[2023-03-15 13:16:05,728] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:16:05,728] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:16:05,728] [INFO] DQC Reference Directory: /var/lib/cwl/stgd406f39c-9d30-48c5-96f5-9b950fb48b95/dqc_reference
[2023-03-15 13:16:06,889] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:16:06,890] [INFO] Task started: Prodigal
[2023-03-15 13:16:06,890] [INFO] Running command: cat /var/lib/cwl/stgf9cc1553-47f9-40d2-a950-0d41a4de4db4/OceanDNA-b46298.fa | prodigal -d OceanDNA-b46298/cds.fna -a OceanDNA-b46298/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:17:04,365] [INFO] Task succeeded: Prodigal
[2023-03-15 13:17:04,366] [INFO] Task started: HMMsearch
[2023-03-15 13:17:04,366] [INFO] Running command: hmmsearch --tblout OceanDNA-b46298/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd406f39c-9d30-48c5-96f5-9b950fb48b95/dqc_reference/reference_markers.hmm OceanDNA-b46298/protein.faa > /dev/null
[2023-03-15 13:17:04,640] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:17:04,641] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf9cc1553-47f9-40d2-a950-0d41a4de4db4/OceanDNA-b46298.fa]
[2023-03-15 13:17:04,684] [INFO] Query marker FASTA was written to OceanDNA-b46298/markers.fasta
[2023-03-15 13:17:04,685] [INFO] Task started: Blastn
[2023-03-15 13:17:04,685] [INFO] Running command: blastn -query OceanDNA-b46298/markers.fasta -db /var/lib/cwl/stgd406f39c-9d30-48c5-96f5-9b950fb48b95/dqc_reference/reference_markers.fasta -out OceanDNA-b46298/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:17:05,237] [INFO] Task succeeded: Blastn
[2023-03-15 13:17:05,237] [INFO] Selected 21 target genomes.
[2023-03-15 13:17:05,238] [INFO] Target genome list was writen to OceanDNA-b46298/target_genomes.txt
[2023-03-15 13:17:05,276] [INFO] Task started: fastANI
[2023-03-15 13:17:05,276] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9cc1553-47f9-40d2-a950-0d41a4de4db4/OceanDNA-b46298.fa --refList OceanDNA-b46298/target_genomes.txt --output OceanDNA-b46298/fastani_result.tsv --threads 1
[2023-03-15 13:17:21,104] [INFO] Task succeeded: fastANI
[2023-03-15 13:17:21,105] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd406f39c-9d30-48c5-96f5-9b950fb48b95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:17:21,105] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd406f39c-9d30-48c5-96f5-9b950fb48b95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:17:21,105] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:17:21,105] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 13:17:21,105] [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 13:17:21,105] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46298/tc_result.tsv
[2023-03-15 13:17:21,105] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:17:21,105] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:17:21,106] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd406f39c-9d30-48c5-96f5-9b950fb48b95/dqc_reference/checkm_data
[2023-03-15 13:17:21,108] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:17:21,117] [INFO] Task started: CheckM
[2023-03-15 13:17:21,117] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46298/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46298/checkm_input OceanDNA-b46298/checkm_result
[2023-03-15 13:19:42,674] [INFO] Task succeeded: CheckM
[2023-03-15 13:19:42,675] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:19:42,679] [INFO] ===== Completeness check finished =====
[2023-03-15 13:19:42,679] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:19:42,679] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46298/markers.fasta)
[2023-03-15 13:19:42,681] [INFO] Task started: Blastn
[2023-03-15 13:19:42,681] [INFO] Running command: blastn -query OceanDNA-b46298/markers.fasta -db /var/lib/cwl/stgd406f39c-9d30-48c5-96f5-9b950fb48b95/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46298/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:19:43,908] [INFO] Task succeeded: Blastn
[2023-03-15 13:19:43,909] [INFO] Selected 25 target genomes.
[2023-03-15 13:19:43,909] [INFO] Target genome list was writen to OceanDNA-b46298/target_genomes_gtdb.txt
[2023-03-15 13:19:43,939] [INFO] Task started: fastANI
[2023-03-15 13:19:43,939] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9cc1553-47f9-40d2-a950-0d41a4de4db4/OceanDNA-b46298.fa --refList OceanDNA-b46298/target_genomes_gtdb.txt --output OceanDNA-b46298/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:20:00,716] [INFO] Task succeeded: fastANI
[2023-03-15 13:20:00,722] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:20:00,722] [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_016779125.1	s__GCA-2715965 sp016779125	76.0123	92	1979	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_016195385.1	s__JACPZS01 sp016195385	76.0006	61	1979	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__JACPZS01;g__JACPZS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013140495.1	s__SCTL01 sp013140495	75.9517	58	1979	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__SCTL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903863315.1	s__SXTU01 sp903863315	75.8748	88	1979	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SXTU01;g__SXTU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002715965.1	s__GCA-2715965 sp002715965	75.7867	105	1979	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_009695395.1	s__SXTU01 sp009695395	75.7345	56	1979	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SXTU01;g__SXTU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525685.1	s__WYBW01 sp011525685	75.685	72	1979	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__WYBW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009695195.1	s__SCTL01 sp009695195	75.6192	63	1979	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__SCTL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200005.1	s__PALSA-1396 sp016200005	75.3792	68	1979	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__PALSA-1396;g__PALSA-1396	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903922605.1	s__CAIVQB01 sp903922605	75.3282	53	1979	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__CAIVQB01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:20:00,723] [INFO] GTDB search result was written to OceanDNA-b46298/result_gtdb.tsv
[2023-03-15 13:20:00,723] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:20:00,723] [INFO] DFAST_QC result json was written to OceanDNA-b46298/dqc_result.json
[2023-03-15 13:20:00,724] [INFO] DFAST_QC completed!
[2023-03-15 13:20:00,724] [INFO] Total running time: 0h3m55s