.1	s__MGIIa-L1 sp8160u	78.5387	143	490	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	97.88	96.83	0.79	0.69	4	-
GCA_009887095.1	s__MGIIa-L1 sp009887095	78.3667	162	490	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_002495535.1	s__MGIIa-L1 sp002495535	78.1739	197	490	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_002506275.1	s__MGIIa-L1 sp002506275	76.5049	65	490	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.51	98.77	0.87	0.72	5	-
--------------------------------------------------------------------------------
[2023-03-16 06:32:07,189] [INFO] GTDB search result was written to OceanDNA-a2222/result_gtdb.tsv
[2023-03-16 06:32:07,191] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:32:07,192] [INFO] DFAST_QC result json was written to OceanDNA-a2222/dqc_result.json
[2023-03-16 06:32:07,192] [INFO] DFAST_QC completed!
[2023-03-16 06:32:07,192] [INFO] Total running time: 0h0m48s