[2023-03-18 01:26:26,348] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:26:26,348] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:26:26,348] [INFO] DQC Reference Directory: /var/lib/cwl/stge925e35c-14c6-4f52-9c01-f93d4d45ce8c/dqc_reference
[2023-03-18 01:26:27,594] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:26:27,595] [INFO] Task started: Prodigal
[2023-03-18 01:26:27,595] [INFO] Running command: cat /var/lib/cwl/stg26233b8e-bfd6-47ed-8683-93a247aa205c/OceanDNA-a2640.fa | prodigal -d OceanDNA-a2640/cds.fna -a OceanDNA-a2640/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:26:36,734] [INFO] Task succeeded: Prodigal
[2023-03-18 01:26:36,734] [INFO] Task started: HMMsearch
[2023-03-18 01:26:36,734] [INFO] Running command: hmmsearch --tblout OceanDNA-a2640/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge925e35c-14c6-4f52-9c01-f93d4d45ce8c/dqc_reference/reference_markers.hmm OceanDNA-a2640/protein.faa > /dev/null
[2023-03-18 01:26:36,946] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:26:36,947] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg26233b8e-bfd6-47ed-8683-93a247aa205c/OceanDNA-a2640.fa]
[2023-03-18 01:26:36,958] [INFO] Query marker FASTA was written to OceanDNA-a2640/markers.fasta
[2023-03-18 01:26:36,958] [INFO] Task started: Blastn
[2023-03-18 01:26:36,958] [INFO] Running command: blastn -query OceanDNA-a2640/markers.fasta -db /var/lib/cwl/stge925e35c-14c6-4f52-9c01-f93d4d45ce8c/dqc_reference/reference_markers.fasta -out OceanDNA-a2640/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:26:37,454] [INFO] Task succeeded: Blastn
[2023-03-18 01:26:37,454] [INFO] Selected 1 target genomes.
[2023-03-18 01:26:37,454] [INFO] Target genome list was writen to OceanDNA-a2640/target_genomes.txt
[2023-03-18 01:26:37,470] [INFO] Task started: fastANI
[2023-03-18 01:26:37,470] [INFO] Running command: fastANI --query /var/lib/cwl/stg26233b8e-bfd6-47ed-8683-93a247aa205c/OceanDNA-a2640.fa --refList OceanDNA-a2640/target_genomes.txt --output OceanDNA-a2640/fastani_result.tsv --threads 1
[2023-03-18 01:26:38,275] [INFO] Task succeeded: fastANI
[2023-03-18 01:26:38,276] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge925e35c-14c6-4f52-9c01-f93d4d45ce8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:26:38,276] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge925e35c-14c6-4f52-9c01-f93d4d45ce8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:26:38,276] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:26:38,276] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 01:26:38,276] [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 01:26:38,276] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2640/tc_result.tsv
[2023-03-18 01:26:38,276] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:26:38,277] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:26:38,277] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge925e35c-14c6-4f52-9c01-f93d4d45ce8c/dqc_reference/checkm_data
[2023-03-18 01:26:38,280] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:26:38,284] [INFO] Task started: CheckM
[2023-03-18 01:26:38,284] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2640/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2640/checkm_input OceanDNA-a2640/checkm_result
[2023-03-18 01:27:07,654] [INFO] Task succeeded: CheckM
[2023-03-18 01:27:07,654] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.71%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:27:07,656] [INFO] ===== Completeness check finished =====
[2023-03-18 01:27:07,656] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:27:07,657] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2640/markers.fasta)
[2023-03-18 01:27:07,658] [INFO] Task started: Blastn
[2023-03-18 01:27:07,658] [INFO] Running command: blastn -query OceanDNA-a2640/markers.fasta -db /var/lib/cwl/stge925e35c-14c6-4f52-9c01-f93d4d45ce8c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2640/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:27:08,215] [INFO] Task succeeded: Blastn
[2023-03-18 01:27:08,216] [INFO] Selected 9 target genomes.
[2023-03-18 01:27:08,216] [INFO] Target genome list was writen to OceanDNA-a2640/target_genomes_gtdb.txt
[2023-03-18 01:27:08,225] [INFO] Task started: fastANI
[2023-03-18 01:27:08,225] [INFO] Running command: fastANI --query /var/lib/cwl/stg26233b8e-bfd6-47ed-8683-93a247aa205c/OceanDNA-a2640.fa --refList OceanDNA-a2640/target_genomes_gtdb.txt --output OceanDNA-a2640/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:27:11,017] [INFO] Task succeeded: fastANI
[2023-03-18 01:27:11,021] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:27:11,021] [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_013329355.1	s__MGIIa-L1 sp9354u	99.1361	356	534	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.57	99.13	0.80	0.62	3	conclusive
GCA_013329865.1	s__MGIIa-L1 sp8725u	91.6047	355	534	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	100.00	100.00	0.97	0.97	2	-
GCA_002505355.1	s__MGIIa-L1 sp002505355	78.5818	171	534	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:27:11,021] [INFO] GTDB search result was written to OceanDNA-a2640/result_gtdb.tsv
[2023-03-18 01:27:11,022] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:27:11,022] [INFO] DFAST_QC result json was written to OceanDNA-a2640/dqc_result.json
[2023-03-18 01:27:11,022] [INFO] DFAST_QC completed!
[2023-03-18 01:27:11,023] [INFO] Total running time: 0h0m45s