[2023-03-17 14:23:21,326] [INFO] DFAST_QC pipeline started.
[2023-03-17 14:23:21,326] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 14:23:21,326] [INFO] DQC Reference Directory: /var/lib/cwl/stg72ed2b1c-07aa-4a4e-b98f-aced8d19279e/dqc_reference
[2023-03-17 14:23:23,906] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 14:23:23,907] [INFO] Task started: Prodigal
[2023-03-17 14:23:23,907] [INFO] Running command: cat /var/lib/cwl/stg678e244b-82da-463b-a400-dc266fdb8dca/OceanDNA-b14324.fa | prodigal -d OceanDNA-b14324/cds.fna -a OceanDNA-b14324/protein.faa -g 11 -q > /dev/null
[2023-03-17 14:23:35,236] [INFO] Task succeeded: Prodigal
[2023-03-17 14:23:35,236] [INFO] Task started: HMMsearch
[2023-03-17 14:23:35,236] [INFO] Running command: hmmsearch --tblout OceanDNA-b14324/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72ed2b1c-07aa-4a4e-b98f-aced8d19279e/dqc_reference/reference_markers.hmm OceanDNA-b14324/protein.faa > /dev/null
[2023-03-17 14:23:35,518] [INFO] Task succeeded: HMMsearch
[2023-03-17 14:23:35,519] [INFO] Found 6/6 markers.
[2023-03-17 14:23:35,534] [INFO] Query marker FASTA was written to OceanDNA-b14324/markers.fasta
[2023-03-17 14:23:35,535] [INFO] Task started: Blastn
[2023-03-17 14:23:35,535] [INFO] Running command: blastn -query OceanDNA-b14324/markers.fasta -db /var/lib/cwl/stg72ed2b1c-07aa-4a4e-b98f-aced8d19279e/dqc_reference/reference_markers.fasta -out OceanDNA-b14324/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 14:23:36,083] [INFO] Task succeeded: Blastn
[2023-03-17 14:23:36,084] [INFO] Selected 8 target genomes.
[2023-03-17 14:23:36,084] [INFO] Target genome list was writen to OceanDNA-b14324/target_genomes.txt
[2023-03-17 14:23:36,088] [INFO] Task started: fastANI
[2023-03-17 14:23:36,088] [INFO] Running command: fastANI --query /var/lib/cwl/stg678e244b-82da-463b-a400-dc266fdb8dca/OceanDNA-b14324.fa --refList OceanDNA-b14324/target_genomes.txt --output OceanDNA-b14324/fastani_result.tsv --threads 1
[2023-03-17 14:23:39,455] [INFO] Task succeeded: fastANI
[2023-03-17 14:23:39,456] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72ed2b1c-07aa-4a4e-b98f-aced8d19279e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 14:23:39,456] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72ed2b1c-07aa-4a4e-b98f-aced8d19279e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 14:23:39,456] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 14:23:39,456] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 14:23:39,456] [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 14:23:39,456] [INFO] DFAST Taxonomy check result was written to OceanDNA-b14324/tc_result.tsv
[2023-03-17 14:23:39,457] [INFO] ===== Taxonomy check completed =====
[2023-03-17 14:23:39,457] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 14:23:39,457] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72ed2b1c-07aa-4a4e-b98f-aced8d19279e/dqc_reference/checkm_data
[2023-03-17 14:23:39,460] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 14:23:39,463] [INFO] Task started: CheckM
[2023-03-17 14:23:39,464] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14324/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14324/checkm_input OceanDNA-b14324/checkm_result
[2023-03-17 14:24:16,512] [INFO] Task succeeded: CheckM
[2023-03-17 14:24:16,513] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 14:24:16,514] [INFO] ===== Completeness check finished =====
[2023-03-17 14:24:16,515] [INFO] ===== Start GTDB Search =====
[2023-03-17 14:24:16,515] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14324/markers.fasta)
[2023-03-17 14:24:16,515] [INFO] Task started: Blastn
[2023-03-17 14:24:16,515] [INFO] Running command: blastn -query OceanDNA-b14324/markers.fasta -db /var/lib/cwl/stg72ed2b1c-07aa-4a4e-b98f-aced8d19279e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14324/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 14:24:17,361] [INFO] Task succeeded: Blastn
[2023-03-17 14:24:17,362] [INFO] Selected 6 target genomes.
[2023-03-17 14:24:17,362] [INFO] Target genome list was writen to OceanDNA-b14324/target_genomes_gtdb.txt
[2023-03-17 14:24:17,387] [INFO] Task started: fastANI
[2023-03-17 14:24:17,387] [INFO] Running command: fastANI --query /var/lib/cwl/stg678e244b-82da-463b-a400-dc266fdb8dca/OceanDNA-b14324.fa --refList OceanDNA-b14324/target_genomes_gtdb.txt --output OceanDNA-b14324/fastani_result_gtdb.tsv --threads 1
[2023-03-17 14:24:20,255] [INFO] Task succeeded: fastANI
[2023-03-17 14:24:20,259] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 14:24:20,259] [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_009392675.1	s__UBA11996 sp009392675	95.8288	395	666	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__UBA11996	95.0	95.66	95.66	0.60	0.60	2	conclusive
GCA_002500485.1	s__UBA11996 sp002500485	88.9741	569	666	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__UBA11996	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002435305.1	s__UBA11996 sp002435305	88.9326	517	666	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__UBA11996	95.0	99.14	98.93	0.85	0.82	4	-
GCA_012965485.1	s__UBA11996 sp012965485	88.7584	315	666	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__UBA11996	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003228105.1	s__UBA11996 sp003228105	88.6731	464	666	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__UBA11996	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 14:24:20,260] [INFO] GTDB search result was written to OceanDNA-b14324/result_gtdb.tsv
[2023-03-17 14:24:20,260] [INFO] ===== GTDB Search completed =====
[2023-03-17 14:24:20,260] [INFO] DFAST_QC result json was written to OceanDNA-b14324/dqc_result.json
[2023-03-17 14:24:20,261] [INFO] DFAST_QC completed!
[2023-03-17 14:24:20,261] [INFO] Total running time: 0h0m59s