[2023-03-18 22:17:12,621] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:17:12,622] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:17:12,622] [INFO] DQC Reference Directory: /var/lib/cwl/stgbddc794b-17ee-4676-a1d4-9365ab27d916/dqc_reference
[2023-03-18 22:17:13,709] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:17:13,709] [INFO] Task started: Prodigal
[2023-03-18 22:17:13,709] [INFO] Running command: cat /var/lib/cwl/stga8228852-bcb3-4c1d-b7c1-c4244664ace5/OceanDNA-b16995.fa | prodigal -d OceanDNA-b16995/cds.fna -a OceanDNA-b16995/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:17:18,814] [INFO] Task succeeded: Prodigal
[2023-03-18 22:17:18,814] [INFO] Task started: HMMsearch
[2023-03-18 22:17:18,814] [INFO] Running command: hmmsearch --tblout OceanDNA-b16995/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbddc794b-17ee-4676-a1d4-9365ab27d916/dqc_reference/reference_markers.hmm OceanDNA-b16995/protein.faa > /dev/null
[2023-03-18 22:17:18,984] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:17:18,985] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga8228852-bcb3-4c1d-b7c1-c4244664ace5/OceanDNA-b16995.fa]
[2023-03-18 22:17:19,005] [INFO] Query marker FASTA was written to OceanDNA-b16995/markers.fasta
[2023-03-18 22:17:19,005] [INFO] Task started: Blastn
[2023-03-18 22:17:19,005] [INFO] Running command: blastn -query OceanDNA-b16995/markers.fasta -db /var/lib/cwl/stgbddc794b-17ee-4676-a1d4-9365ab27d916/dqc_reference/reference_markers.fasta -out OceanDNA-b16995/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:17:19,484] [INFO] Task succeeded: Blastn
[2023-03-18 22:17:19,485] [INFO] Selected 15 target genomes.
[2023-03-18 22:17:19,485] [INFO] Target genome list was writen to OceanDNA-b16995/target_genomes.txt
[2023-03-18 22:17:19,492] [INFO] Task started: fastANI
[2023-03-18 22:17:19,492] [INFO] Running command: fastANI --query /var/lib/cwl/stga8228852-bcb3-4c1d-b7c1-c4244664ace5/OceanDNA-b16995.fa --refList OceanDNA-b16995/target_genomes.txt --output OceanDNA-b16995/fastani_result.tsv --threads 1
[2023-03-18 22:17:23,981] [INFO] Task succeeded: fastANI
[2023-03-18 22:17:23,982] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbddc794b-17ee-4676-a1d4-9365ab27d916/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:17:23,982] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbddc794b-17ee-4676-a1d4-9365ab27d916/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:17:23,982] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:17:23,982] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:17:23,982] [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 22:17:23,985] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16995/tc_result.tsv
[2023-03-18 22:17:23,992] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:17:23,993] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:17:23,993] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbddc794b-17ee-4676-a1d4-9365ab27d916/dqc_reference/checkm_data
[2023-03-18 22:17:23,996] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:17:24,024] [INFO] Task started: CheckM
[2023-03-18 22:17:24,024] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16995/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16995/checkm_input OceanDNA-b16995/checkm_result
[2023-03-18 22:17:42,708] [INFO] Task succeeded: CheckM
[2023-03-18 22:17:42,709] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:17:42,804] [INFO] ===== Completeness check finished =====
[2023-03-18 22:17:42,804] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:17:42,804] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16995/markers.fasta)
[2023-03-18 22:17:42,806] [INFO] Task started: Blastn
[2023-03-18 22:17:42,806] [INFO] Running command: blastn -query OceanDNA-b16995/markers.fasta -db /var/lib/cwl/stgbddc794b-17ee-4676-a1d4-9365ab27d916/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16995/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:17:43,438] [INFO] Task succeeded: Blastn
[2023-03-18 22:17:43,504] [INFO] Selected 14 target genomes.
[2023-03-18 22:17:43,504] [INFO] Target genome list was writen to OceanDNA-b16995/target_genomes_gtdb.txt
[2023-03-18 22:17:43,523] [INFO] Task started: fastANI
[2023-03-18 22:17:43,523] [INFO] Running command: fastANI --query /var/lib/cwl/stga8228852-bcb3-4c1d-b7c1-c4244664ace5/OceanDNA-b16995.fa --refList OceanDNA-b16995/target_genomes_gtdb.txt --output OceanDNA-b16995/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:17:47,034] [INFO] Task succeeded: fastANI
[2023-03-18 22:17:47,039] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 22:17:47,039] [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_002167555.2	s__TMED58 sp002167555	99.699	315	331	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__UBA1144;f__UBA1144;g__TMED58	95.0	97.87	96.79	0.94	0.92	5	conclusive
GCA_002701865.2	s__TMED58 sp002701865	79.167	158	331	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__UBA1144;f__UBA1144;g__TMED58	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002708105.2	s__TMED58 sp002708105	78.7345	148	331	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__UBA1144;f__UBA1144;g__TMED58	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018654605.1	s__TMED58 sp018654605	78.6446	150	331	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__UBA1144;f__UBA1144;g__TMED58	95.0	99.90	99.90	0.96	0.96	2	-
GCA_905181755.1	s__TMED58 sp905181755	78.2628	95	331	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__UBA1144;f__UBA1144;g__TMED58	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701925.2	s__GCA-2701925 sp002701925	77.5201	88	331	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__UBA1144;f__UBA1144;g__GCA-2701925	95.0	97.33	97.15	0.95	0.94	4	-
--------------------------------------------------------------------------------
[2023-03-18 22:17:47,040] [INFO] GTDB search result was written to OceanDNA-b16995/result_gtdb.tsv
[2023-03-18 22:17:47,040] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:17:47,040] [INFO] DFAST_QC result json was written to OceanDNA-b16995/dqc_result.json
[2023-03-18 22:17:47,041] [INFO] DFAST_QC completed!
[2023-03-18 22:17:47,041] [INFO] Total running time: 0h0m34s