[2023-03-19 00:40:34,807] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:40:34,808] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:40:34,808] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f752409-87ac-4c6e-9629-36eaa76d8460/dqc_reference
[2023-03-19 00:40:35,930] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:40:35,931] [INFO] Task started: Prodigal
[2023-03-19 00:40:35,931] [INFO] Running command: cat /var/lib/cwl/stgc4a2aa87-dcd9-4580-b696-5d5bf077b5e3/OceanDNA-a4860.fa | prodigal -d OceanDNA-a4860/cds.fna -a OceanDNA-a4860/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:40:40,634] [INFO] Task succeeded: Prodigal
[2023-03-19 00:40:40,635] [INFO] Task started: HMMsearch
[2023-03-19 00:40:40,635] [INFO] Running command: hmmsearch --tblout OceanDNA-a4860/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f752409-87ac-4c6e-9629-36eaa76d8460/dqc_reference/reference_markers.hmm OceanDNA-a4860/protein.faa > /dev/null
[2023-03-19 00:40:40,786] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:40:40,786] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgc4a2aa87-dcd9-4580-b696-5d5bf077b5e3/OceanDNA-a4860.fa]
[2023-03-19 00:40:40,799] [INFO] Query marker FASTA was written to OceanDNA-a4860/markers.fasta
[2023-03-19 00:40:40,800] [INFO] Task started: Blastn
[2023-03-19 00:40:40,800] [INFO] Running command: blastn -query OceanDNA-a4860/markers.fasta -db /var/lib/cwl/stg9f752409-87ac-4c6e-9629-36eaa76d8460/dqc_reference/reference_markers.fasta -out OceanDNA-a4860/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:40:41,263] [INFO] Task succeeded: Blastn
[2023-03-19 00:40:41,267] [INFO] Selected 1 target genomes.
[2023-03-19 00:40:41,268] [INFO] Target genome list was writen to OceanDNA-a4860/target_genomes.txt
[2023-03-19 00:40:41,268] [INFO] Task started: fastANI
[2023-03-19 00:40:41,268] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4a2aa87-dcd9-4580-b696-5d5bf077b5e3/OceanDNA-a4860.fa --refList OceanDNA-a4860/target_genomes.txt --output OceanDNA-a4860/fastani_result.tsv --threads 1
[2023-03-19 00:40:41,658] [INFO] Task succeeded: fastANI
[2023-03-19 00:40:41,658] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f752409-87ac-4c6e-9629-36eaa76d8460/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:40:41,658] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f752409-87ac-4c6e-9629-36eaa76d8460/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:40:41,659] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:40:41,659] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:40:41,659] [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
--------------------------------------------------------------------------------
[2023-03-19 00:40:41,659] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4860/tc_result.tsv
[2023-03-19 00:40:41,659] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:40:41,659] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:40:41,659] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f752409-87ac-4c6e-9629-36eaa76d8460/dqc_reference/checkm_data
[2023-03-19 00:40:41,662] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:40:41,935] [INFO] Task started: CheckM
[2023-03-19 00:40:41,935] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4860/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4860/checkm_input OceanDNA-a4860/checkm_result
[2023-03-19 00:41:00,091] [INFO] Task succeeded: CheckM
[2023-03-19 00:41:00,091] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.90%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:41:00,111] [INFO] ===== Completeness check finished =====
[2023-03-19 00:41:00,111] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:41:00,111] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4860/markers.fasta)
[2023-03-19 00:41:00,111] [INFO] Task started: Blastn
[2023-03-19 00:41:00,111] [INFO] Running command: blastn -query OceanDNA-a4860/markers.fasta -db /var/lib/cwl/stg9f752409-87ac-4c6e-9629-36eaa76d8460/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4860/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:41:00,669] [INFO] Task succeeded: Blastn
[2023-03-19 00:41:00,671] [INFO] Selected 5 target genomes.
[2023-03-19 00:41:00,671] [INFO] Target genome list was writen to OceanDNA-a4860/target_genomes_gtdb.txt
[2023-03-19 00:41:00,677] [INFO] Task started: fastANI
[2023-03-19 00:41:00,677] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4a2aa87-dcd9-4580-b696-5d5bf077b5e3/OceanDNA-a4860.fa --refList OceanDNA-a4860/target_genomes_gtdb.txt --output OceanDNA-a4860/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:41:02,543] [INFO] Task succeeded: fastANI
[2023-03-19 00:41:02,546] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:41:02,546] [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_002714745.1	s__Thalassarchaeum sp002714745	94.2538	195	246	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	97.82	95.69	0.77	0.69	7	-
GCA_002727275.1	s__Thalassarchaeum sp002727275	81.6044	187	246	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698225.1	s__Thalassarchaeum sp002698225	80.9957	163	246	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	99.66	99.66	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-03-19 00:41:02,547] [INFO] GTDB search result was written to OceanDNA-a4860/result_gtdb.tsv
[2023-03-19 00:41:02,547] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:41:02,547] [INFO] DFAST_QC result json was written to OceanDNA-a4860/dqc_result.json
[2023-03-19 00:41:02,547] [INFO] DFAST_QC completed!
[2023-03-19 00:41:02,547] [INFO] Total running time: 0h0m28s