[2023-03-17 23:28:36,177] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:28:36,177] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:28:36,177] [INFO] DQC Reference Directory: /var/lib/cwl/stg712ab4ce-e133-4fd4-8fbf-dc04e2176461/dqc_reference
[2023-03-17 23:28:37,326] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:28:37,327] [INFO] Task started: Prodigal
[2023-03-17 23:28:37,327] [INFO] Running command: cat /var/lib/cwl/stg6441c3d4-2107-4164-8c47-d8cf87b9be8f/OceanDNA-b5657.fa | prodigal -d OceanDNA-b5657/cds.fna -a OceanDNA-b5657/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:28:42,577] [INFO] Task succeeded: Prodigal
[2023-03-17 23:28:42,577] [INFO] Task started: HMMsearch
[2023-03-17 23:28:42,577] [INFO] Running command: hmmsearch --tblout OceanDNA-b5657/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg712ab4ce-e133-4fd4-8fbf-dc04e2176461/dqc_reference/reference_markers.hmm OceanDNA-b5657/protein.faa > /dev/null
[2023-03-17 23:28:42,735] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:28:42,736] [INFO] Found 6/6 markers.
[2023-03-17 23:28:42,747] [INFO] Query marker FASTA was written to OceanDNA-b5657/markers.fasta
[2023-03-17 23:28:42,748] [INFO] Task started: Blastn
[2023-03-17 23:28:42,748] [INFO] Running command: blastn -query OceanDNA-b5657/markers.fasta -db /var/lib/cwl/stg712ab4ce-e133-4fd4-8fbf-dc04e2176461/dqc_reference/reference_markers.fasta -out OceanDNA-b5657/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:28:43,251] [INFO] Task succeeded: Blastn
[2023-03-17 23:28:43,252] [INFO] Selected 23 target genomes.
[2023-03-17 23:28:43,252] [INFO] Target genome list was writen to OceanDNA-b5657/target_genomes.txt
[2023-03-17 23:28:43,280] [INFO] Task started: fastANI
[2023-03-17 23:28:43,280] [INFO] Running command: fastANI --query /var/lib/cwl/stg6441c3d4-2107-4164-8c47-d8cf87b9be8f/OceanDNA-b5657.fa --refList OceanDNA-b5657/target_genomes.txt --output OceanDNA-b5657/fastani_result.tsv --threads 1
[2023-03-17 23:28:55,322] [INFO] Task succeeded: fastANI
[2023-03-17 23:28:55,323] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg712ab4ce-e133-4fd4-8fbf-dc04e2176461/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:28:55,323] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg712ab4ce-e133-4fd4-8fbf-dc04e2176461/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:28:55,323] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:28:55,323] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 23:28:55,323] [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
--------------------------------------------------------------------------------
[2023-03-17 23:28:55,323] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5657/tc_result.tsv
[2023-03-17 23:28:55,323] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:28:55,323] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:28:55,323] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg712ab4ce-e133-4fd4-8fbf-dc04e2176461/dqc_reference/checkm_data
[2023-03-17 23:28:55,326] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:28:55,329] [INFO] Task started: CheckM
[2023-03-17 23:28:55,329] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5657/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5657/checkm_input OceanDNA-b5657/checkm_result
[2023-03-17 23:29:14,810] [INFO] Task succeeded: CheckM
[2023-03-17 23:29:14,810] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.20%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:29:14,812] [INFO] ===== Completeness check finished =====
[2023-03-17 23:29:14,812] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:29:14,812] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5657/markers.fasta)
[2023-03-17 23:29:14,813] [INFO] Task started: Blastn
[2023-03-17 23:29:14,813] [INFO] Running command: blastn -query OceanDNA-b5657/markers.fasta -db /var/lib/cwl/stg712ab4ce-e133-4fd4-8fbf-dc04e2176461/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5657/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:29:15,534] [INFO] Task succeeded: Blastn
[2023-03-17 23:29:15,535] [INFO] Selected 21 target genomes.
[2023-03-17 23:29:15,535] [INFO] Target genome list was writen to OceanDNA-b5657/target_genomes_gtdb.txt
[2023-03-17 23:29:15,748] [INFO] Task started: fastANI
[2023-03-17 23:29:15,748] [INFO] Running command: fastANI --query /var/lib/cwl/stg6441c3d4-2107-4164-8c47-d8cf87b9be8f/OceanDNA-b5657.fa --refList OceanDNA-b5657/target_genomes_gtdb.txt --output OceanDNA-b5657/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:29:23,713] [INFO] Task succeeded: fastANI
[2023-03-17 23:29:23,715] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 23:29:23,716] [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_002167805.1	s__TMED14 sp002167805	93.2802	164	171	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__TMED14	95.0	95.87	95.87	0.92	0.92	2	-
GCA_002682945.1	s__TMED14 sp002682945	93.2268	156	171	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__TMED14	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:29:23,716] [INFO] GTDB search result was written to OceanDNA-b5657/result_gtdb.tsv
[2023-03-17 23:29:23,716] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:29:23,716] [INFO] DFAST_QC result json was written to OceanDNA-b5657/dqc_result.json
[2023-03-17 23:29:23,716] [INFO] DFAST_QC completed!
[2023-03-17 23:29:23,716] [INFO] Total running time: 0h0m48s