[2023-03-18 08:31:56,316] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:31:56,317] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:31:56,317] [INFO] DQC Reference Directory: /var/lib/cwl/stg88951355-2325-4e37-8a9e-235e9537f605/dqc_reference
[2023-03-18 08:31:57,410] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:31:57,411] [INFO] Task started: Prodigal
[2023-03-18 08:31:57,411] [INFO] Running command: cat /var/lib/cwl/stg23c1c786-1940-4f9b-8b3e-513c07ece04a/OceanDNA-b15853.fa | prodigal -d OceanDNA-b15853/cds.fna -a OceanDNA-b15853/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:32:14,631] [INFO] Task succeeded: Prodigal
[2023-03-18 08:32:14,631] [INFO] Task started: HMMsearch
[2023-03-18 08:32:14,631] [INFO] Running command: hmmsearch --tblout OceanDNA-b15853/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg88951355-2325-4e37-8a9e-235e9537f605/dqc_reference/reference_markers.hmm OceanDNA-b15853/protein.faa > /dev/null
[2023-03-18 08:32:14,802] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:32:14,803] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg23c1c786-1940-4f9b-8b3e-513c07ece04a/OceanDNA-b15853.fa]
[2023-03-18 08:32:14,821] [INFO] Query marker FASTA was written to OceanDNA-b15853/markers.fasta
[2023-03-18 08:32:14,821] [INFO] Task started: Blastn
[2023-03-18 08:32:14,821] [INFO] Running command: blastn -query OceanDNA-b15853/markers.fasta -db /var/lib/cwl/stg88951355-2325-4e37-8a9e-235e9537f605/dqc_reference/reference_markers.fasta -out OceanDNA-b15853/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:32:15,331] [INFO] Task succeeded: Blastn
[2023-03-18 08:32:15,331] [INFO] Selected 19 target genomes.
[2023-03-18 08:32:15,331] [INFO] Target genome list was writen to OceanDNA-b15853/target_genomes.txt
[2023-03-18 08:32:15,341] [INFO] Task started: fastANI
[2023-03-18 08:32:15,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg23c1c786-1940-4f9b-8b3e-513c07ece04a/OceanDNA-b15853.fa --refList OceanDNA-b15853/target_genomes.txt --output OceanDNA-b15853/fastani_result.tsv --threads 1
[2023-03-18 08:32:26,698] [INFO] Task succeeded: fastANI
[2023-03-18 08:32:26,699] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg88951355-2325-4e37-8a9e-235e9537f605/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:32:26,699] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg88951355-2325-4e37-8a9e-235e9537f605/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:32:26,699] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:32:26,699] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:32:26,699] [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 08:32:26,699] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15853/tc_result.tsv
[2023-03-18 08:32:26,699] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:32:26,700] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:32:26,700] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg88951355-2325-4e37-8a9e-235e9537f605/dqc_reference/checkm_data
[2023-03-18 08:32:26,702] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:32:26,706] [INFO] Task started: CheckM
[2023-03-18 08:32:26,707] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15853/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15853/checkm_input OceanDNA-b15853/checkm_result
[2023-03-18 08:33:11,138] [INFO] Task succeeded: CheckM
[2023-03-18 08:33:11,138] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:33:11,141] [INFO] ===== Completeness check finished =====
[2023-03-18 08:33:11,141] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:33:11,141] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15853/markers.fasta)
[2023-03-18 08:33:11,141] [INFO] Task started: Blastn
[2023-03-18 08:33:11,141] [INFO] Running command: blastn -query OceanDNA-b15853/markers.fasta -db /var/lib/cwl/stg88951355-2325-4e37-8a9e-235e9537f605/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15853/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:33:11,868] [INFO] Task succeeded: Blastn
[2023-03-18 08:33:11,869] [INFO] Selected 7 target genomes.
[2023-03-18 08:33:11,869] [INFO] Target genome list was writen to OceanDNA-b15853/target_genomes_gtdb.txt
[2023-03-18 08:33:11,878] [INFO] Task started: fastANI
[2023-03-18 08:33:11,878] [INFO] Running command: fastANI --query /var/lib/cwl/stg23c1c786-1940-4f9b-8b3e-513c07ece04a/OceanDNA-b15853.fa --refList OceanDNA-b15853/target_genomes_gtdb.txt --output OceanDNA-b15853/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:33:16,238] [INFO] Task succeeded: fastANI
[2023-03-18 08:33:16,243] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 08:33:16,243] [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_002746355.1	s__UBA9611 sp002746355	99.2026	889	932	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.11	98.97	0.93	0.85	6	conclusive
GCA_002698265.1	s__UBA9611 sp002698265	87.2361	532	932	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	98.74	98.13	0.78	0.72	6	-
GCA_002328185.1	s__UBA9611 sp002328185	80.9739	662	932	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.09	98.06	0.94	0.90	6	-
GCA_009392075.1	s__UBA9611 sp009392075	80.9336	421	932	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	96.71	96.71	0.58	0.58	2	-
GCA_009392095.1	s__UBA9611 sp009391975	80.5912	513	932	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	98.46	97.52	0.83	0.73	9	-
GCA_002816585.1	s__UBA9611 sp002816585	79.1621	388	932	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013204585.1	s__UBA9611 sp013204585	78.1128	414	932	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:33:16,243] [INFO] GTDB search result was written to OceanDNA-b15853/result_gtdb.tsv
[2023-03-18 08:33:16,244] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:33:16,244] [INFO] DFAST_QC result json was written to OceanDNA-b15853/dqc_result.json
[2023-03-18 08:33:16,244] [INFO] DFAST_QC completed!
[2023-03-18 08:33:16,244] [INFO] Total running time: 0h1m20s