[2023-03-16 05:52:41,096] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:52:41,096] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:52:41,096] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f422b00-cf97-4d0a-8e4d-195503947ae7/dqc_reference
[2023-03-16 05:52:42,202] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:52:42,202] [INFO] Task started: Prodigal
[2023-03-16 05:52:42,202] [INFO] Running command: cat /var/lib/cwl/stg6f7c278c-2a0b-48a0-ac73-17f08116d974/OceanDNA-b31123.fa | prodigal -d OceanDNA-b31123/cds.fna -a OceanDNA-b31123/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:52:57,019] [INFO] Task succeeded: Prodigal
[2023-03-16 05:52:57,020] [INFO] Task started: HMMsearch
[2023-03-16 05:52:57,020] [INFO] Running command: hmmsearch --tblout OceanDNA-b31123/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f422b00-cf97-4d0a-8e4d-195503947ae7/dqc_reference/reference_markers.hmm OceanDNA-b31123/protein.faa > /dev/null
[2023-03-16 05:52:57,216] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:52:57,216] [INFO] Found 6/6 markers.
[2023-03-16 05:52:57,237] [INFO] Query marker FASTA was written to OceanDNA-b31123/markers.fasta
[2023-03-16 05:52:57,237] [INFO] Task started: Blastn
[2023-03-16 05:52:57,237] [INFO] Running command: blastn -query OceanDNA-b31123/markers.fasta -db /var/lib/cwl/stg6f422b00-cf97-4d0a-8e4d-195503947ae7/dqc_reference/reference_markers.fasta -out OceanDNA-b31123/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:52:57,811] [INFO] Task succeeded: Blastn
[2023-03-16 05:52:57,813] [INFO] Selected 23 target genomes.
[2023-03-16 05:52:57,813] [INFO] Target genome list was writen to OceanDNA-b31123/target_genomes.txt
[2023-03-16 05:52:57,827] [INFO] Task started: fastANI
[2023-03-16 05:52:57,827] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f7c278c-2a0b-48a0-ac73-17f08116d974/OceanDNA-b31123.fa --refList OceanDNA-b31123/target_genomes.txt --output OceanDNA-b31123/fastani_result.tsv --threads 1
[2023-03-16 05:53:12,499] [INFO] Task succeeded: fastANI
[2023-03-16 05:53:12,499] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f422b00-cf97-4d0a-8e4d-195503947ae7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:53:12,499] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f422b00-cf97-4d0a-8e4d-195503947ae7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:53:12,500] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:53:12,500] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 05:53:12,500] [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 05:53:12,500] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31123/tc_result.tsv
[2023-03-16 05:53:12,500] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:53:12,501] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:53:12,501] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f422b00-cf97-4d0a-8e4d-195503947ae7/dqc_reference/checkm_data
[2023-03-16 05:53:12,503] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:53:12,508] [INFO] Task started: CheckM
[2023-03-16 05:53:12,508] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31123/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31123/checkm_input OceanDNA-b31123/checkm_result
[2023-03-16 05:53:52,559] [INFO] Task succeeded: CheckM
[2023-03-16 05:53:52,559] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.76%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 05:53:52,565] [INFO] ===== Completeness check finished =====
[2023-03-16 05:53:52,565] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:53:52,566] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31123/markers.fasta)
[2023-03-16 05:53:52,566] [INFO] Task started: Blastn
[2023-03-16 05:53:52,566] [INFO] Running command: blastn -query OceanDNA-b31123/markers.fasta -db /var/lib/cwl/stg6f422b00-cf97-4d0a-8e4d-195503947ae7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31123/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:53:53,547] [INFO] Task succeeded: Blastn
[2023-03-16 05:53:53,550] [INFO] Selected 23 target genomes.
[2023-03-16 05:53:53,550] [INFO] Target genome list was writen to OceanDNA-b31123/target_genomes_gtdb.txt
[2023-03-16 05:53:53,574] [INFO] Task started: fastANI
[2023-03-16 05:53:53,574] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f7c278c-2a0b-48a0-ac73-17f08116d974/OceanDNA-b31123.fa --refList OceanDNA-b31123/target_genomes_gtdb.txt --output OceanDNA-b31123/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:54:06,194] [INFO] Task succeeded: fastANI
[2023-03-16 05:54:06,196] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 05:54:06,196] [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_002723345.1	s__TMED167 sp002723345	99.9354	734	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__TMED167	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002170915.1	s__TMED167 sp002170915	81.781	454	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__TMED167	95.0	100.00	100.00	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-03-16 05:54:06,198] [INFO] GTDB search result was written to OceanDNA-b31123/result_gtdb.tsv
[2023-03-16 05:54:06,199] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:54:06,200] [INFO] DFAST_QC result json was written to OceanDNA-b31123/dqc_result.json
[2023-03-16 05:54:06,201] [INFO] DFAST_QC completed!
[2023-03-16 05:54:06,201] [INFO] Total running time: 0h1m25s