[2023-03-15 21:48:08,696] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:48:08,696] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:48:08,696] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ec0a812-550a-409d-a620-56e74c8a6637/dqc_reference
[2023-03-15 21:48:09,791] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:48:09,791] [INFO] Task started: Prodigal
[2023-03-15 21:48:09,791] [INFO] Running command: cat /var/lib/cwl/stg9f5fa4e4-0a14-4691-bff8-c271d4e07fea/OceanDNA-b23165.fa | prodigal -d OceanDNA-b23165/cds.fna -a OceanDNA-b23165/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:48:33,992] [INFO] Task succeeded: Prodigal
[2023-03-15 21:48:33,992] [INFO] Task started: HMMsearch
[2023-03-15 21:48:33,992] [INFO] Running command: hmmsearch --tblout OceanDNA-b23165/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ec0a812-550a-409d-a620-56e74c8a6637/dqc_reference/reference_markers.hmm OceanDNA-b23165/protein.faa > /dev/null
[2023-03-15 21:48:34,226] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:48:34,227] [INFO] Found 6/6 markers.
[2023-03-15 21:48:34,252] [INFO] Query marker FASTA was written to OceanDNA-b23165/markers.fasta
[2023-03-15 21:48:34,254] [INFO] Task started: Blastn
[2023-03-15 21:48:34,254] [INFO] Running command: blastn -query OceanDNA-b23165/markers.fasta -db /var/lib/cwl/stg2ec0a812-550a-409d-a620-56e74c8a6637/dqc_reference/reference_markers.fasta -out OceanDNA-b23165/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:48:38,604] [INFO] Task succeeded: Blastn
[2023-03-15 21:48:38,608] [INFO] Selected 28 target genomes.
[2023-03-15 21:48:38,608] [INFO] Target genome list was writen to OceanDNA-b23165/target_genomes.txt
[2023-03-15 21:48:38,677] [INFO] Task started: fastANI
[2023-03-15 21:48:38,677] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f5fa4e4-0a14-4691-bff8-c271d4e07fea/OceanDNA-b23165.fa --refList OceanDNA-b23165/target_genomes.txt --output OceanDNA-b23165/fastani_result.tsv --threads 1
[2023-03-15 21:48:57,803] [INFO] Task succeeded: fastANI
[2023-03-15 21:48:57,804] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ec0a812-550a-409d-a620-56e74c8a6637/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:48:57,804] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ec0a812-550a-409d-a620-56e74c8a6637/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:48:57,808] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:48:57,808] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:48:57,808] [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
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	74.7919	59	1383	95	below_threshold
Actinocorallia herbida	strain=DSM 44254	GCA_003751225.1	58109	58109	type	True	74.5967	55	1383	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:48:57,810] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23165/tc_result.tsv
[2023-03-15 21:48:57,814] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:48:57,814] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:48:57,814] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ec0a812-550a-409d-a620-56e74c8a6637/dqc_reference/checkm_data
[2023-03-15 21:48:57,814] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:48:57,823] [INFO] Task started: CheckM
[2023-03-15 21:48:57,823] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23165/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23165/checkm_input OceanDNA-b23165/checkm_result
[2023-03-15 21:49:56,891] [INFO] Task succeeded: CheckM
[2023-03-15 21:49:56,891] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:49:56,899] [INFO] ===== Completeness check finished =====
[2023-03-15 21:49:56,900] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:49:56,900] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23165/markers.fasta)
[2023-03-15 21:49:56,901] [INFO] Task started: Blastn
[2023-03-15 21:49:56,901] [INFO] Running command: blastn -query OceanDNA-b23165/markers.fasta -db /var/lib/cwl/stg2ec0a812-550a-409d-a620-56e74c8a6637/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23165/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:49:57,653] [INFO] Task succeeded: Blastn
[2023-03-15 21:49:57,656] [INFO] Selected 27 target genomes.
[2023-03-15 21:49:57,656] [INFO] Target genome list was writen to OceanDNA-b23165/target_genomes_gtdb.txt
[2023-03-15 21:49:57,813] [INFO] Task started: fastANI
[2023-03-15 21:49:57,813] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f5fa4e4-0a14-4691-bff8-c271d4e07fea/OceanDNA-b23165.fa --refList OceanDNA-b23165/target_genomes_gtdb.txt --output OceanDNA-b23165/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:50:17,484] [INFO] Task succeeded: fastANI
[2023-03-15 21:50:17,488] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 21:50:17,488] [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_002695115.1	s__UBA8108 sp002695115	98.9029	901	1383	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA8108;f__UBA8108;g__UBA8108	95.0	98.97	98.97	0.70	0.70	2	conclusive
GCA_002708465.1	s__UBA8108 sp002708465	81.0008	522	1383	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA8108;f__UBA8108;g__UBA8108	95.0	95.06	95.06	0.65	0.65	2	-
GCA_002320775.1	s__UBA8108 sp002320775	80.4901	847	1383	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA8108;f__UBA8108;g__UBA8108	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016209605.1	s__JACQVS01 sp016209605	75.202	55	1383	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA8108;f__JACQVS01;g__JACQVS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016209535.1	s__JACQVW01 sp016209535	74.9953	97	1383	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA8108;f__SXIK01;g__JACQVW01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:50:17,491] [INFO] GTDB search result was written to OceanDNA-b23165/result_gtdb.tsv
[2023-03-15 21:50:17,494] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:50:17,498] [INFO] DFAST_QC result json was written to OceanDNA-b23165/dqc_result.json
[2023-03-15 21:50:17,498] [INFO] DFAST_QC completed!
[2023-03-15 21:50:17,498] [INFO] Total running time: 0h2m9s