[2023-03-15 08:25:09,336] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:25:09,336] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:25:09,336] [INFO] DQC Reference Directory: /var/lib/cwl/stgefb0bbf6-e6be-4b7a-a0d4-b7bb2d57111a/dqc_reference
[2023-03-15 08:25:10,418] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:25:10,419] [INFO] Task started: Prodigal
[2023-03-15 08:25:10,419] [INFO] Running command: cat /var/lib/cwl/stg28df6ef7-3ef2-46ac-9672-9c8c4ebfc895/OceanDNA-b13912.fa | prodigal -d OceanDNA-b13912/cds.fna -a OceanDNA-b13912/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:25:29,031] [INFO] Task succeeded: Prodigal
[2023-03-15 08:25:29,031] [INFO] Task started: HMMsearch
[2023-03-15 08:25:29,031] [INFO] Running command: hmmsearch --tblout OceanDNA-b13912/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgefb0bbf6-e6be-4b7a-a0d4-b7bb2d57111a/dqc_reference/reference_markers.hmm OceanDNA-b13912/protein.faa > /dev/null
[2023-03-15 08:25:29,194] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:25:29,195] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg28df6ef7-3ef2-46ac-9672-9c8c4ebfc895/OceanDNA-b13912.fa]
[2023-03-15 08:25:29,215] [INFO] Query marker FASTA was written to OceanDNA-b13912/markers.fasta
[2023-03-15 08:25:29,215] [INFO] Task started: Blastn
[2023-03-15 08:25:29,215] [INFO] Running command: blastn -query OceanDNA-b13912/markers.fasta -db /var/lib/cwl/stgefb0bbf6-e6be-4b7a-a0d4-b7bb2d57111a/dqc_reference/reference_markers.fasta -out OceanDNA-b13912/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:25:29,730] [INFO] Task succeeded: Blastn
[2023-03-15 08:25:29,732] [INFO] Selected 12 target genomes.
[2023-03-15 08:25:29,732] [INFO] Target genome list was writen to OceanDNA-b13912/target_genomes.txt
[2023-03-15 08:25:29,739] [INFO] Task started: fastANI
[2023-03-15 08:25:29,739] [INFO] Running command: fastANI --query /var/lib/cwl/stg28df6ef7-3ef2-46ac-9672-9c8c4ebfc895/OceanDNA-b13912.fa --refList OceanDNA-b13912/target_genomes.txt --output OceanDNA-b13912/fastani_result.tsv --threads 1
[2023-03-15 08:25:36,104] [INFO] Task succeeded: fastANI
[2023-03-15 08:25:36,104] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgefb0bbf6-e6be-4b7a-a0d4-b7bb2d57111a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:25:36,104] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgefb0bbf6-e6be-4b7a-a0d4-b7bb2d57111a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:25:36,104] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:25:36,105] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 08:25:36,105] [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
--------------------------------------------------------------------------------
[2023-03-15 08:25:36,105] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13912/tc_result.tsv
[2023-03-15 08:25:36,106] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:25:36,106] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:25:36,106] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgefb0bbf6-e6be-4b7a-a0d4-b7bb2d57111a/dqc_reference/checkm_data
[2023-03-15 08:25:36,109] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:25:36,146] [INFO] Task started: CheckM
[2023-03-15 08:25:36,147] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13912/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13912/checkm_input OceanDNA-b13912/checkm_result
[2023-03-15 08:26:24,052] [INFO] Task succeeded: CheckM
[2023-03-15 08:26:24,053] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:26:24,056] [INFO] ===== Completeness check finished =====
[2023-03-15 08:26:24,056] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:26:24,056] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13912/markers.fasta)
[2023-03-15 08:26:24,057] [INFO] Task started: Blastn
[2023-03-15 08:26:24,057] [INFO] Running command: blastn -query OceanDNA-b13912/markers.fasta -db /var/lib/cwl/stgefb0bbf6-e6be-4b7a-a0d4-b7bb2d57111a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13912/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:26:24,778] [INFO] Task succeeded: Blastn
[2023-03-15 08:26:24,779] [INFO] Selected 11 target genomes.
[2023-03-15 08:26:24,779] [INFO] Target genome list was writen to OceanDNA-b13912/target_genomes_gtdb.txt
[2023-03-15 08:26:24,787] [INFO] Task started: fastANI
[2023-03-15 08:26:24,787] [INFO] Running command: fastANI --query /var/lib/cwl/stg28df6ef7-3ef2-46ac-9672-9c8c4ebfc895/OceanDNA-b13912.fa --refList OceanDNA-b13912/target_genomes_gtdb.txt --output OceanDNA-b13912/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:26:29,999] [INFO] Task succeeded: fastANI
[2023-03-15 08:26:30,002] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 08:26:30,002] [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_002710885.1	s__UBA1123 sp002710885	97.5481	604	995	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA11138;g__UBA1123	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002313895.1	s__UBA1123 sp002313895	94.6894	815	995	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA11138;g__UBA1123	95.0	98.51	97.41	0.87	0.77	6	-
GCA_002328865.1	s__UBA2160 sp002328865	75.9953	79	995	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA11138;g__UBA2160	95.0	99.82	99.77	0.91	0.88	7	-
--------------------------------------------------------------------------------
[2023-03-15 08:26:30,003] [INFO] GTDB search result was written to OceanDNA-b13912/result_gtdb.tsv
[2023-03-15 08:26:30,003] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:26:30,004] [INFO] DFAST_QC result json was written to OceanDNA-b13912/dqc_result.json
[2023-03-15 08:26:30,004] [INFO] DFAST_QC completed!
[2023-03-15 08:26:30,004] [INFO] Total running time: 0h1m21s