[2023-03-18 09:41:07,189] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:41:07,189] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:41:07,189] [INFO] DQC Reference Directory: /var/lib/cwl/stg54d65266-52c5-4212-a115-3a42b1384e8d/dqc_reference
[2023-03-18 09:41:08,297] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:41:08,297] [INFO] Task started: Prodigal
[2023-03-18 09:41:08,297] [INFO] Running command: cat /var/lib/cwl/stgaaaa5e69-ff68-44f8-9524-2f48fa53f0e6/OceanDNA-b46406.fa | prodigal -d OceanDNA-b46406/cds.fna -a OceanDNA-b46406/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:41:21,839] [INFO] Task succeeded: Prodigal
[2023-03-18 09:41:21,840] [INFO] Task started: HMMsearch
[2023-03-18 09:41:21,840] [INFO] Running command: hmmsearch --tblout OceanDNA-b46406/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54d65266-52c5-4212-a115-3a42b1384e8d/dqc_reference/reference_markers.hmm OceanDNA-b46406/protein.faa > /dev/null
[2023-03-18 09:41:21,972] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:41:21,972] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgaaaa5e69-ff68-44f8-9524-2f48fa53f0e6/OceanDNA-b46406.fa]
[2023-03-18 09:41:21,983] [INFO] Query marker FASTA was written to OceanDNA-b46406/markers.fasta
[2023-03-18 09:41:21,984] [INFO] Task started: Blastn
[2023-03-18 09:41:21,984] [INFO] Running command: blastn -query OceanDNA-b46406/markers.fasta -db /var/lib/cwl/stg54d65266-52c5-4212-a115-3a42b1384e8d/dqc_reference/reference_markers.fasta -out OceanDNA-b46406/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:41:22,521] [INFO] Task succeeded: Blastn
[2023-03-18 09:41:22,522] [INFO] Selected 10 target genomes.
[2023-03-18 09:41:22,522] [INFO] Target genome list was writen to OceanDNA-b46406/target_genomes.txt
[2023-03-18 09:41:22,529] [INFO] Task started: fastANI
[2023-03-18 09:41:22,529] [INFO] Running command: fastANI --query /var/lib/cwl/stgaaaa5e69-ff68-44f8-9524-2f48fa53f0e6/OceanDNA-b46406.fa --refList OceanDNA-b46406/target_genomes.txt --output OceanDNA-b46406/fastani_result.tsv --threads 1
[2023-03-18 09:41:30,644] [INFO] Task succeeded: fastANI
[2023-03-18 09:41:30,645] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54d65266-52c5-4212-a115-3a42b1384e8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:41:30,645] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54d65266-52c5-4212-a115-3a42b1384e8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:41:30,645] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:41:30,645] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:41:30,645] [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 09:41:30,645] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46406/tc_result.tsv
[2023-03-18 09:41:30,645] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:41:30,645] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:41:30,646] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54d65266-52c5-4212-a115-3a42b1384e8d/dqc_reference/checkm_data
[2023-03-18 09:41:30,648] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:41:30,651] [INFO] Task started: CheckM
[2023-03-18 09:41:30,652] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46406/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46406/checkm_input OceanDNA-b46406/checkm_result
[2023-03-18 09:42:07,420] [INFO] Task succeeded: CheckM
[2023-03-18 09:42:07,421] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.53%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:42:07,422] [INFO] ===== Completeness check finished =====
[2023-03-18 09:42:07,423] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:42:07,423] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46406/markers.fasta)
[2023-03-18 09:42:07,423] [INFO] Task started: Blastn
[2023-03-18 09:42:07,423] [INFO] Running command: blastn -query OceanDNA-b46406/markers.fasta -db /var/lib/cwl/stg54d65266-52c5-4212-a115-3a42b1384e8d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46406/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:42:08,151] [INFO] Task succeeded: Blastn
[2023-03-18 09:42:08,151] [INFO] Selected 7 target genomes.
[2023-03-18 09:42:08,152] [INFO] Target genome list was writen to OceanDNA-b46406/target_genomes_gtdb.txt
[2023-03-18 09:42:08,160] [INFO] Task started: fastANI
[2023-03-18 09:42:08,160] [INFO] Running command: fastANI --query /var/lib/cwl/stgaaaa5e69-ff68-44f8-9524-2f48fa53f0e6/OceanDNA-b46406.fa --refList OceanDNA-b46406/target_genomes_gtdb.txt --output OceanDNA-b46406/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:42:11,836] [INFO] Task succeeded: fastANI
[2023-03-18 09:42:11,841] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:42:11,841] [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_003972865.1	s__UBA1096 sp003972865	88.4269	274	416	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015658765.1	s__UBA1096 sp015658765	86.3969	260	416	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018674955.1	s__UBA1096 sp018674955	85.7692	327	416	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	98.88	98.74	0.86	0.81	14	-
GCA_014382705.1	s__UBA1096 sp014382705	85.1247	369	416	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002299785.1	s__UBA1096 sp002299785	83.5172	233	416	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686755.1	s__UBA1096 sp002686755	83.014	324	416	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523195.1	s__UBA1096 sp011523195	78.1866	141	416	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:42:11,841] [INFO] GTDB search result was written to OceanDNA-b46406/result_gtdb.tsv
[2023-03-18 09:42:11,842] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:42:11,842] [INFO] DFAST_QC result json was written to OceanDNA-b46406/dqc_result.json
[2023-03-18 09:42:11,842] [INFO] DFAST_QC completed!
[2023-03-18 09:42:11,842] [INFO] Total running time: 0h1m5s