[2023-03-17 08:39:27,184] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:39:27,184] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:39:27,184] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ce86c1f-8543-4edd-a802-e4948d7d7dca/dqc_reference
[2023-03-17 08:39:28,404] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:39:28,404] [INFO] Task started: Prodigal
[2023-03-17 08:39:28,404] [INFO] Running command: cat /var/lib/cwl/stg86c2b028-b549-49bf-aa8f-637490c84d75/OceanDNA-b4489.fa | prodigal -d OceanDNA-b4489/cds.fna -a OceanDNA-b4489/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:39:41,092] [INFO] Task succeeded: Prodigal
[2023-03-17 08:39:41,093] [INFO] Task started: HMMsearch
[2023-03-17 08:39:41,093] [INFO] Running command: hmmsearch --tblout OceanDNA-b4489/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ce86c1f-8543-4edd-a802-e4948d7d7dca/dqc_reference/reference_markers.hmm OceanDNA-b4489/protein.faa > /dev/null
[2023-03-17 08:39:41,265] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:39:41,265] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg86c2b028-b549-49bf-aa8f-637490c84d75/OceanDNA-b4489.fa]
[2023-03-17 08:39:41,285] [INFO] Query marker FASTA was written to OceanDNA-b4489/markers.fasta
[2023-03-17 08:39:41,286] [INFO] Task started: Blastn
[2023-03-17 08:39:41,286] [INFO] Running command: blastn -query OceanDNA-b4489/markers.fasta -db /var/lib/cwl/stg3ce86c1f-8543-4edd-a802-e4948d7d7dca/dqc_reference/reference_markers.fasta -out OceanDNA-b4489/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:39:41,823] [INFO] Task succeeded: Blastn
[2023-03-17 08:39:41,825] [INFO] Selected 23 target genomes.
[2023-03-17 08:39:41,826] [INFO] Target genome list was writen to OceanDNA-b4489/target_genomes.txt
[2023-03-17 08:39:42,090] [INFO] Task started: fastANI
[2023-03-17 08:39:42,090] [INFO] Running command: fastANI --query /var/lib/cwl/stg86c2b028-b549-49bf-aa8f-637490c84d75/OceanDNA-b4489.fa --refList OceanDNA-b4489/target_genomes.txt --output OceanDNA-b4489/fastani_result.tsv --threads 1
[2023-03-17 08:39:57,762] [INFO] Task succeeded: fastANI
[2023-03-17 08:39:57,762] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ce86c1f-8543-4edd-a802-e4948d7d7dca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:39:57,762] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ce86c1f-8543-4edd-a802-e4948d7d7dca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:39:57,766] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 08:39:57,767] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 08:39:57,767] [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
Arcticibacterium luteifluviistationis	strain=SM1504	GCA_003258705.1	1784714	1784714	type	True	76.9709	51	446	95	below_threshold
Jiulongibacter sediminis	strain=JN14-9	GCA_004329705.1	1605367	1605367	type	True	76.5253	54	446	95	below_threshold
Jiulongibacter sediminis	strain=JN14-9	GCA_001306455.1	1605367	1605367	type	True	76.5253	54	446	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 08:39:57,768] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4489/tc_result.tsv
[2023-03-17 08:39:57,768] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:39:57,768] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:39:57,768] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ce86c1f-8543-4edd-a802-e4948d7d7dca/dqc_reference/checkm_data
[2023-03-17 08:39:57,769] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:39:57,785] [INFO] Task started: CheckM
[2023-03-17 08:39:57,785] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4489/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4489/checkm_input OceanDNA-b4489/checkm_result
[2023-03-17 08:40:34,080] [INFO] Task succeeded: CheckM
[2023-03-17 08:40:34,081] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 08:40:34,083] [INFO] ===== Completeness check finished =====
[2023-03-17 08:40:34,083] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:40:34,083] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4489/markers.fasta)
[2023-03-17 08:40:34,085] [INFO] Task started: Blastn
[2023-03-17 08:40:34,085] [INFO] Running command: blastn -query OceanDNA-b4489/markers.fasta -db /var/lib/cwl/stg3ce86c1f-8543-4edd-a802-e4948d7d7dca/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4489/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:40:34,908] [INFO] Task succeeded: Blastn
[2023-03-17 08:40:34,909] [INFO] Selected 25 target genomes.
[2023-03-17 08:40:34,909] [INFO] Target genome list was writen to OceanDNA-b4489/target_genomes_gtdb.txt
[2023-03-17 08:40:35,858] [INFO] Task started: fastANI
[2023-03-17 08:40:35,858] [INFO] Running command: fastANI --query /var/lib/cwl/stg86c2b028-b549-49bf-aa8f-637490c84d75/OceanDNA-b4489.fa --refList OceanDNA-b4489/target_genomes_gtdb.txt --output OceanDNA-b4489/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:40:53,053] [INFO] Task succeeded: fastANI
[2023-03-17 08:40:53,055] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 08:40:53,055] [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
GCF_003258705.1	s__Arcticibacterium luteifluviistationis	76.9709	51	446	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Arcticibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001306455.1	s__Jiulongibacter sediminis	76.5253	54	446	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Jiulongibacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-17 08:40:53,055] [INFO] GTDB search result was written to OceanDNA-b4489/result_gtdb.tsv
[2023-03-17 08:40:53,056] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:40:53,056] [INFO] DFAST_QC result json was written to OceanDNA-b4489/dqc_result.json
[2023-03-17 08:40:53,056] [INFO] DFAST_QC completed!
[2023-03-17 08:40:53,056] [INFO] Total running time: 0h1m26s