[2023-03-18 03:59:27,744] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:59:27,744] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:59:27,744] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f57c94a-6838-4e21-b687-304b363cc080/dqc_reference
[2023-03-18 03:59:29,369] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:59:29,369] [INFO] Task started: Prodigal
[2023-03-18 03:59:29,369] [INFO] Running command: cat /var/lib/cwl/stg3a26dc6b-2c66-44e3-aa8f-3bfe5d81eeb4/OceanDNA-a1029.fa | prodigal -d OceanDNA-a1029/cds.fna -a OceanDNA-a1029/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:59:31,857] [INFO] Task succeeded: Prodigal
[2023-03-18 03:59:31,857] [INFO] Task started: HMMsearch
[2023-03-18 03:59:31,857] [INFO] Running command: hmmsearch --tblout OceanDNA-a1029/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f57c94a-6838-4e21-b687-304b363cc080/dqc_reference/reference_markers.hmm OceanDNA-a1029/protein.faa > /dev/null
[2023-03-18 03:59:31,962] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:59:31,963] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg3a26dc6b-2c66-44e3-aa8f-3bfe5d81eeb4/OceanDNA-a1029.fa]
[2023-03-18 03:59:31,967] [INFO] Query marker FASTA was written to OceanDNA-a1029/markers.fasta
[2023-03-18 03:59:31,969] [INFO] Task started: Blastn
[2023-03-18 03:59:31,969] [INFO] Running command: blastn -query OceanDNA-a1029/markers.fasta -db /var/lib/cwl/stg2f57c94a-6838-4e21-b687-304b363cc080/dqc_reference/reference_markers.fasta -out OceanDNA-a1029/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:59:34,776] [INFO] Task succeeded: Blastn
[2023-03-18 03:59:34,777] [INFO] Selected 5 target genomes.
[2023-03-18 03:59:34,777] [INFO] Target genome list was writen to OceanDNA-a1029/target_genomes.txt
[2023-03-18 03:59:34,781] [INFO] Task started: fastANI
[2023-03-18 03:59:34,781] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a26dc6b-2c66-44e3-aa8f-3bfe5d81eeb4/OceanDNA-a1029.fa --refList OceanDNA-a1029/target_genomes.txt --output OceanDNA-a1029/fastani_result.tsv --threads 1
[2023-03-18 03:59:36,142] [INFO] Task succeeded: fastANI
[2023-03-18 03:59:36,143] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f57c94a-6838-4e21-b687-304b363cc080/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:59:36,143] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f57c94a-6838-4e21-b687-304b363cc080/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:59:36,143] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:59:36,143] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 03:59:36,143] [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 03:59:36,143] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1029/tc_result.tsv
[2023-03-18 03:59:36,143] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:59:36,144] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:59:36,144] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f57c94a-6838-4e21-b687-304b363cc080/dqc_reference/checkm_data
[2023-03-18 03:59:36,146] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:59:36,148] [INFO] Task started: CheckM
[2023-03-18 03:59:36,148] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1029/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1029/checkm_input OceanDNA-a1029/checkm_result
[2023-03-18 03:59:48,867] [INFO] Task succeeded: CheckM
[2023-03-18 03:59:48,867] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.39%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:59:48,868] [INFO] ===== Completeness check finished =====
[2023-03-18 03:59:48,868] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:59:48,868] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1029/markers.fasta)
[2023-03-18 03:59:48,870] [INFO] Task started: Blastn
[2023-03-18 03:59:48,871] [INFO] Running command: blastn -query OceanDNA-a1029/markers.fasta -db /var/lib/cwl/stg2f57c94a-6838-4e21-b687-304b363cc080/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1029/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:59:49,707] [INFO] Task succeeded: Blastn
[2023-03-18 03:59:49,708] [INFO] Selected 5 target genomes.
[2023-03-18 03:59:49,708] [INFO] Target genome list was writen to OceanDNA-a1029/target_genomes_gtdb.txt
[2023-03-18 03:59:49,715] [INFO] Task started: fastANI
[2023-03-18 03:59:49,715] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a26dc6b-2c66-44e3-aa8f-3bfe5d81eeb4/OceanDNA-a1029.fa --refList OceanDNA-a1029/target_genomes_gtdb.txt --output OceanDNA-a1029/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:59:50,492] [INFO] Task succeeded: fastANI
[2023-03-18 03:59:50,494] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 03:59:50,495] [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_017609795.1	s__JAFCDM01 sp017609795	78.1319	72	143	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Pacearchaeales;f__GW2011-AR1;g__JAFCDM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018653485.1	s__JABIDS01 sp018653485	77.4019	54	143	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Pacearchaeales;f__GW2011-AR1;g__JABIDS01	95.0	99.99	99.99	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2023-03-18 03:59:50,495] [INFO] GTDB search result was written to OceanDNA-a1029/result_gtdb.tsv
[2023-03-18 03:59:50,495] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:59:50,495] [INFO] DFAST_QC result json was written to OceanDNA-a1029/dqc_result.json
[2023-03-18 03:59:50,495] [INFO] DFAST_QC completed!
[2023-03-18 03:59:50,495] [INFO] Total running time: 0h0m23s