[2023-03-18 07:29:29,825] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:29:29,825] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:29:29,825] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0886f15-25c1-4966-b40c-0b500652d416/dqc_reference
[2023-03-18 07:29:30,929] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:29:30,929] [INFO] Task started: Prodigal
[2023-03-18 07:29:30,929] [INFO] Running command: cat /var/lib/cwl/stg6b53bdc7-c629-4ce1-8f43-f516c8c891cd/OceanDNA-b24145.fa | prodigal -d OceanDNA-b24145/cds.fna -a OceanDNA-b24145/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:29:38,830] [INFO] Task succeeded: Prodigal
[2023-03-18 07:29:38,831] [INFO] Task started: HMMsearch
[2023-03-18 07:29:38,831] [INFO] Running command: hmmsearch --tblout OceanDNA-b24145/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0886f15-25c1-4966-b40c-0b500652d416/dqc_reference/reference_markers.hmm OceanDNA-b24145/protein.faa > /dev/null
[2023-03-18 07:29:38,979] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:29:38,979] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6b53bdc7-c629-4ce1-8f43-f516c8c891cd/OceanDNA-b24145.fa]
[2023-03-18 07:29:38,994] [INFO] Query marker FASTA was written to OceanDNA-b24145/markers.fasta
[2023-03-18 07:29:38,994] [INFO] Task started: Blastn
[2023-03-18 07:29:38,994] [INFO] Running command: blastn -query OceanDNA-b24145/markers.fasta -db /var/lib/cwl/stgb0886f15-25c1-4966-b40c-0b500652d416/dqc_reference/reference_markers.fasta -out OceanDNA-b24145/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:29:39,546] [INFO] Task succeeded: Blastn
[2023-03-18 07:29:39,547] [INFO] Selected 24 target genomes.
[2023-03-18 07:29:39,547] [INFO] Target genome list was writen to OceanDNA-b24145/target_genomes.txt
[2023-03-18 07:29:39,559] [INFO] Task started: fastANI
[2023-03-18 07:29:39,559] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b53bdc7-c629-4ce1-8f43-f516c8c891cd/OceanDNA-b24145.fa --refList OceanDNA-b24145/target_genomes.txt --output OceanDNA-b24145/fastani_result.tsv --threads 1
[2023-03-18 07:29:54,903] [INFO] Task succeeded: fastANI
[2023-03-18 07:29:54,904] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0886f15-25c1-4966-b40c-0b500652d416/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:29:54,904] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0886f15-25c1-4966-b40c-0b500652d416/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:29:54,904] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:29:54,904] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 07:29:54,904] [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 07:29:54,904] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24145/tc_result.tsv
[2023-03-18 07:29:54,904] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:29:54,905] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:29:54,905] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0886f15-25c1-4966-b40c-0b500652d416/dqc_reference/checkm_data
[2023-03-18 07:29:54,907] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:29:54,914] [INFO] Task started: CheckM
[2023-03-18 07:29:54,914] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24145/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24145/checkm_input OceanDNA-b24145/checkm_result
[2023-03-18 07:30:20,090] [INFO] Task succeeded: CheckM
[2023-03-18 07:30:20,090] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.81%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:30:20,092] [INFO] ===== Completeness check finished =====
[2023-03-18 07:30:20,092] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:30:20,092] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24145/markers.fasta)
[2023-03-18 07:30:20,093] [INFO] Task started: Blastn
[2023-03-18 07:30:20,093] [INFO] Running command: blastn -query OceanDNA-b24145/markers.fasta -db /var/lib/cwl/stgb0886f15-25c1-4966-b40c-0b500652d416/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24145/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:30:20,948] [INFO] Task succeeded: Blastn
[2023-03-18 07:30:20,949] [INFO] Selected 19 target genomes.
[2023-03-18 07:30:20,949] [INFO] Target genome list was writen to OceanDNA-b24145/target_genomes_gtdb.txt
[2023-03-18 07:30:21,298] [INFO] Task started: fastANI
[2023-03-18 07:30:21,298] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b53bdc7-c629-4ce1-8f43-f516c8c891cd/OceanDNA-b24145.fa --refList OceanDNA-b24145/target_genomes_gtdb.txt --output OceanDNA-b24145/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:30:31,592] [INFO] Task succeeded: fastANI
[2023-03-18 07:30:31,596] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 07:30:31,596] [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_002471575.1	s__UBA830 sp002471575	80.0642	212	334	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	97.90	95.90	0.91	0.84	7	-
GCA_905479125.1	s__UBA830 sp905479125	78.2062	122	334	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	98.22	98.19	0.84	0.83	3	-
GCA_905181725.1	s__UBA830 sp905181725	77.8779	147	334	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377375.1	s__WHUE01 sp009377375	76.6207	75	334	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WHUE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002239065.1	s__MPNO01 sp002239065	76.4491	57	334	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__MPNO01;g__MPNO01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:30:31,596] [INFO] GTDB search result was written to OceanDNA-b24145/result_gtdb.tsv
[2023-03-18 07:30:31,596] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:30:31,597] [INFO] DFAST_QC result json was written to OceanDNA-b24145/dqc_result.json
[2023-03-18 07:30:31,597] [INFO] DFAST_QC completed!
[2023-03-18 07:30:31,597] [INFO] Total running time: 0h1m2s