[2023-03-16 08:30:41,129] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:30:41,130] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:30:41,130] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c3b7670-ba6a-401c-b7ce-3d2579930cdd/dqc_reference
[2023-03-16 08:30:43,995] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:30:43,996] [INFO] Task started: Prodigal
[2023-03-16 08:30:43,996] [INFO] Running command: cat /var/lib/cwl/stga7e64a22-60ab-4ec0-82f4-abc0a4d2e43c/OceanDNA-b15526.fa | prodigal -d OceanDNA-b15526/cds.fna -a OceanDNA-b15526/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:31:09,048] [INFO] Task succeeded: Prodigal
[2023-03-16 08:31:09,048] [INFO] Task started: HMMsearch
[2023-03-16 08:31:09,048] [INFO] Running command: hmmsearch --tblout OceanDNA-b15526/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c3b7670-ba6a-401c-b7ce-3d2579930cdd/dqc_reference/reference_markers.hmm OceanDNA-b15526/protein.faa > /dev/null
[2023-03-16 08:31:09,252] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:31:09,253] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga7e64a22-60ab-4ec0-82f4-abc0a4d2e43c/OceanDNA-b15526.fa]
[2023-03-16 08:31:09,283] [INFO] Query marker FASTA was written to OceanDNA-b15526/markers.fasta
[2023-03-16 08:31:09,284] [INFO] Task started: Blastn
[2023-03-16 08:31:09,284] [INFO] Running command: blastn -query OceanDNA-b15526/markers.fasta -db /var/lib/cwl/stg3c3b7670-ba6a-401c-b7ce-3d2579930cdd/dqc_reference/reference_markers.fasta -out OceanDNA-b15526/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:31:09,799] [INFO] Task succeeded: Blastn
[2023-03-16 08:31:09,803] [INFO] Selected 16 target genomes.
[2023-03-16 08:31:09,804] [INFO] Target genome list was writen to OceanDNA-b15526/target_genomes.txt
[2023-03-16 08:31:09,825] [INFO] Task started: fastANI
[2023-03-16 08:31:09,825] [INFO] Running command: fastANI --query /var/lib/cwl/stga7e64a22-60ab-4ec0-82f4-abc0a4d2e43c/OceanDNA-b15526.fa --refList OceanDNA-b15526/target_genomes.txt --output OceanDNA-b15526/fastani_result.tsv --threads 1
[2023-03-16 08:31:18,477] [INFO] Task succeeded: fastANI
[2023-03-16 08:31:18,477] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c3b7670-ba6a-401c-b7ce-3d2579930cdd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:31:18,477] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c3b7670-ba6a-401c-b7ce-3d2579930cdd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:31:18,478] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:31:18,478] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 08:31:18,478] [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 08:31:18,479] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15526/tc_result.tsv
[2023-03-16 08:31:18,479] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:31:18,480] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:31:18,480] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c3b7670-ba6a-401c-b7ce-3d2579930cdd/dqc_reference/checkm_data
[2023-03-16 08:31:18,483] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:31:18,492] [INFO] Task started: CheckM
[2023-03-16 08:31:18,492] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15526/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15526/checkm_input OceanDNA-b15526/checkm_result
[2023-03-16 08:32:20,053] [INFO] Task succeeded: CheckM
[2023-03-16 08:32:20,054] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:32:20,059] [INFO] ===== Completeness check finished =====
[2023-03-16 08:32:20,059] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:32:20,059] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15526/markers.fasta)
[2023-03-16 08:32:20,060] [INFO] Task started: Blastn
[2023-03-16 08:32:20,060] [INFO] Running command: blastn -query OceanDNA-b15526/markers.fasta -db /var/lib/cwl/stg3c3b7670-ba6a-401c-b7ce-3d2579930cdd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15526/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:32:20,752] [INFO] Task succeeded: Blastn
[2023-03-16 08:32:20,753] [INFO] Selected 17 target genomes.
[2023-03-16 08:32:20,753] [INFO] Target genome list was writen to OceanDNA-b15526/target_genomes_gtdb.txt
[2023-03-16 08:32:20,906] [INFO] Task started: fastANI
[2023-03-16 08:32:20,906] [INFO] Running command: fastANI --query /var/lib/cwl/stga7e64a22-60ab-4ec0-82f4-abc0a4d2e43c/OceanDNA-b15526.fa --refList OceanDNA-b15526/target_genomes_gtdb.txt --output OceanDNA-b15526/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:32:29,584] [INFO] Task succeeded: fastANI
[2023-03-16 08:32:29,589] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 08:32:29,589] [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_002817055.1	s__UBA1141 sp002817055	99.6326	399	1392	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA1141	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002816455.1	s__UBA1141 sp002816455	78.1238	286	1392	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA1141	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002311385.1	s__UBA1141 sp002311385	77.4419	448	1392	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA1141	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002746355.1	s__UBA9611 sp002746355	76.1184	99	1392	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.11	98.97	0.93	0.85	6	-
GCA_009692925.1	s__SHYG01 sp009692925	75.802	58	1392	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__SHYG01	95.0	99.84	99.84	0.93	0.93	2	-
GCA_002721995.1	s__UBA9611 sp002721995	75.6634	72	1392	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.09	98.66	0.88	0.85	7	-
--------------------------------------------------------------------------------
[2023-03-16 08:32:29,589] [INFO] GTDB search result was written to OceanDNA-b15526/result_gtdb.tsv
[2023-03-16 08:32:29,589] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:32:29,590] [INFO] DFAST_QC result json was written to OceanDNA-b15526/dqc_result.json
[2023-03-16 08:32:29,590] [INFO] DFAST_QC completed!
[2023-03-16 08:32:29,590] [INFO] Total running time: 0h1m48s