[2023-03-19 03:05:33,110] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:05:33,110] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:05:33,110] [INFO] DQC Reference Directory: /var/lib/cwl/stg24fed939-466a-473d-8bef-ab1d21ec1318/dqc_reference
[2023-03-19 03:05:34,250] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:05:34,250] [INFO] Task started: Prodigal
[2023-03-19 03:05:34,251] [INFO] Running command: cat /var/lib/cwl/stgd15fe626-2ecf-43a3-9e03-8cb0068c258c/OceanDNA-b46303.fa | prodigal -d OceanDNA-b46303/cds.fna -a OceanDNA-b46303/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:06:26,334] [INFO] Task succeeded: Prodigal
[2023-03-19 03:06:26,334] [INFO] Task started: HMMsearch
[2023-03-19 03:06:26,334] [INFO] Running command: hmmsearch --tblout OceanDNA-b46303/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24fed939-466a-473d-8bef-ab1d21ec1318/dqc_reference/reference_markers.hmm OceanDNA-b46303/protein.faa > /dev/null
[2023-03-19 03:06:26,586] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:06:26,587] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd15fe626-2ecf-43a3-9e03-8cb0068c258c/OceanDNA-b46303.fa]
[2023-03-19 03:06:26,626] [INFO] Query marker FASTA was written to OceanDNA-b46303/markers.fasta
[2023-03-19 03:06:26,628] [INFO] Task started: Blastn
[2023-03-19 03:06:26,628] [INFO] Running command: blastn -query OceanDNA-b46303/markers.fasta -db /var/lib/cwl/stg24fed939-466a-473d-8bef-ab1d21ec1318/dqc_reference/reference_markers.fasta -out OceanDNA-b46303/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:06:27,226] [INFO] Task succeeded: Blastn
[2023-03-19 03:06:27,230] [INFO] Selected 20 target genomes.
[2023-03-19 03:06:27,230] [INFO] Target genome list was writen to OceanDNA-b46303/target_genomes.txt
[2023-03-19 03:06:27,242] [INFO] Task started: fastANI
[2023-03-19 03:06:27,242] [INFO] Running command: fastANI --query /var/lib/cwl/stgd15fe626-2ecf-43a3-9e03-8cb0068c258c/OceanDNA-b46303.fa --refList OceanDNA-b46303/target_genomes.txt --output OceanDNA-b46303/fastani_result.tsv --threads 1
[2023-03-19 03:06:42,756] [INFO] Task succeeded: fastANI
[2023-03-19 03:06:42,756] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24fed939-466a-473d-8bef-ab1d21ec1318/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:06:42,757] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24fed939-466a-473d-8bef-ab1d21ec1318/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:06:42,757] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:06:42,757] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 03:06:42,757] [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
--------------------------------------------------------------------------------
[2023-03-19 03:06:42,759] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46303/tc_result.tsv
[2023-03-19 03:06:42,759] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:06:42,759] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:06:42,759] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24fed939-466a-473d-8bef-ab1d21ec1318/dqc_reference/checkm_data
[2023-03-19 03:06:42,762] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:06:42,931] [INFO] Task started: CheckM
[2023-03-19 03:06:42,931] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46303/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46303/checkm_input OceanDNA-b46303/checkm_result
[2023-03-19 03:08:51,522] [INFO] Task succeeded: CheckM
[2023-03-19 03:08:51,523] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:08:51,544] [INFO] ===== Completeness check finished =====
[2023-03-19 03:08:51,544] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:08:51,544] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46303/markers.fasta)
[2023-03-19 03:08:51,546] [INFO] Task started: Blastn
[2023-03-19 03:08:51,546] [INFO] Running command: blastn -query OceanDNA-b46303/markers.fasta -db /var/lib/cwl/stg24fed939-466a-473d-8bef-ab1d21ec1318/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46303/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:08:52,405] [INFO] Task succeeded: Blastn
[2023-03-19 03:08:52,408] [INFO] Selected 20 target genomes.
[2023-03-19 03:08:52,408] [INFO] Target genome list was writen to OceanDNA-b46303/target_genomes_gtdb.txt
[2023-03-19 03:08:52,427] [INFO] Task started: fastANI
[2023-03-19 03:08:52,427] [INFO] Running command: fastANI --query /var/lib/cwl/stgd15fe626-2ecf-43a3-9e03-8cb0068c258c/OceanDNA-b46303.fa --refList OceanDNA-b46303/target_genomes_gtdb.txt --output OceanDNA-b46303/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:09:06,827] [INFO] Task succeeded: fastANI
[2023-03-19 03:09:06,833] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 03:09:06,833] [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_002715965.1	s__GCA-2715965 sp002715965	99.8275	1785	1885	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__GCA-2715965;g__GCA-2715965	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016779125.1	s__GCA-2715965 sp016779125	76.2164	122	1885	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__GCA-2715965;g__GCA-2715965	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903916195.1	s__CAIVQB01 sp903916195	75.7981	58	1885	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__CAIVQB01	95.0	99.38	98.88	0.92	0.89	6	-
GCA_016871675.1	s__VHCN01 sp016871675	75.7784	67	1885	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__VHCN01;g__VHCN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009695395.1	s__SXTU01 sp009695395	75.6989	52	1885	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SXTU01;g__SXTU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009922615.1	s__SXTU01 sp009922615	75.6415	88	1885	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SXTU01;g__SXTU01	95.0	99.88	99.88	0.94	0.94	2	-
GCA_008933025.1	s__UBA6176 sp008933025	75.2693	53	1885	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__UBA6176	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005791875.1	s__SXTU01 sp005791875	75.2556	76	1885	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SXTU01;g__SXTU01	95.0	99.67	99.31	0.92	0.90	5	-
GCA_014193395.1	s__BJHT01 sp014193395	75.2222	99	1885	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__BJHT01;g__BJHT01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 03:09:06,835] [INFO] GTDB search result was written to OceanDNA-b46303/result_gtdb.tsv
[2023-03-19 03:09:06,839] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:09:06,841] [INFO] DFAST_QC result json was written to OceanDNA-b46303/dqc_result.json
[2023-03-19 03:09:06,841] [INFO] DFAST_QC completed!
[2023-03-19 03:09:06,841] [INFO] Total running time: 0h3m34s