[2023-03-18 06:43:44,054] [INFO] DFAST_QC pipeline started.
[2023-03-18 06:43:44,054] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 06:43:44,054] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b815fa0-b12b-4865-8b33-78dfc7b748b6/dqc_reference
[2023-03-18 06:43:47,808] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 06:43:47,809] [INFO] Task started: Prodigal
[2023-03-18 06:43:47,809] [INFO] Running command: cat /var/lib/cwl/stge9593ca3-4abd-4a95-8e7d-cb5bf32dcf7d/OceanDNA-b20707.fa | prodigal -d OceanDNA-b20707/cds.fna -a OceanDNA-b20707/protein.faa -g 11 -q > /dev/null
[2023-03-18 06:43:54,059] [INFO] Task succeeded: Prodigal
[2023-03-18 06:43:54,060] [INFO] Task started: HMMsearch
[2023-03-18 06:43:54,060] [INFO] Running command: hmmsearch --tblout OceanDNA-b20707/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b815fa0-b12b-4865-8b33-78dfc7b748b6/dqc_reference/reference_markers.hmm OceanDNA-b20707/protein.faa > /dev/null
[2023-03-18 06:43:54,289] [INFO] Task succeeded: HMMsearch
[2023-03-18 06:43:54,290] [INFO] Found 6/6 markers.
[2023-03-18 06:43:54,299] [INFO] Query marker FASTA was written to OceanDNA-b20707/markers.fasta
[2023-03-18 06:43:54,301] [INFO] Task started: Blastn
[2023-03-18 06:43:54,302] [INFO] Running command: blastn -query OceanDNA-b20707/markers.fasta -db /var/lib/cwl/stg7b815fa0-b12b-4865-8b33-78dfc7b748b6/dqc_reference/reference_markers.fasta -out OceanDNA-b20707/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:43:56,898] [INFO] Task succeeded: Blastn
[2023-03-18 06:43:56,899] [INFO] Selected 18 target genomes.
[2023-03-18 06:43:56,899] [INFO] Target genome list was writen to OceanDNA-b20707/target_genomes.txt
[2023-03-18 06:43:56,939] [INFO] Task started: fastANI
[2023-03-18 06:43:56,939] [INFO] Running command: fastANI --query /var/lib/cwl/stge9593ca3-4abd-4a95-8e7d-cb5bf32dcf7d/OceanDNA-b20707.fa --refList OceanDNA-b20707/target_genomes.txt --output OceanDNA-b20707/fastani_result.tsv --threads 1
[2023-03-18 06:44:06,809] [INFO] Task succeeded: fastANI
[2023-03-18 06:44:06,810] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b815fa0-b12b-4865-8b33-78dfc7b748b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 06:44:06,810] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b815fa0-b12b-4865-8b33-78dfc7b748b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 06:44:06,810] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 06:44:06,810] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 06:44:06,810] [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 06:44:06,810] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20707/tc_result.tsv
[2023-03-18 06:44:06,810] [INFO] ===== Taxonomy check completed =====
[2023-03-18 06:44:06,810] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 06:44:06,811] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b815fa0-b12b-4865-8b33-78dfc7b748b6/dqc_reference/checkm_data
[2023-03-18 06:44:06,814] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 06:44:06,816] [INFO] Task started: CheckM
[2023-03-18 06:44:06,817] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20707/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20707/checkm_input OceanDNA-b20707/checkm_result
[2023-03-18 06:44:32,862] [INFO] Task succeeded: CheckM
[2023-03-18 06:44:32,862] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 06:44:32,864] [INFO] ===== Completeness check finished =====
[2023-03-18 06:44:32,864] [INFO] ===== Start GTDB Search =====
[2023-03-18 06:44:32,864] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20707/markers.fasta)
[2023-03-18 06:44:32,866] [INFO] Task started: Blastn
[2023-03-18 06:44:32,866] [INFO] Running command: blastn -query OceanDNA-b20707/markers.fasta -db /var/lib/cwl/stg7b815fa0-b12b-4865-8b33-78dfc7b748b6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20707/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:44:34,323] [INFO] Task succeeded: Blastn
[2023-03-18 06:44:34,324] [INFO] Selected 24 target genomes.
[2023-03-18 06:44:34,324] [INFO] Target genome list was writen to OceanDNA-b20707/target_genomes_gtdb.txt
[2023-03-18 06:44:35,254] [INFO] Task started: fastANI
[2023-03-18 06:44:35,255] [INFO] Running command: fastANI --query /var/lib/cwl/stge9593ca3-4abd-4a95-8e7d-cb5bf32dcf7d/OceanDNA-b20707.fa --refList OceanDNA-b20707/target_genomes_gtdb.txt --output OceanDNA-b20707/fastani_result_gtdb.tsv --threads 1
[2023-03-18 06:44:41,264] [INFO] Task succeeded: fastANI
[2023-03-18 06:44:41,267] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 06:44:41,268] [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_002701185.1	s__TMED6 sp002701185	77.3479	113	420	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED6;g__TMED6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239355.1	s__TMED6 sp014239355	77.1641	133	420	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED6;g__TMED6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002710085.1	s__TMED6 sp002710085	76.9263	81	420	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED6;g__TMED6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002711465.1	s__TMED6 sp002711465	76.8573	107	420	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED6;g__TMED6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002704685.1	s__GCA-002707645 sp002704685	75.7177	50	420	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002707645	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 06:44:41,268] [INFO] GTDB search result was written to OceanDNA-b20707/result_gtdb.tsv
[2023-03-18 06:44:41,268] [INFO] ===== GTDB Search completed =====
[2023-03-18 06:44:41,269] [INFO] DFAST_QC result json was written to OceanDNA-b20707/dqc_result.json
[2023-03-18 06:44:41,269] [INFO] DFAST_QC completed!
[2023-03-18 06:44:41,269] [INFO] Total running time: 0h0m57s