[2023-03-18 00:25:18,088] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:25:18,089] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:25:18,089] [INFO] DQC Reference Directory: /var/lib/cwl/stg47df29a4-f3f1-48f0-8a54-380a82023411/dqc_reference
[2023-03-18 00:25:19,178] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:25:19,179] [INFO] Task started: Prodigal
[2023-03-18 00:25:19,179] [INFO] Running command: cat /var/lib/cwl/stgecb5a048-cd2f-44e8-ac6b-531fa3a1e710/OceanDNA-b22835.fa | prodigal -d OceanDNA-b22835/cds.fna -a OceanDNA-b22835/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:26:01,472] [INFO] Task succeeded: Prodigal
[2023-03-18 00:26:01,472] [INFO] Task started: HMMsearch
[2023-03-18 00:26:01,472] [INFO] Running command: hmmsearch --tblout OceanDNA-b22835/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47df29a4-f3f1-48f0-8a54-380a82023411/dqc_reference/reference_markers.hmm OceanDNA-b22835/protein.faa > /dev/null
[2023-03-18 00:26:01,741] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:26:01,741] [INFO] Found 6/6 markers.
[2023-03-18 00:26:01,781] [INFO] Query marker FASTA was written to OceanDNA-b22835/markers.fasta
[2023-03-18 00:26:01,782] [INFO] Task started: Blastn
[2023-03-18 00:26:01,783] [INFO] Running command: blastn -query OceanDNA-b22835/markers.fasta -db /var/lib/cwl/stg47df29a4-f3f1-48f0-8a54-380a82023411/dqc_reference/reference_markers.fasta -out OceanDNA-b22835/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:26:02,321] [INFO] Task succeeded: Blastn
[2023-03-18 00:26:02,322] [INFO] Selected 21 target genomes.
[2023-03-18 00:26:02,322] [INFO] Target genome list was writen to OceanDNA-b22835/target_genomes.txt
[2023-03-18 00:26:02,383] [INFO] Task started: fastANI
[2023-03-18 00:26:02,383] [INFO] Running command: fastANI --query /var/lib/cwl/stgecb5a048-cd2f-44e8-ac6b-531fa3a1e710/OceanDNA-b22835.fa --refList OceanDNA-b22835/target_genomes.txt --output OceanDNA-b22835/fastani_result.tsv --threads 1
[2023-03-18 00:26:16,822] [INFO] Task succeeded: fastANI
[2023-03-18 00:26:16,822] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47df29a4-f3f1-48f0-8a54-380a82023411/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:26:16,822] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47df29a4-f3f1-48f0-8a54-380a82023411/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:26:16,825] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:26:16,825] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:26:16,825] [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
Maioricimonas rarisocia	strain=Mal4	GCA_007747795.1	2528026	2528026	type	True	74.8725	77	2299	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:26:16,826] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22835/tc_result.tsv
[2023-03-18 00:26:16,826] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:26:16,826] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:26:16,826] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47df29a4-f3f1-48f0-8a54-380a82023411/dqc_reference/checkm_data
[2023-03-18 00:26:16,827] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:26:16,835] [INFO] Task started: CheckM
[2023-03-18 00:26:16,835] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22835/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22835/checkm_input OceanDNA-b22835/checkm_result
[2023-03-18 00:27:58,253] [INFO] Task succeeded: CheckM
[2023-03-18 00:27:58,253] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.03%
Contamintation: 8.80%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-18 00:27:58,257] [INFO] ===== Completeness check finished =====
[2023-03-18 00:27:58,257] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:27:58,257] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22835/markers.fasta)
[2023-03-18 00:27:58,258] [INFO] Task started: Blastn
[2023-03-18 00:27:58,258] [INFO] Running command: blastn -query OceanDNA-b22835/markers.fasta -db /var/lib/cwl/stg47df29a4-f3f1-48f0-8a54-380a82023411/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22835/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:27:59,211] [INFO] Task succeeded: Blastn
[2023-03-18 00:27:59,212] [INFO] Selected 15 target genomes.
[2023-03-18 00:27:59,212] [INFO] Target genome list was writen to OceanDNA-b22835/target_genomes_gtdb.txt
[2023-03-18 00:27:59,367] [INFO] Task started: fastANI
[2023-03-18 00:27:59,368] [INFO] Running command: fastANI --query /var/lib/cwl/stgecb5a048-cd2f-44e8-ac6b-531fa3a1e710/OceanDNA-b22835.fa --refList OceanDNA-b22835/target_genomes_gtdb.txt --output OceanDNA-b22835/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:28:14,255] [INFO] Task succeeded: fastANI
[2023-03-18 00:28:14,260] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:28:14,260] [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_016779365.1	s__JABMPE01 sp016779365	79.2255	512	2299	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABMPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013203845.1	s__JABMPE01 sp013203845	78.5351	843	2299	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABMPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018699955.1	s__JABISG01 sp018699955	76.2865	69	2299	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABISG01	95.0	99.95	99.95	0.96	0.96	3	-
GCA_016124895.1	s__JABMPE01 sp016124895	75.8501	229	2299	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABMPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722955.1	s__GCA-2722955 sp002722955	75.4182	75	2299	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__GCA-2722955	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724315.1	s__UBA8437 sp002724315	75.3515	52	2299	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__UBA8437	95.0	97.85	97.85	0.87	0.87	2	-
GCA_900299185.1	s__AM-0621 sp900299185	75.1493	66	2299	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__AM-0621	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:28:14,260] [INFO] GTDB search result was written to OceanDNA-b22835/result_gtdb.tsv
[2023-03-18 00:28:14,260] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:28:14,261] [INFO] DFAST_QC result json was written to OceanDNA-b22835/dqc_result.json
[2023-03-18 00:28:14,261] [INFO] DFAST_QC completed!
[2023-03-18 00:28:14,261] [INFO] Total running time: 0h2m56s