[2023-03-16 19:29:06,181] [INFO] DFAST_QC pipeline started.
[2023-03-16 19:29:06,181] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 19:29:06,181] [INFO] DQC Reference Directory: /var/lib/cwl/stg87a2d8d6-16c8-4391-bd66-68102da75fb3/dqc_reference
[2023-03-16 19:29:07,382] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 19:29:07,383] [INFO] Task started: Prodigal
[2023-03-16 19:29:07,383] [INFO] Running command: cat /var/lib/cwl/stg8e6d4584-3b4d-4e13-a1cd-47a205a3e519/OceanDNA-a1656.fa | prodigal -d OceanDNA-a1656/cds.fna -a OceanDNA-a1656/protein.faa -g 11 -q > /dev/null
[2023-03-16 19:29:10,813] [INFO] Task succeeded: Prodigal
[2023-03-16 19:29:10,813] [INFO] Task started: HMMsearch
[2023-03-16 19:29:10,813] [INFO] Running command: hmmsearch --tblout OceanDNA-a1656/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87a2d8d6-16c8-4391-bd66-68102da75fb3/dqc_reference/reference_markers.hmm OceanDNA-a1656/protein.faa > /dev/null
[2023-03-16 19:29:10,951] [INFO] Task succeeded: HMMsearch
[2023-03-16 19:29:10,951] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg8e6d4584-3b4d-4e13-a1cd-47a205a3e519/OceanDNA-a1656.fa]
[2023-03-16 19:29:10,962] [INFO] Query marker FASTA was written to OceanDNA-a1656/markers.fasta
[2023-03-16 19:29:10,964] [INFO] Task started: Blastn
[2023-03-16 19:29:10,964] [INFO] Running command: blastn -query OceanDNA-a1656/markers.fasta -db /var/lib/cwl/stg87a2d8d6-16c8-4391-bd66-68102da75fb3/dqc_reference/reference_markers.fasta -out OceanDNA-a1656/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:29:11,475] [INFO] Task succeeded: Blastn
[2023-03-16 19:29:11,476] [INFO] Selected 5 target genomes.
[2023-03-16 19:29:11,477] [INFO] Target genome list was writen to OceanDNA-a1656/target_genomes.txt
[2023-03-16 19:29:11,482] [INFO] Task started: fastANI
[2023-03-16 19:29:11,483] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e6d4584-3b4d-4e13-a1cd-47a205a3e519/OceanDNA-a1656.fa --refList OceanDNA-a1656/target_genomes.txt --output OceanDNA-a1656/fastani_result.tsv --threads 1
[2023-03-16 19:29:13,571] [INFO] Task succeeded: fastANI
[2023-03-16 19:29:13,571] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87a2d8d6-16c8-4391-bd66-68102da75fb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 19:29:13,572] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87a2d8d6-16c8-4391-bd66-68102da75fb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 19:29:13,572] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 19:29:13,572] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 19:29:13,572] [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 19:29:13,573] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1656/tc_result.tsv
[2023-03-16 19:29:13,573] [INFO] ===== Taxonomy check completed =====
[2023-03-16 19:29:13,573] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 19:29:13,573] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87a2d8d6-16c8-4391-bd66-68102da75fb3/dqc_reference/checkm_data
[2023-03-16 19:29:13,577] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 19:29:13,743] [INFO] Task started: CheckM
[2023-03-16 19:29:13,743] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1656/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1656/checkm_input OceanDNA-a1656/checkm_result
[2023-03-16 19:29:39,510] [INFO] Task succeeded: CheckM
[2023-03-16 19:29:39,510] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.75%
Contamintation: 6.71%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 19:29:39,513] [INFO] ===== Completeness check finished =====
[2023-03-16 19:29:39,513] [INFO] ===== Start GTDB Search =====
[2023-03-16 19:29:39,513] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1656/markers.fasta)
[2023-03-16 19:29:39,515] [INFO] Task started: Blastn
[2023-03-16 19:29:39,515] [INFO] Running command: blastn -query OceanDNA-a1656/markers.fasta -db /var/lib/cwl/stg87a2d8d6-16c8-4391-bd66-68102da75fb3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1656/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:29:40,157] [INFO] Task succeeded: Blastn
[2023-03-16 19:29:40,158] [INFO] Selected 11 target genomes.
[2023-03-16 19:29:40,158] [INFO] Target genome list was writen to OceanDNA-a1656/target_genomes_gtdb.txt
[2023-03-16 19:29:40,173] [INFO] Task started: fastANI
[2023-03-16 19:29:40,173] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e6d4584-3b4d-4e13-a1cd-47a205a3e519/OceanDNA-a1656.fa --refList OceanDNA-a1656/target_genomes_gtdb.txt --output OceanDNA-a1656/fastani_result_gtdb.tsv --threads 1
[2023-03-16 19:29:42,787] [INFO] Task succeeded: fastANI
[2023-03-16 19:29:42,792] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 19:29:42,793] [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_902533295.1	s__CG-Epi1 sp902533295	83.8377	78	152	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902531985.1	s__CG-Epi1 sp902531985	81.0608	76	152	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014240055.1	s__CG-Epi1 sp014240055	78.8119	66	152	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002718915.1	s__CG-Epi1 sp002718915	78.7331	50	152	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014240255.1	s__CG-Epi1 sp014240255	78.5737	71	152	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001875345.1	s__CG-Epi1 sp001875345	77.7635	56	152	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845825.1	s__CG-Epi1 sp016845825	77.519	51	152	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724775.1	s__CG-Epi1 sp002724775	76.8456	56	152	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	96.65	95.92	0.84	0.84	3	-
--------------------------------------------------------------------------------
[2023-03-16 19:29:42,793] [INFO] GTDB search result was written to OceanDNA-a1656/result_gtdb.tsv
[2023-03-16 19:29:42,793] [INFO] ===== GTDB Search completed =====
[2023-03-16 19:29:42,795] [INFO] DFAST_QC result json was written to OceanDNA-a1656/dqc_result.json
[2023-03-16 19:29:42,795] [INFO] DFAST_QC completed!
[2023-03-16 19:29:42,795] [INFO] Total running time: 0h0m37s