[2023-03-17 07:47:46,513] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:47:46,513] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:47:46,513] [INFO] DQC Reference Directory: /var/lib/cwl/stg44d80139-63db-44fa-9851-470095190e36/dqc_reference
[2023-03-17 07:47:47,597] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:47:47,598] [INFO] Task started: Prodigal
[2023-03-17 07:47:47,598] [INFO] Running command: cat /var/lib/cwl/stg7d2737c9-b0b7-407b-b6fc-acb7a14b945c/OceanDNA-b31138.fa | prodigal -d OceanDNA-b31138/cds.fna -a OceanDNA-b31138/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:47:57,741] [INFO] Task succeeded: Prodigal
[2023-03-17 07:47:57,741] [INFO] Task started: HMMsearch
[2023-03-17 07:47:57,741] [INFO] Running command: hmmsearch --tblout OceanDNA-b31138/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44d80139-63db-44fa-9851-470095190e36/dqc_reference/reference_markers.hmm OceanDNA-b31138/protein.faa > /dev/null
[2023-03-17 07:47:57,929] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:47:57,930] [INFO] Found 6/6 markers.
[2023-03-17 07:47:57,947] [INFO] Query marker FASTA was written to OceanDNA-b31138/markers.fasta
[2023-03-17 07:47:57,947] [INFO] Task started: Blastn
[2023-03-17 07:47:57,947] [INFO] Running command: blastn -query OceanDNA-b31138/markers.fasta -db /var/lib/cwl/stg44d80139-63db-44fa-9851-470095190e36/dqc_reference/reference_markers.fasta -out OceanDNA-b31138/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:47:58,487] [INFO] Task succeeded: Blastn
[2023-03-17 07:47:58,488] [INFO] Selected 15 target genomes.
[2023-03-17 07:47:58,488] [INFO] Target genome list was writen to OceanDNA-b31138/target_genomes.txt
[2023-03-17 07:47:58,495] [INFO] Task started: fastANI
[2023-03-17 07:47:58,495] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d2737c9-b0b7-407b-b6fc-acb7a14b945c/OceanDNA-b31138.fa --refList OceanDNA-b31138/target_genomes.txt --output OceanDNA-b31138/fastani_result.tsv --threads 1
[2023-03-17 07:48:06,465] [INFO] Task succeeded: fastANI
[2023-03-17 07:48:06,466] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44d80139-63db-44fa-9851-470095190e36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:48:06,466] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44d80139-63db-44fa-9851-470095190e36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:48:06,466] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:48:06,466] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 07:48:06,466] [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
--------------------------------------------------------------------------------
[2023-03-17 07:48:06,466] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31138/tc_result.tsv
[2023-03-17 07:48:06,466] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:48:06,466] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:48:06,466] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44d80139-63db-44fa-9851-470095190e36/dqc_reference/checkm_data
[2023-03-17 07:48:06,469] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:48:06,479] [INFO] Task started: CheckM
[2023-03-17 07:48:06,479] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31138/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31138/checkm_input OceanDNA-b31138/checkm_result
[2023-03-17 07:48:35,957] [INFO] Task succeeded: CheckM
[2023-03-17 07:48:35,957] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:48:35,959] [INFO] ===== Completeness check finished =====
[2023-03-17 07:48:35,959] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:48:35,960] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31138/markers.fasta)
[2023-03-17 07:48:35,960] [INFO] Task started: Blastn
[2023-03-17 07:48:35,960] [INFO] Running command: blastn -query OceanDNA-b31138/markers.fasta -db /var/lib/cwl/stg44d80139-63db-44fa-9851-470095190e36/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31138/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:48:36,853] [INFO] Task succeeded: Blastn
[2023-03-17 07:48:36,854] [INFO] Selected 20 target genomes.
[2023-03-17 07:48:36,854] [INFO] Target genome list was writen to OceanDNA-b31138/target_genomes_gtdb.txt
[2023-03-17 07:48:37,144] [INFO] Task started: fastANI
[2023-03-17 07:48:37,144] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d2737c9-b0b7-407b-b6fc-acb7a14b945c/OceanDNA-b31138.fa --refList OceanDNA-b31138/target_genomes_gtdb.txt --output OceanDNA-b31138/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:48:43,977] [INFO] Task succeeded: fastANI
[2023-03-17 07:48:43,979] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 07:48:43,979] [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_016777585.1	s__TMED23 sp016777585	98.5568	479	604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__TMED23	95.0	95.71	95.71	0.75	0.75	2	conclusive
GCA_002168115.1	s__TMED23 sp002168115	85.6307	487	604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__TMED23	95.0	100.00	100.00	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-03-17 07:48:43,979] [INFO] GTDB search result was written to OceanDNA-b31138/result_gtdb.tsv
[2023-03-17 07:48:43,979] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:48:43,980] [INFO] DFAST_QC result json was written to OceanDNA-b31138/dqc_result.json
[2023-03-17 07:48:43,980] [INFO] DFAST_QC completed!
[2023-03-17 07:48:43,980] [INFO] Total running time: 0h0m57s