[2023-03-18 02:27:37,206] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:27:37,207] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:27:37,207] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc9cc934-3286-4a89-96d6-edccd27869da/dqc_reference
[2023-03-18 02:27:38,490] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:27:38,490] [INFO] Task started: Prodigal
[2023-03-18 02:27:38,490] [INFO] Running command: cat /var/lib/cwl/stg8cabccea-0045-451f-b895-62d717d7cedb/OceanDNA-b3424.fa | prodigal -d OceanDNA-b3424/cds.fna -a OceanDNA-b3424/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:27:56,271] [INFO] Task succeeded: Prodigal
[2023-03-18 02:27:56,271] [INFO] Task started: HMMsearch
[2023-03-18 02:27:56,271] [INFO] Running command: hmmsearch --tblout OceanDNA-b3424/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc9cc934-3286-4a89-96d6-edccd27869da/dqc_reference/reference_markers.hmm OceanDNA-b3424/protein.faa > /dev/null
[2023-03-18 02:27:56,491] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:27:56,492] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8cabccea-0045-451f-b895-62d717d7cedb/OceanDNA-b3424.fa]
[2023-03-18 02:27:56,514] [INFO] Query marker FASTA was written to OceanDNA-b3424/markers.fasta
[2023-03-18 02:27:56,515] [INFO] Task started: Blastn
[2023-03-18 02:27:56,515] [INFO] Running command: blastn -query OceanDNA-b3424/markers.fasta -db /var/lib/cwl/stgcc9cc934-3286-4a89-96d6-edccd27869da/dqc_reference/reference_markers.fasta -out OceanDNA-b3424/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:27:57,014] [INFO] Task succeeded: Blastn
[2023-03-18 02:27:57,015] [INFO] Selected 15 target genomes.
[2023-03-18 02:27:57,015] [INFO] Target genome list was writen to OceanDNA-b3424/target_genomes.txt
[2023-03-18 02:27:57,022] [INFO] Task started: fastANI
[2023-03-18 02:27:57,023] [INFO] Running command: fastANI --query /var/lib/cwl/stg8cabccea-0045-451f-b895-62d717d7cedb/OceanDNA-b3424.fa --refList OceanDNA-b3424/target_genomes.txt --output OceanDNA-b3424/fastani_result.tsv --threads 1
[2023-03-18 02:28:06,704] [INFO] Task succeeded: fastANI
[2023-03-18 02:28:06,704] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc9cc934-3286-4a89-96d6-edccd27869da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:28:06,704] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc9cc934-3286-4a89-96d6-edccd27869da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:28:06,705] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:28:06,705] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 02:28:06,705] [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
--------------------------------------------------------------------------------
[2023-03-18 02:28:06,705] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3424/tc_result.tsv
[2023-03-18 02:28:06,705] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:28:06,705] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:28:06,705] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc9cc934-3286-4a89-96d6-edccd27869da/dqc_reference/checkm_data
[2023-03-18 02:28:06,707] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:28:06,712] [INFO] Task started: CheckM
[2023-03-18 02:28:06,712] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3424/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3424/checkm_input OceanDNA-b3424/checkm_result
[2023-03-18 02:28:53,414] [INFO] Task succeeded: CheckM
[2023-03-18 02:28:53,414] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.81%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:28:53,417] [INFO] ===== Completeness check finished =====
[2023-03-18 02:28:53,417] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:28:53,417] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3424/markers.fasta)
[2023-03-18 02:28:53,417] [INFO] Task started: Blastn
[2023-03-18 02:28:53,417] [INFO] Running command: blastn -query OceanDNA-b3424/markers.fasta -db /var/lib/cwl/stgcc9cc934-3286-4a89-96d6-edccd27869da/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3424/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:28:54,096] [INFO] Task succeeded: Blastn
[2023-03-18 02:28:54,096] [INFO] Selected 22 target genomes.
[2023-03-18 02:28:54,096] [INFO] Target genome list was writen to OceanDNA-b3424/target_genomes_gtdb.txt
[2023-03-18 02:28:54,119] [INFO] Task started: fastANI
[2023-03-18 02:28:54,119] [INFO] Running command: fastANI --query /var/lib/cwl/stg8cabccea-0045-451f-b895-62d717d7cedb/OceanDNA-b3424.fa --refList OceanDNA-b3424/target_genomes_gtdb.txt --output OceanDNA-b3424/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:29:07,173] [INFO] Task succeeded: fastANI
[2023-03-18 02:29:07,176] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:29:07,177] [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_002162075.1	s__UphvI-Ar2 sp002162075	77.9106	307	986	d__Bacteria;p__Armatimonadota;c__Fimbriimonadia;o__Fimbriimonadales;f__Fimbriimonadaceae;g__UphvI-Ar2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823945.1	s__UphvI-Ar2 sp013823945	77.5689	282	986	d__Bacteria;p__Armatimonadota;c__Fimbriimonadia;o__Fimbriimonadales;f__Fimbriimonadaceae;g__UphvI-Ar2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789105.1	s__UphvI-Ar2 sp016789105	76.9372	137	986	d__Bacteria;p__Armatimonadota;c__Fimbriimonadia;o__Fimbriimonadales;f__Fimbriimonadaceae;g__UphvI-Ar2	95.0	99.57	99.57	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-18 02:29:07,177] [INFO] GTDB search result was written to OceanDNA-b3424/result_gtdb.tsv
[2023-03-18 02:29:07,177] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:29:07,177] [INFO] DFAST_QC result json was written to OceanDNA-b3424/dqc_result.json
[2023-03-18 02:29:07,177] [INFO] DFAST_QC completed!
[2023-03-18 02:29:07,178] [INFO] Total running time: 0h1m30s