[2023-03-16 20:45:16,518] [INFO] DFAST_QC pipeline started.
[2023-03-16 20:45:16,518] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 20:45:16,518] [INFO] DQC Reference Directory: /var/lib/cwl/stg128b4724-6030-466d-ac71-d4233d71a4cb/dqc_reference
[2023-03-16 20:45:17,618] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 20:45:17,618] [INFO] Task started: Prodigal
[2023-03-16 20:45:17,618] [INFO] Running command: cat /var/lib/cwl/stge2e32503-e798-4dd0-b008-6270eb6008a0/OceanDNA-b45507.fa | prodigal -d OceanDNA-b45507/cds.fna -a OceanDNA-b45507/protein.faa -g 11 -q > /dev/null
[2023-03-16 20:45:43,436] [INFO] Task succeeded: Prodigal
[2023-03-16 20:45:43,436] [INFO] Task started: HMMsearch
[2023-03-16 20:45:43,436] [INFO] Running command: hmmsearch --tblout OceanDNA-b45507/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg128b4724-6030-466d-ac71-d4233d71a4cb/dqc_reference/reference_markers.hmm OceanDNA-b45507/protein.faa > /dev/null
[2023-03-16 20:45:43,617] [INFO] Task succeeded: HMMsearch
[2023-03-16 20:45:43,618] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge2e32503-e798-4dd0-b008-6270eb6008a0/OceanDNA-b45507.fa]
[2023-03-16 20:45:43,639] [INFO] Query marker FASTA was written to OceanDNA-b45507/markers.fasta
[2023-03-16 20:45:43,640] [INFO] Task started: Blastn
[2023-03-16 20:45:43,640] [INFO] Running command: blastn -query OceanDNA-b45507/markers.fasta -db /var/lib/cwl/stg128b4724-6030-466d-ac71-d4233d71a4cb/dqc_reference/reference_markers.fasta -out OceanDNA-b45507/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:45:44,196] [INFO] Task succeeded: Blastn
[2023-03-16 20:45:44,197] [INFO] Selected 19 target genomes.
[2023-03-16 20:45:44,197] [INFO] Target genome list was writen to OceanDNA-b45507/target_genomes.txt
[2023-03-16 20:45:44,211] [INFO] Task started: fastANI
[2023-03-16 20:45:44,212] [INFO] Running command: fastANI --query /var/lib/cwl/stge2e32503-e798-4dd0-b008-6270eb6008a0/OceanDNA-b45507.fa --refList OceanDNA-b45507/target_genomes.txt --output OceanDNA-b45507/fastani_result.tsv --threads 1
[2023-03-16 20:46:03,382] [INFO] Task succeeded: fastANI
[2023-03-16 20:46:03,383] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg128b4724-6030-466d-ac71-d4233d71a4cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 20:46:03,383] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg128b4724-6030-466d-ac71-d4233d71a4cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 20:46:03,383] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 20:46:03,383] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 20:46:03,383] [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
--------------------------------------------------------------------------------
[2023-03-16 20:46:03,383] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45507/tc_result.tsv
[2023-03-16 20:46:03,384] [INFO] ===== Taxonomy check completed =====
[2023-03-16 20:46:03,384] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 20:46:03,384] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg128b4724-6030-466d-ac71-d4233d71a4cb/dqc_reference/checkm_data
[2023-03-16 20:46:03,387] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 20:46:03,701] [INFO] Task started: CheckM
[2023-03-16 20:46:03,701] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45507/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45507/checkm_input OceanDNA-b45507/checkm_result
[2023-03-16 20:47:11,299] [INFO] Task succeeded: CheckM
[2023-03-16 20:47:11,300] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 20:47:11,302] [INFO] ===== Completeness check finished =====
[2023-03-16 20:47:11,302] [INFO] ===== Start GTDB Search =====
[2023-03-16 20:47:11,303] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45507/markers.fasta)
[2023-03-16 20:47:11,304] [INFO] Task started: Blastn
[2023-03-16 20:47:11,304] [INFO] Running command: blastn -query OceanDNA-b45507/markers.fasta -db /var/lib/cwl/stg128b4724-6030-466d-ac71-d4233d71a4cb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45507/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:47:12,152] [INFO] Task succeeded: Blastn
[2023-03-16 20:47:12,153] [INFO] Selected 14 target genomes.
[2023-03-16 20:47:12,153] [INFO] Target genome list was writen to OceanDNA-b45507/target_genomes_gtdb.txt
[2023-03-16 20:47:12,171] [INFO] Task started: fastANI
[2023-03-16 20:47:12,171] [INFO] Running command: fastANI --query /var/lib/cwl/stge2e32503-e798-4dd0-b008-6270eb6008a0/OceanDNA-b45507.fa --refList OceanDNA-b45507/target_genomes_gtdb.txt --output OceanDNA-b45507/fastani_result_gtdb.tsv --threads 1
[2023-03-16 20:47:20,200] [INFO] Task succeeded: fastANI
[2023-03-16 20:47:20,204] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 20:47:20,204] [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_905612515.1	s__GCA-2730975 sp905612515	93.3717	282	773	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__GCA-2730975	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382645.1	s__GCA-2730975 sp014382645	88.6386	546	773	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__GCA-2730975	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018695085.1	s__GCA-2730975 sp018695085	88.1183	424	773	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__GCA-2730975	95.0	98.14	98.04	0.72	0.68	4	-
GCA_002730975.1	s__GCA-2730975 sp002730975	87.733	571	773	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__GCA-2730975	95.0	99.68	99.68	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2023-03-16 20:47:20,204] [INFO] GTDB search result was written to OceanDNA-b45507/result_gtdb.tsv
[2023-03-16 20:47:20,204] [INFO] ===== GTDB Search completed =====
[2023-03-16 20:47:20,205] [INFO] DFAST_QC result json was written to OceanDNA-b45507/dqc_result.json
[2023-03-16 20:47:20,205] [INFO] DFAST_QC completed!
[2023-03-16 20:47:20,205] [INFO] Total running time: 0h2m4s