[2023-03-16 09:47:30,759] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:47:30,760] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:47:30,760] [INFO] DQC Reference Directory: /var/lib/cwl/stg84afcfcb-e15b-41c9-95b9-c3723c78c59c/dqc_reference
[2023-03-16 09:47:31,857] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:47:31,857] [INFO] Task started: Prodigal
[2023-03-16 09:47:31,858] [INFO] Running command: cat /var/lib/cwl/stg576188f7-29a2-4637-b9c3-805297baa676/OceanDNA-a1489.fa | prodigal -d OceanDNA-a1489/cds.fna -a OceanDNA-a1489/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:47:38,723] [INFO] Task succeeded: Prodigal
[2023-03-16 09:47:38,724] [INFO] Task started: HMMsearch
[2023-03-16 09:47:38,724] [INFO] Running command: hmmsearch --tblout OceanDNA-a1489/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84afcfcb-e15b-41c9-95b9-c3723c78c59c/dqc_reference/reference_markers.hmm OceanDNA-a1489/protein.faa > /dev/null
[2023-03-16 09:47:38,861] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:47:38,861] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg576188f7-29a2-4637-b9c3-805297baa676/OceanDNA-a1489.fa]
[2023-03-16 09:47:38,874] [INFO] Query marker FASTA was written to OceanDNA-a1489/markers.fasta
[2023-03-16 09:47:38,874] [INFO] Task started: Blastn
[2023-03-16 09:47:38,874] [INFO] Running command: blastn -query OceanDNA-a1489/markers.fasta -db /var/lib/cwl/stg84afcfcb-e15b-41c9-95b9-c3723c78c59c/dqc_reference/reference_markers.fasta -out OceanDNA-a1489/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:47:39,321] [INFO] Task succeeded: Blastn
[2023-03-16 09:47:39,323] [INFO] Selected 5 target genomes.
[2023-03-16 09:47:39,323] [INFO] Target genome list was writen to OceanDNA-a1489/target_genomes.txt
[2023-03-16 09:47:39,326] [INFO] Task started: fastANI
[2023-03-16 09:47:39,326] [INFO] Running command: fastANI --query /var/lib/cwl/stg576188f7-29a2-4637-b9c3-805297baa676/OceanDNA-a1489.fa --refList OceanDNA-a1489/target_genomes.txt --output OceanDNA-a1489/fastani_result.tsv --threads 1
[2023-03-16 09:47:41,585] [INFO] Task succeeded: fastANI
[2023-03-16 09:47:41,586] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84afcfcb-e15b-41c9-95b9-c3723c78c59c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:47:41,586] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84afcfcb-e15b-41c9-95b9-c3723c78c59c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:47:41,586] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:47:41,586] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 09:47:41,586] [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 09:47:41,587] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1489/tc_result.tsv
[2023-03-16 09:47:41,588] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:47:41,588] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:47:41,588] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84afcfcb-e15b-41c9-95b9-c3723c78c59c/dqc_reference/checkm_data
[2023-03-16 09:47:41,590] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:47:41,610] [INFO] Task started: CheckM
[2023-03-16 09:47:41,610] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1489/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1489/checkm_input OceanDNA-a1489/checkm_result
[2023-03-16 09:48:03,957] [INFO] Task succeeded: CheckM
[2023-03-16 09:48:03,957] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:48:03,960] [INFO] ===== Completeness check finished =====
[2023-03-16 09:48:03,961] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:48:03,961] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1489/markers.fasta)
[2023-03-16 09:48:03,962] [INFO] Task started: Blastn
[2023-03-16 09:48:03,962] [INFO] Running command: blastn -query OceanDNA-a1489/markers.fasta -db /var/lib/cwl/stg84afcfcb-e15b-41c9-95b9-c3723c78c59c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1489/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:48:04,411] [INFO] Task succeeded: Blastn
[2023-03-16 09:48:04,413] [INFO] Selected 5 target genomes.
[2023-03-16 09:48:04,413] [INFO] Target genome list was writen to OceanDNA-a1489/target_genomes_gtdb.txt
[2023-03-16 09:48:04,489] [INFO] Task started: fastANI
[2023-03-16 09:48:04,489] [INFO] Running command: fastANI --query /var/lib/cwl/stg576188f7-29a2-4637-b9c3-805297baa676/OceanDNA-a1489.fa --refList OceanDNA-a1489/target_genomes_gtdb.txt --output OceanDNA-a1489/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:48:06,070] [INFO] Task succeeded: fastANI
[2023-03-16 09:48:06,072] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 09:48:06,072] [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_018646625.1	s__JABGUJ01 sp018646625	99.9871	419	426	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Woesearchaeales;f__JABGUJ01;g__JABGUJ01	95.0	100.00	99.99	0.98	0.92	6	conclusive
--------------------------------------------------------------------------------
[2023-03-16 09:48:06,074] [INFO] GTDB search result was written to OceanDNA-a1489/result_gtdb.tsv
[2023-03-16 09:48:06,074] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:48:06,075] [INFO] DFAST_QC result json was written to OceanDNA-a1489/dqc_result.json
[2023-03-16 09:48:06,075] [INFO] DFAST_QC completed!
[2023-03-16 09:48:06,075] [INFO] Total running time: 0h0m35s