[2023-03-15 07:58:33,367] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:58:33,369] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:58:33,369] [INFO] DQC Reference Directory: /var/lib/cwl/stg552baf2a-201a-468c-97e2-ea0040c02b9e/dqc_reference
[2023-03-15 07:58:35,137] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:58:35,137] [INFO] Task started: Prodigal
[2023-03-15 07:58:35,137] [INFO] Running command: cat /var/lib/cwl/stg9f88b16a-0d9f-4ceb-8c57-7b5e751708e4/OceanDNA-b17387.fa | prodigal -d OceanDNA-b17387/cds.fna -a OceanDNA-b17387/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:58:51,242] [INFO] Task succeeded: Prodigal
[2023-03-15 07:58:51,242] [INFO] Task started: HMMsearch
[2023-03-15 07:58:51,243] [INFO] Running command: hmmsearch --tblout OceanDNA-b17387/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg552baf2a-201a-468c-97e2-ea0040c02b9e/dqc_reference/reference_markers.hmm OceanDNA-b17387/protein.faa > /dev/null
[2023-03-15 07:58:51,434] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:58:51,435] [INFO] Found 6/6 markers.
[2023-03-15 07:58:51,475] [INFO] Query marker FASTA was written to OceanDNA-b17387/markers.fasta
[2023-03-15 07:58:51,476] [INFO] Task started: Blastn
[2023-03-15 07:58:51,476] [INFO] Running command: blastn -query OceanDNA-b17387/markers.fasta -db /var/lib/cwl/stg552baf2a-201a-468c-97e2-ea0040c02b9e/dqc_reference/reference_markers.fasta -out OceanDNA-b17387/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:58:52,008] [INFO] Task succeeded: Blastn
[2023-03-15 07:58:52,013] [INFO] Selected 27 target genomes.
[2023-03-15 07:58:52,013] [INFO] Target genome list was writen to OceanDNA-b17387/target_genomes.txt
[2023-03-15 07:58:52,025] [INFO] Task started: fastANI
[2023-03-15 07:58:52,026] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f88b16a-0d9f-4ceb-8c57-7b5e751708e4/OceanDNA-b17387.fa --refList OceanDNA-b17387/target_genomes.txt --output OceanDNA-b17387/fastani_result.tsv --threads 1
[2023-03-15 07:59:12,147] [INFO] Task succeeded: fastANI
[2023-03-15 07:59:12,147] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg552baf2a-201a-468c-97e2-ea0040c02b9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:59:12,148] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg552baf2a-201a-468c-97e2-ea0040c02b9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:59:12,148] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:59:12,148] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 07:59:12,148] [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
--------------------------------------------------------------------------------
[2023-03-15 07:59:12,151] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17387/tc_result.tsv
[2023-03-15 07:59:12,154] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:59:12,154] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:59:12,154] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg552baf2a-201a-468c-97e2-ea0040c02b9e/dqc_reference/checkm_data
[2023-03-15 07:59:12,157] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:59:12,164] [INFO] Task started: CheckM
[2023-03-15 07:59:12,164] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17387/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17387/checkm_input OceanDNA-b17387/checkm_result
[2023-03-15 07:59:54,321] [INFO] Task succeeded: CheckM
[2023-03-15 07:59:54,321] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.39%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-15 07:59:54,368] [INFO] ===== Completeness check finished =====
[2023-03-15 07:59:54,368] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:59:54,369] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17387/markers.fasta)
[2023-03-15 07:59:54,370] [INFO] Task started: Blastn
[2023-03-15 07:59:54,370] [INFO] Running command: blastn -query OceanDNA-b17387/markers.fasta -db /var/lib/cwl/stg552baf2a-201a-468c-97e2-ea0040c02b9e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17387/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:59:55,109] [INFO] Task succeeded: Blastn
[2023-03-15 07:59:55,115] [INFO] Selected 27 target genomes.
[2023-03-15 07:59:55,115] [INFO] Target genome list was writen to OceanDNA-b17387/target_genomes_gtdb.txt
[2023-03-15 07:59:55,204] [INFO] Task started: fastANI
[2023-03-15 07:59:55,204] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f88b16a-0d9f-4ceb-8c57-7b5e751708e4/OceanDNA-b17387.fa --refList OceanDNA-b17387/target_genomes_gtdb.txt --output OceanDNA-b17387/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:00:09,003] [INFO] Task succeeded: fastANI
[2023-03-15 08:00:09,006] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 08:00:09,007] [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_015664885.1	s__UBA1138 sp003447875	77.0143	58	865	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA1138	95.0	99.72	99.64	0.94	0.92	3	-
GCA_002731735.1	s__UBA822 sp002731735	76.2125	62	865	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA822	95.0	97.30	96.95	0.68	0.67	5	-
GCA_003695865.1	s__J028 sp003695865	76.1391	54	865	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__J028	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873995.1	s__UBA2982 sp016873995	75.827	51	865	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2982	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 08:00:09,009] [INFO] GTDB search result was written to OceanDNA-b17387/result_gtdb.tsv
[2023-03-15 08:00:09,012] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:00:09,017] [INFO] DFAST_QC result json was written to OceanDNA-b17387/dqc_result.json
[2023-03-15 08:00:09,017] [INFO] DFAST_QC completed!
[2023-03-15 08:00:09,017] [INFO] Total running time: 0h1m36s